The Human Microbiome: Emerging Themes at the Horizon of the 21st Century (Day 3)
24
August

By Adem Lewis / in , , /


SO IT’S MY PLEASURE TO INTRODUCE ERIC A.M., OUR THIRD KEYNOTE SPEAKER FOR THIS WORKSHOP. ERIC CAME ORIGINALLY FROM — DID UNDERGRADUATE AT UNIVERSITY OF ILLINOIS AND A MASTER’S DEGREE AT THE UNIVERSITY OF CALIFORNIA RIVER SIDE WITH A PH.D. FROM THE UNIVERSITY OF WASHINGTON AND SEATTLE AND FINISHED UP HIS TRAINING AT BERKELEY. ERIC IS THE PROFESSOR OF BIOLOGICAL ENGINEERING AT MIT AND CO-DIRECTOR OF THE CENTER FOR MICROBIOME INFORMATICS AND IN 2013, HIS LABORATORY LAUNCHED AS A NON-PROFIT, OPEN BIOME, TO MEET THE CLINICAL DEMAND FOR FECAL TRANSPLANTATION. AND AS OF THE WRITING OF THIS BIO, THE TREATMENT THAT IS OPEN BIOME HAS SENT OUT HAVE TREATED OVER 25,000 PATIENTS. SO HIS RESEARCH IS PRIMARILY FOCUSED ON TRANSLATING THE MICROBIOME RESEARCH INTO THE CLINIC. I HEARD ERIC SPEAK IN FEBRUARY AT KEYSTONE MEETING AND I THOUGHT IT WAS FANTASTIC. SO, WITH THAT AND WITHOUT ANY FURTHER ADIEU, I’D LIKE TO INTRODUCE ERIC ALM FROM MIT WHOSE TALK IS ON MICROBIOME INTERVENTIONS FROM FECAL TRANSPLANTS TO SYNTHETIC MICROBIAL THERAPEUTICS.>>DR. ALM: THANK YOU, RYAN. THANK YOU EVERYBODY WHO IS HERE. SO A REAL SPECIAL TREAT AND QUITE AN HONOR TO BE INCLUDED IN THE LINE UP AT THE WORKSHOP WHEN I STARTED AT MIT ABOUT 11 YEARS AGO, THE ONE THINGS I SAID I WOULDN’T DO IS GET INVOLVED IN MEDICAL RESEARCH. I WAS AN ENVIRONMENTAL MICROBIOLOGIST AND I SAID THERE IS ENOUGH PEOPLE DOING THIS STUFF AND MICROBETOLOGISTS AREN’T NEEDED. ALREADY ENOUGH PEOPLE WORKING ON IT. AND I GOT DRAWN IN BY A COLLEAGUE WHO WAS WORKING ON THE HUMAN MICROBIOME PROJECT AND SAID THEY WANTED HELP WITH STATISTICS. I SAID THAT DOESN’T SOUND BIOMEDICAL AT ALL. SOUNDS PRETTY SAFE. AND I STARTED WORKING ON IT AND IT WAS SO EXCITING, I’VE CHANGED MY ENTIRE DIRECTION AND THAT IS ALL WE DO NOW. SO, IN MANY WAYS, IT’S A SPECIAL HONOR AND A SPECIAL TREAT FOR ME TO SPEAK HERE ABOUT THE HMP BECAUSE IT WAS REALLY WHAT ENDED UP DIRECTING IN A LARGE WAY, MY ONGOING RESEARCH PROGRAM. SO, FOLKS WHO HAVE SEEN ME TALK BEFORE HAVE SEEN THIS SLIDE. AND THIS IS THE FIRST PROJECT THAT I WORKED ON IN HUMAN MICROBIOME WHEN I SAMPLED MY MICROBIOME AND GOT IT EVERY DAY, ALONG WITH REALLY TALENTED GRADUATE STUDENT, NOW AN ASSISTANT PROFESSOR AT DUKE. AND ON THE TOP IS MY MICROBIOME OVER THE COURSE OF THE YEAR AND ON THE BOTTOM IS LAWRENCE’S MICROBIOME. IF WE DIVE DEEPER INTO MY MICROBIOME, ONE OF THE INTERESTING THINGS, THERE ARE INTERESTING THINGS THAT HAPPEN TO BOTH ME AND LAWRENCE DURING THE STUDY. ONE OF THE INTERESTING THINGS THAT HAPPENED TO ME WAS THE SALMONELLA INFECTION. SO I GOT FOOD POISONING AFTER ORDERING SOME UNDER COOKED FRENCH TOAST ABOUT THREE-QUARTERS OF THE WAY THROUGH THE STUDY AND I GOT SALMONELLA. I DIDN’T GET ANTIBIOTICS SO I GOT TO SEE THE INFECTION RUN ITS COURSE. ONE OF THE REALLY INTERESTING THINGS THAT HAPPENED — ON THIS PLOT, THE ROWS ARE THE DIFFERENT BACK STEERIA. THE WARMER COLORS INDICATE THERE IS MORE OF THAT BACTERIA ON THAT PARTICULAR DAY. COOLER COLORS INDICATE THERE IS LESS. AND YOU CAN SEE ONCE I GOT SALMONELLA, ALL OF THESE BACTERIA WHO HAD BEEN THE MAJOR PLAYERS IN MY MICROBIOME UP UNTIL THAT POINT, SORT OF WENT AWAY AND MOST NEVER CAME BACK. THEY WERE REPLACED BY THESE BACTERIA DOWN HERE, SOME OF WHICH WERE BRAND NEW AND NEVER SEEN IN THE 170-ODD DAYS WE SAMPLED. AND SOMEWHERE PRESENT BUT VERY LOW ABUNDANCE AND NEVER REALLY ABLE TO GET A FOOTHOLD IN WHATEVER NICHE THEY WERE SUPPOSED TO POPULATE. THIS REALLY GOT ME THINKING. IF THE MICROBIOME CAN BE REPROGRAMMED LIKE THAT, AND WE CAN FIGURE OUT WHAT IS THE DIFFERENCE BETWEEN A HEALTHY AND SICK MICROBIOME, MAYBE WE CAN GO I AND USE THIS CLINICALLY. WE CAN FIX A BROKEN MICROBIOME BY PUTTING NEW STRAINS IN. ONE OF THE THINGS THAT REINFORCE THAT IS BELIEF IS THESE BACTERIA UP HERE THAT WENT AWAY, THESE BACTERIA THAT REPLACED THEM, WERE VERY, VERY SIMILAR. THEY WERE VERY CLOSELY RELATED TO EACH OTHER. AND SO HERE IS SORT OF AN OVERVIEW OF THE TREE OF LIFE FOR THE BACTER.>>>THAT WERE LIVING IN MY GUT. AND THE BLUE IS SORT OF THE BLUE FROM THE PREVIOUS PLOT SO THESE WERE THE MICROBES THAT WENT EXTINCT IN MY GUT AND THE ORANGE ONES WERE THE ONES THAT REPLACED THEM. SO FOR EACH BACTERIA THAT LEFT, IT WAS REPLACED WITH ANOTHER BACTERIA THAT WAS VERY SIMILAR. AND SO THIS SORT OF FUNCTIONAL CAPABILITIES THE MICROBIOME DIDN’T REALLY CHANGE VERY MUCH. AND THE OTHER THING THEY WANTED YOU TO NOTICE, AND I’LL COME TO THIS LATER — IS THAT ALL OF THESE BACTERIA THAT INITIALLY WENT ALMOST COMPLETELY EXTINCT EXCEPT FOR THESE WHITE SPOTS HERE AND THEN WERE ALMOST COMPLETELY REPLACED, WERE A SUB SET OF THE FIRM CUTES AND I’M COME BACK LATER AND SHOW YOU FUNCTIONALLY WHAT THAT SUBSET IS. BEFORE WE GET THERE, ONE OF THE NEXT PROJECTS I GOT INVOLVED IN THIS KIND OF FOLLOWS DIRECTLY FROM THIS AREA MAYBE WE CAN ENGINEER TRANSMISSION AND USING FECAL TRANSPLANTS. IN SOME WAYS, C DIFIS ANTIBIOTIC USAGE AND A VERY STRONG RISK FACTOR FOR C DIF. THE WAY I THINK ABOUT IT IS, ANTIBIOTIC USAGE IS OUR CRUDE ATTEMPT AT ENGINEERING THE MICROBIOME AND IT’S AN ATTEMPT GONE AWRY BECAUSE THEN IT LEADS TO HIGHER RISK FOR INFECTIOUS DISEASE AFTERWARDS. SO, CAN WE TRY OTHER METHODS OF ENGINEERING? SO, OFTENTIMES WE HAVE THIS HEALTHY MICROBIAL GUT ECOSYSTEM, APPLY ANTIBIOTICS IT’S CLEAR-CUTTING THAT ECOSYSTEM, WE GET INVASIVE SPECIES AND WE CAN GET CAUGHT IN A CYCLE HERE. AND IF WE GO THROUGH THE CYCLE THREE TIMES, NOW OUR C DIF, INFECTION AND A RECURRENT ONE AND WE ARE ALLOWED TO TREAT IT USING FECAL TRANSPLANT. THAT’S SORT WHAT HAVE WE DO AT OPEN BIOME AND INVOLVED IN A STUDY RUN BY LIBBY HOME AN OVER AT MGH AND TOGETHER WITH DIRK JEANERS AND RON XAVIER AT THE BRODE, COLLECTED GENOMIC DATA IN PARTICULAR, METAGENOMIC DATA ON THIS COHORT. SO WE HAD FOUR HEALTHY DONORS TREATING 20 PATIENTS WITH ABOUT A 90% SUCCESS RATE. IMPORTANTLY, AT LEAST ONE OF OUR DONORS TREATED 12 PATIENTS SO WE GOT TO SEE THIS SORT OF IN-HUMAN EXPERIMENT REPEATED MULTIPLE TIMES. WE GOT TO USE THE DATA TO BUILD MODELS. AND ONE OF THE MODELS THAT WE WANTED TO LOOK AT WAS WORK DONE BY CHRIS, A GRADUATE STUDENT IN MY LAB. ONE OF THE PROBLEMS THAT WE WANTED TO SOLVE AND MODEL IS, IF WE LOOK AT THE STRAINS THAT ARE IN A MICROBIOME AND SO THIS IS A C DIFPATIENT BEFORE FECAL TRANSPLANT. HERE IS OUR HEALTHY DONOR. SO YOU CAN SEE THOSE PROFILES ARE PRETTY DIFFERENT. I’M NOT SHOWING YOU ALL THE DIFFERENT NAMES OF THE BUGS AND NO PARTICULAR ORDER BUT DARKER CONSIDERS MEANS THERE IS MORE OF THAT BACTERIA IN THAT PARTICULAR SAMPLE. THIS IS WHAT OUR PATIENT LOOKS LIKE AFTER A FECAL TRANSPLANT. SO WE STARTED THAT AND WE SAID, GOSH, IT DOESN’T LOOK LIKE THERE IS ANY VERY SIMPLE RULES. IT DOESN’T LOOK LIKE IT IS A +B=THE COMBINATION. IT DOESN’T SEEM TO BE LIKE ANY OF THE SIMPLE RULES THAT WE CAN PUT TOGETHER. BUT CHRIS WANTED TO SEE IF HE COULD USE MACHINE LEARNING TO BUILD A MODEL THAT WOULD PREDICT WHETHER OR NOT A SPECIES WOULD ENGRAFT AND IF IT DID ENGRAFT FROM THE DONOR TO THE PATIENT, WHAT WOULD LITTLE ABUNDANCE BE? WHEN WE START TO THINK ABOUT SYNTHETIC MICROBIAL THERAPEUTICS IN THE FUTURE, GETTING AWAY FROM A FECAL TRANSPLANT AND TAKING BUGS INTO CULTURE AND FEEDING THEM TO PATIENTS AND HOPING THEY ENGRAFT. FOR A LOT OF MECHANISMS THAT IS WE CARE ABOUT, WE NEED THEM TO BE ABUNDANT. WE RANDOMLY PICK A BACTERIAL SPECIES FROM HUMAN MICROBIOME. THEY ARE ENRICHED AT THE LOW END OF THE CURVE IN TERMS OF ABUNDANCE. SO YOU’RE AVERAGE SPECIES IS NOT GOING TO BE VERY ABUNDANT AT ALL AND IF YOU WANT YOUR SPECKITIES PRODUCE A COMMODITY GOOD — SPECIES, IF IT’S PRESENT AT .0001% OF YOUR TOTAL BIOMASS, IT’S NOT GOING TO BE A VERY COMPETITIVE PRODUCER. IT’S NOT GOING TO ALTER THE OVERALL POOL OF THAT VERY MUCH. SO, PREDICTING ABUNDANCE IS IMPORTANT AND WHAT WE FOUND IS THAT WE COULD PREDICT WHETHER THINGS ENGRAFTED QUITE WELL AND WE COULD ALSO PREDICT ABUNDANCE AND IMPORTANTLY IF WE SAY, HERE IS OUR CUTOFF, ANYTHING LOWER THAN THIS, WE DON’T WANT TO USE IN A SYNTHETIC THERAPEUTIC, IF WE PICKED THESE STRAINS, FOR THE MOST PART, WE WOULD GET THINGS THAT ACTUALLY WERE QUITE ABUNDANT IN THE PATIENT. SO BECAUSE WE CAN DO THIS, IT SORT OF PAVES THE ROAD FROM GOING FROM FECAL TRANSPLANTS FORWARD TO MORE SYNTHETIC TREATMENTS. SO, WE BUILT A MODEL. THIS IS WHAT IT LOOKS LIKE AND THE DATASET I JUST SHOWED YOU. SO A LOT OF THINGS THAT SEEMED HARD TO PREDICT HERE, THE MODEL IS RIGHT AND IT HAS A FEW THINGS WRONG. AND IT GETS A FEW THINGS RIGHT THAT ARE VERY SURPRISING. THE FIRST TIME I GAVE THIS TALK I WAS SHOT SHOCKED BY MY OWN DATA AND I THOUGHT, THERE IS AN ERROR? SOMEONE IN THE AUDIENCE PEOPLE WAS KIND ENOUGH TO POINT IT OUT TO ME. WE HAVE GONE AND LOOKED AND IF YOU LOOK AT THIS SPECIES, IT’S NOT PRESENT IN THE PATIENT OR DONOR. AND YET, IT’S PRESENT AFTER THE FMT. THE SURPRISING THING IS IT WAS PREDICTED BY THE MODEL AND IT WAS PREDICTED BY THE MODEL BECAUSE HERE IS SAY STRAIN THAT IS RARELY PRESENT IN OUR PATIENTS OR DONORS BUT OFTEN SHOWS UP IN PATIENTS AFTER FECAL TRANSPLANTS AND THE MODEL IS ABLE TO PULL THAT OUT. SO THERE IS A SPECIES THAT PLAY AN IMPORTANT ROLE POTENTIALLY IN SUCCESSION AND THINGS LIKE THAT. AND THESE ARE THINGS THAT WE ARE SORT OF LEARNING BY MINING THESE DATA. SO THAT WAS ALL GENERALLY THE OTU LEVEL. WE WANTED TO LOOK A LITTLE BIT CLOSER AT THE SPECIES LEVEL AND EVEN DRILL DOWN TO THE STRAIN LEVEL. SO, CHRIS WROTE A PROGRAM CALLED STRAIN FINDER AND WHAT STRAIN FINDER DOES, IS IT TAKES METAGENOMIC DATA, WHICH ARE THESE VERY SHORT READS AND THEN TRIES TO INFER WHAT IS THE STRAIN CONTENT. AND IF YOU APPLY STRAIN FINDER TO A SINGLE SAMPLE, IT’S PRETTY GOOD AT TELLING YOU HOW MANY STRAINS THERE ARE. IT CAN’T TELL YOU WHAT IS THE GENOTYPE OF THOSE STRAINS BECAUSE THERE IS NOT ENOUGH INFORMATION. BUT, IF YOUR NUMBER OF SAMPLES IS GENERALLY SPEAKING YOUR NUMBER OF SAMPLES IS GREATER THAN YOUR NUMBER OF DIFFERENT STRAINS IN THOSE SAMPLES, SO YOU HAVE STRAINS OF APPEARING ACROSS MULTIPLE SAMPLES, THEN STATISTICS WORK OUT SUCH THAT YOU CAN OFTEN PREDICT NOT ONLY HOW MUCH OR HOW MANY STRAINS THERE ARE AND HOW ABUNDANT THEY ARE IN EACH INDIVIDUAL SAMPLE, BUT WHAT THE GENOTYPE IS FOR EACH OF THOSE STRAINS. AND HERE IS JUST AN EXAMPLE OF STRAIN FINDER. HERE WE HAVE DIFFERENT NUMBERS OF SAMPLES FROM TWO SAMPLES ALL THE WAY UP TO 64 AND FROM TWO STRAINS ALL THE WAY UP TO 32 STRAINS. SO WE ARE NOT DOING VERY GOOD. THE BLUE COLORS ARE BETTER LIKE DARK BLUE IS ESSENTIALLY PERFECT PREDICTION BUT WE ARE GETTING VERY GOOD PREDICTIONS ACROSS MOST OF THE COMBINATIONS OF DIFFERENT NUMBER SYSTEM OF SAMPLES AND STRAINS AND HERE IS SOME EXAMPLE DATA WHERE RED IS THE PREDICTED GENOTYPE OF THE STRAIN AND BLACK IS THE TRUE GENOTYPE OF THE STRAIN. AND YOU CAN SEE THAT FOR EVERY TRUE STRAIN, THERE IS A PREDICTED STRAIN THAT MATCHES IT VERY CLOSELY. SO WE APPLIED THIS TO THE SAME STUDY, THE FECAL TRANSPLANT STUDY. SO HERE WE ARE LOOKING AT STRAINS IN A SPECIES AND HERE WE HAVE OUR DONOR NUMBER 1 HAS TWO STRAINS. THE BLUE ONE IS ABOUT TWICE AS ABUNDANT AS THE GREEN ONE. IT GOES INTO A DONOR OVER HERE AND THREE DIFFERENT TIME POINTS. AND YOU CAN SEE BOTH OF THE STRAINS HERE TRANSFERRED OVER TO THE PATIENT AND THIS WAS A CASE WHERE THE DONOR HAD THIS PARTICULAR OTU IN THE RECIPIENT PATIENT DID NOT. SO THE STRAINS GET TRANSFERRED OVER. HERE THE DONOR HAS FOUR DIFFERENT STRAINS AND THOSE STRAINS GET TRANSFERRED OVER AS WELL BUT A LOT MORE FLUCTUATION IN THEIR RELATIVE ABUNDANCE. HERE IS A CASE WHERE THE DONOR HAD FOUR STRAINS. 9 RECIPIENT PICKED UP THE FOUR STRAINS BUT THEN EVEN THOUGH THAT RECIPIENT NEVER HAD FPRAU PRIOR TO THE FECAL TRANSPLANT, ONCE THEY GOT IT, THEY WERE ABLE TO ACQUIRE NEW STRAINS. THIS RED STRAIN HERE, FROM SOMEWHERE, FROM THE ENVIRONMENT OR SOMETHING MAYBE VERY, VERY LOW ABUNDANCE INITIALLY THAT WAS ABLE TO THRIVE ONCE THERE WAS SORT OF A CRITICAL MASS OF SIMILAR STRAINS OF THE SAME SPECIES. AND THIS IS SOMETHING THAT WE SAW OVER AND OVER AGAIN. SO WE HAVE THESE STRAINS OF DONOR ORIGIN AND THEN THESE STRAINS THAT ARE ENVIRONMENTAL BECAUSE THEY ARE FROM SOME OTHER SOURCE. ANOTHER CASE WAS WHERE THE DONOR HAD A STRAIN AND THE RECIPIENT ALSO HAD A STRAIN OF THE SAME OTU. SOME OF THE TIMES WE WOULD SEE THAT PREFMT AND POST FMT, DIDN’T CHANGE VERY WELL MUCH. SO DONOR STRAINS WERE NOT ABLE TO GET MUCH OF A FOOTHOLD IN THE PATIENT AND SOMETIMES WE SAW THE OPPOSITE BEHAVIOR. SO, AFTER FECAL TRANSPLANT, THE PATIENT LOOKED A LOT MORE — THE DONOR AT THE STRAIN LEVEL. SO WE SAW THE COMPETITION CAN HAPPEN AND AT THE END, I’LL TELL YOU A LITTLE BIT ABOUT SOME OF THE RULES THAT WE ARE STARTING TO DISCOVER ABOUT WHAT EFFECTS THAT COMPETITION. THE OTHER INTERESTING THING WE NOTICED AND YOU SAW THIS ON THE DIAGRAMS ALREADY, IF A STRAIN EN GRAFTS IN THE PATIENT AND ONLY ABOUT 30% ENGRAFT IN THE PATIENT, BUT WHEN THEY DO, THE PATIENT GETS ESSENTIALLY 100% OF THE STRAINS THAT WERE IN THE DONOR, VERY RARELY DO THEY ONLY PICK UP SOME OF THE STRAINS. SO IT’S THIS ALL OR NOTHING BEHAVIOR. MOST OF THE TIME IT DOESN’T ENGRAFT BUT WHEN IT DOES, ALL THE DIFFERENT STRAINS ENGRAFT. YOU CAN SEE SOME EXAMPLES OF THAT HERE, EVEN THE REALLY QUITE COMPLEX COMMUNITIES SEEM TO ENGRAFT IN ALL THE DIFFERENT MEMBERS COMING ACROSS. AND THIS IS SURPRISING SINCE IN& GENERAL IF YOU LOOK AT ANY ONE OF THE STRAINS, SMALL PROBABILITY THAT THEY ENGRAFT BUT IF YOU KNOW THEY ARE CLOSELY RELATED BUGS ENGRAFT, THEN IS THERE A HIGH PROBABILITY. SO A INTERACTION THERE DEFINITELY. THIS IS AN OVERVIEW AND THE ONLY THING I WANT YOU TO TAKE AWAY FROM THIS SLIDE, THIS IS FOR ALL THE DIFFERENT FECAL TRANSPLANTS WE LOOKED AT, CAN WE ASSIGN THE STRAINS TO BEING EITHER FROM THE PATIENT INITIALLY FROM THE DONOR OR STRAINS THAT WERE NEVER SEEN IN EITHER AND THOSE ARE WHAT WE ARE CALLING ENVIRONMENTAL. SO, THE ENVIRONMENT SAL SHOWN IN BLUE AND YOU CAN SEE IT’S A SIGNIFICANT PORTION, ALMOST A THIRD OF ALL THE STRAINS. THEY CAN’T ENGRAFT UNTIL THE FECAL TRANSPLANT AND THEY NEED SOME OF THE DONOR STRAINS THERE TO MAKE THE ENVIRONMENT FAVORABLE BUT ONCE THE STRAINS ARE THERE, THEN THESE ENVIRONMENTAL STRAINS CAN GET A FOOTHOLD. SO, ABOUT A YEAR AND A HALF AGO, WE GOT A GRANT FROM THE BROAD INSTITUTE TO DIVE A LITTLE BIT DEEPER AND REALLY INVESTIGATE ALL THESE DIFFERENCES BETWEEN STRAINS AND SO, WHAT WE DID IS WE TOOK THE OPEN BIOME DONORS, AND TOOK THE COLLECTION AND STARTED TO GENERATE ISOLATES. WE GOT ABOUT 7000 ISOLATES, WHOLE GENOME SEQUENCES FOR THEM, METAGENOMIC TIME SERIES, 16S TIME SERIES AND METABOLOMICS TO CHARACTERIZE AND IN A LOT MOREY DO TAIL WHAT ARE THE PHENOTYPES IN GENOTYPES OF THESE STRAINS. SHAUN GIBBINS IS A TALENTED POSTDOC WHO LED UP THIS PROJECT AND THIS WAS HIS SAMPLE PLAN FOR 16S IN METAGENOME I THINK SO. SO FROM THESE DONORS, THEY COME IN ABOUT FOUR TIMES PER WEEK AND SO FOR A NUMBER OF THEM, WE WERE ABLE TO GET VERY LONG TIME SERIES UP TO TWO YEARS AND FOLLOW WITH 16S AND METAGENOMICS SO, THE ADVANTAGES OF THIS IS NOW WE HAVE THESE. WE HAVE THEM STORED AND WE CAN REVIVE THEM AND IF FOLKS ARE INTERESTED IN PARTICULAR STRAINS , WE ARE HOPING TO BE ABLE TO MAKE THOSE WIDELY AVAILABLE AS SOON AS WE HIRE SOMEBODY TO MAINTAIN THE COLLECTION AND START MAILING IT OUT. BUT THESE ARE GOING TO BE VERY WELL CHARACTERIZED COLLECTION THAT WE HOPE IS A VALUABLE RESOURCE TO THE RESEARCH COMMUNITY. IT’S PRETTY COMPREHENSIVE SO IF WE SORT OF WEIGHT THE DIFFERENT STRAINS BY THEIR RELATIVE BIOMASS, YOU CAN SEE THAT WE ACTUALLY HAVE VERY GOOD COVERAGE. SO THE DARKER PARTS OF THE PIE HERE ARE THE STRAINS, PERCENTAGE OF THOSE STRAINS WE HAVE IN THE FREEZER FROM 11 DIFFERENT DONORS AND THE SHADED PARTS, THESE ARE THE STRAINS THAT WE DON’T YET HAVE. SO YOU CAN SEE WE HAVE VERY GOOD COVERAGE. AND THE ONES WE DON’T HAVE IS BECAUSE THEY ARE NOT VERY ABUNDANT AND THE IT SAYS THAT WE ARE NOT FUNDAMENTALLY MISSING ANYTHING IN OUR APPROACH. WE JUST NEED TO DO A LOT MORE ISOLATIONS BECAUSE THEY ARE LESS FREQUENT. SOME OF THESE INCLUDE STRAIN THAT IS HAVE BEEN DIFFICULT TO CULTURE PREVIOUSLY. SO HUMAN ISOLATES OF — ONLY ONE THAT WAS ISOLATED ABOUT 12 YEARS AGO, NOW WE HAVE DOZENS IN THE FREEZERS AND HOPE THAT THAT IS GOING TO BE PRETTY USEFUL. AND SO WE HAVE OTHER SPECIES BEYOND ACKER MANSIA THAT ARE HUMAN ORIGIN. THERESEY BACK TER, AS FAR AS I KNOW THERE IS JUST ONE HUMAN ISOLATE AND WE HAVE OVER 500 OF THESE AND WE KNOW FROM CULTURE INDEPENDENT SURVEYS THAT THEY ARE A FAIRLY IMPORTANT PART OF THE SPORE FORMING PART OF THE MICROBIOME. SO I WANT TO DIVE A LITTLE BIT DEEPER ON WHAT WE ARE STARTING TO DO WITH THIS COLLECTION. SO HERE WE ARE LOOKING AT 12 DIFFERENT DONORS AND LOOKING AT B FIR JILLIS IN EACH OF THESE DONORS, I HAVEN’T PUT THE TREES TOGETHER ON ONE LARGE TREE BECAUSE THE STRUCTURE IS VERY SIMPLE. ALL OF THE GENETIC DIVERSITY IN B FER JILLIS WITHIN EACH DONOR IS CLUSTERED WITHIN THAT DONOR. AND THERE IS A RELATIVELY SMALL, AT MOST, DOZENS OF MUTATIONS FROM THE LAST COMMON ANCESTOR TO EACH OF THE ISOLATES. AND SO, WE ARE FAIRLY CERTAIN THAT EACH OR ALL THE DIVERSITY IN B FIR JILLIS IN ANY GIVEN PERSON EVOLVED DURING THE COURSE OF THAT PERSON’S LIFETIME. SO IS THAT PERSON WAS IN OCALATESSED BY THAT STRAIN OR MULTIPLE STRAINS AND ONLY ONE OUT COMPETED THE LITTLER. BUT WHEN WE LOOK AT THESE ISOLATES, WE SEE THERE ARE DISTINCT TREES ONE FOR EACH DONOR. SO, WHAT WE DID IS WE DID A DEEP DIVE ON B FIR JILLIS, CULTURED A NUMBER OF ISOLATES FROM INDIVIDUALS, DID METAGENOMICS EUGENE SEQUENCING, TO INFER WHOLE GENOME SEQUENCING AND THEN METAGENOME SEQUENCING WAS DONE FOR THIS LIBRARY SO WE CAN GO BACK AND SEE WITH DAILY RESOLUTION HOW THESE DIFFERENT STRAINS WERE COMPETING WITH EACH OTHER. SO, HERE IS AN EXAMPLE. SO THIS IS AGAIN OUR B FRAGILEIS, AND THIS THE DISTANCE TO MOST COMMON RECENT ANCESTOR IN TERMS OF SNPS. SOME OF THEM HAD LIKE UP TO 10 SNPS SOME ONLY HAD A FEW. SO THESE MIGHT HAVE THOSE INDIVIDUALS MIGHT HAVE BEEN INOCULATED WITH THAT PARTICULAR BUG MORE RECENTLY. AND THIS IS ONE DONOR, DONOR 44 WE HAD THE EXTREMELY LONG TWO-YEAR TIME SERIES FOR. SO THAT WORKED OUT PRETTY WELL AND I’LL SHOW YOU SOME OF THE DYNAMICS THERE. DONOR 440 WAS PRETTY INTERESTING BECAUSE ACTUALLY HAD THE HIGHEST NUMBER OF SNPS FROM THE ISOLATES TO THE MOST RECENT COMMON ANCESTOR BUT WHEN WE LOOKED AT THE TREE, ALL THE SNPS WERE ON THE ONE BRANCH OF THE TREE. AND WHEN WE STARTED TO LOOK AT WHAT TYPE OF SNPS THOSE ARE, WE SAW THAT THEY WERE VERY HIGHLY ENRICHED IN TRANSITIONS AND EVEN A SPECIFIC TYPE OF TRANSITIONS. IT REALLY LOOKS LIKE MAYBE A DEFECT IN ERROR CORRECTION AND WE ESSENTIALLY HAVE A HYPERMUTATOR THAT EINVOLVED HYPERMUTATION WITHIN THE HUMAN HOST. THE THING WE ARE MOST INTERESTED IN WAS NOT LOOKING AT THE TRANSITION TRANSVERSION RATIO BUT TRYING TO IDENTIFY WHICH OF THESE POINT MUTATIONS THAT WERE OCCURRING WERE DUE TO POSITIVE SELECTION. IT’S DIFFICULT TO USE POSITIVE SELECTION BUT WHAT WE REASONED IS IF WE START TO SEE MULTIPLE HITS IN THE SAME GENE OR IN A SIMILAR GENE IN THE SAME PATHWAY, THAT GIVES US SOME CONFIDENCE THAT THE REASON THAT WE ARE SEEING EXCESS HITS IN THE SAME GENE IS BECAUSE IT IS CONFERRING A SELECTIVE ADVANTAGE. AND SO, IF WE LOOK AT ALL OF OUR SNPS, THE SNPS THAT SEPARATE THE STRAINS IN ONE PERSON FROM THE STRAINS IN ANOTHER PERSON, WE SEE THAT THE RATIO IS QUITE LOW. IT’S WHAT YOU EXPECT FOR SNPS THAT DIFFERENTIATE TWO DIFFERENT SPECIES. SO, MANY MORE NON SYNONYMOUS OR MANY MORE SYNONYMOUS MUTATIONS THAN NON SYNONYMOUS. ON THE OTHER HAND IF WE LOOK AT STRAINS THAT WHERE WE GET MULTIPLE HITS IN THE SAME GENE, OR MULTIPLE HITS IN THE SAME GENE BUT IN A DIFFERENT STRAIN, MAYBE EVEN IN A DIFFERENT PERSON. AND THEN WE LOOK AT THE RATIO, WE SEE THAT THEY ARE MOSTLY NON SYNONYMOUS. THIS REALLY WAS THE SMOKING GUN FOR US THAT YES, THERE IS A QUALITATIVE DIFFERENCE HERE AND WHEN GENES ARE HIT MULTIPLE TIMES, THEY TEND TO BE ENRICHED IN THESE NON SYNONYMOUS HITS. SUGGESTING POSITIVE SELECTION. THE OTHER ANALYSIS WE DID IS, THEY ARE ALSO HIGHLY ENRICHED IF THEY ARE HIT MULTIPLE TIMES IN MEMBRANE PROTEIN GENES. SO, THIS IS A LIST JUST FOR THE GENES THAT CROSSED OUR THRESHOLD AS BEING PRETTY INTERESTING. AND YOU CAN SEE, THERE IS A LOT OF THINGS THAT — PERHAPS NOT SURPRISING. SO CAPSULE POLYSACCHARIDE, BIOSYNTHESIS AND SOME TRANSCRIPTIONAL REGULATORS AND SENSORS, BUT THE THING THAT REALLY GRABBED US WAS THESE FAMILY PROTEINS. WE HEARD A GREAT TALK YESTERDAY ON WHAT SOME OF THESE PROTEINS ARE DOING. AND WE SEE THAT THIS, AT LEAST IN B FRAGILEIS, THIS IS A CLASS OF GENES OR PATHWAY THAT IS THE ABSOLUTELY THE MOST ENRICHED IN WITHIN PERSON EVOLUTION. SO, WHAT YOU CAN SEE HERE, ALL THE RED DOTS ARE THE NON SYNONYMOUS SO ONLY ONE SYNONYMOUS MUTATION. AND THESE ARE DIFFERENT STRAINS, THE ROWS AND COLUMNS ARE DIFFERENT PEOPLE. AND THE Xs ARE THE GENES BEING LOST. SO THERE IS A LOT OF GENE GAIN AND GENE LOSS IN ADDITION TO ACCUMULATION OF POINT MUTATIONS. AND I’LL GOAT THAT IN JUST A MINUTE. WE CAN LOOK AT WHERE THESE MUTATIONS ARE OCCURRING IN THE THREE-DIMENSIONAL STRUCTURE AND THEY SEEM TO BE OCCURRING IN THE INNER FACE REGION BETWEEN SUSC AND D AND THAT MAKES A LOT OF SENSE BECAUSE THOSE WOULD BE TWO PRETTY IMPORTANT REGIONS FOR GENES. WE DON’T YET KNOW IF FOLLOWING YESTERDAY’S TALK, ARE THESE SNPS ACTUALLY HELPING DIFFERENT PEOPLE MORE EFFICIENTLY USE LET’S SAY DIFFERENT TYPES OF STARCH? SOMETHING LIKE THAT? ARE THEY ADAPTING TO AN INDIVIDUAL PERSON’S DIET? HOST COLONIZATION? OR ARE THESE GENES SO IMPORTANT AND THEY ARE EXPRESSED SO HIGHLY ON THE CELL SURFACE THAT THEY ARE A GOOD TARGET FOR PHAGE? AND THEY ARE CONSTANTLY EVOLVING TO SORT OF OUT WIT THE PHAGE THAT ARE EVOLVING TO KILL THEM? SO WE HAVE A NUMBER OF EXPERIMENTS GOING TO NOW TO FLUSH OUT THIS QUESTION AND IT MAY TURN OUT THAT IT IS A LITTLE BIT OF BOTH. SO, NOW WE’LL DIVE INTO ONE DONOR. THIS IS OUR DONOR WHERE WE HAD TWO YEARS WORTH OF METAGENOMIC SAMPLES. HERE ARE ALL THE ISOLATES FROM THAT DONOR. AND ON THE TREE, I HAVE JUST COLORED WHERE THE DIFFERENT MUTATIONS HAPPENED. I COLORED IT BY BRANCH. AND WE GO TO THE MEAT GENOMIC DATA AND WE CAN TRACK EACH SNP AND SEE THEY HAVE A DYNAMIC PATTERN. WE CAN SEE THAT THESE TWO MUTATIONS CAME UP RELATIVELY LATE, PROBABLY DURING THE COURSE OF OUR STUDY AND THEN THEY GREW AND THEY REALLY TOOK OVER BUT THEY ONLY TOOK OVER ONE OF THESE BRANCHES. AND SO, BECAUSE WE HAVE SO FEW SNPS, WE CAN BUILD A PERFECT TREE AND THEN WE CAN MAP THOSE SNPS. AND WE CAN REALLY BUILD A MODEL OF EVEN THOUGH WE ARE STARTING WITH MEAT GENOMIC DATA, WE DON’T HAVE WHOLE GENOMES. WE CAN MAKE VERY GOOD INFERENCES ABOUT WHAT ALL THE STRAINS ARE AND WHAT THEIR ABUNDANCE IS AT ANY POINT IN TIME. AND SO, WE CAN ONLY MAKE GENERAL INFERENCES ABOUT WHAT HAPPENED IN THE YEARS PREDATING OUR SAMPLING BUT DURING OUR SAMPLING, WE CAN BUILD A FAIRLY PRECISE MODEL OF HOW MUCH OF EACH STRAIN WE SEE AT DIFFERENT TIMES. WE CAN SEE SOMETIMES WE GET MUTATIONS THAT CROP UP AND THEN DIE-OFF OVER HERE. AND SOMETIMES WE GET MUTATIONS THAT CROP UP AND REALLY TAKE OVER BUT THEY ONLY TAKE OVER SORT OF ONE OF THE ARMS. AND WE HAVE THIS CONSTANT COEXISTENCE OF THE TWO DIFFERENT STRAIN TYPES THAT I SHOWED YOU IN THE PREVIOUS SLIDE. SO, WE TALKED A LOT ABOUT POINT MUTATION. ONE THING MY GROUP IS ALWAYS REALLY INTERESTED IN IS HORIZONTAL GENE TRANSFER AND WE GOT INSPIRED BY THIS STUDY ON K ZYMES WHICH SHOWED THAT IN MOST LIKELY IN THE JAPANESE MICROBIOME SORT OF MOBILE GENE POOL, THERE ARE THESE GENES TO DIGEST A POLYSACCHARIDE THAT MAKES UP THESE SUSHI WRAPPERS. AND IT WAS HORIZONTALLY ACQUIRED FROM A MARINE BACTERIA THAT WAS FEEDING ON THE SEAWEED. SO WE BUILT THIS AND THIS WAS REALLY THE FIRST-EVER MAP OF HORIZONTAL GENE TRANSFER AND HOTSPOTS. AND THE THING WE FOUND, EVEN THOUGH WE INCLUDED ALL THE DIFFERENT GENES, ALL THE DIFFERENT GENOMES AND GEN BANK AT THE TIME WHEN WE HAD A LOT OF NON-HUMAN ENVIRONMENTS, WE SAW IS THAT THE HUMAN MICROBIOME WAS THE REAL HOTSPOT OF HORIZONTAL GENE TRANSFERS, WHERE WE SAW MOST OF OUR HITS. I WAS FORTUNATE ENOUGH TO WORK WITH A REALLY — AN ASSSTANT PROFESSOR AT CORNELL WHO TOOK THIS STUDY OUT TO SOME RURAL VILLAGES IN FIJI WHERE SHE COLLECTED SAMPLES FROM ABOUT 300 DIFFERENT INDIVIDUALS, CAME BACK AND ANALYZED THOSE FOR COMMUNITY STRUCTURE AND GENE TRANSFER. WHAT SHE FOUND IS ALTHOUGH THE HMT MEAT GENOME CLUSTER TOGETHER AND FIJI MEAT GENOMES CLUSTER TOGETHER, WHEN SHE LOOK WITHIN VILLAGES — METAGENOMES — THEY WERE ESSENTIALLY ON TOP OF EACH OTHER. AND ONE OF THE THINGS THAT WAS CAUSING THE METAGENOMES TO CLUSTER TOGETHER WAS THAT THERE ARE THESE POPULATIONS-SPECIFIC GENES THAT WERE — YOU CAN SEE SOME OVER HERE AND THESE ARE MOBILE GENES. BUT THEY ARE SPECIFIC TO THE HM. AND THEY ARE RARELY FOUND IN FIJIANS AND THEN WE HAVE THOSE THAT ARE HIGHLY ENRICHED BUT SPECIFIC TO FIJIANS AND RARELY FOUND IN THE HMP. AND WE CAN LOOK AT WHAT THOSE GENES ARE AND THEY TEND TO BE ENRICHED IN THESE GLYCOSIDE HYDROLACES THAT ALLOW THEIR THEFT ACCESS DIFFERENT PARTS OF THE DIET AND THEY EAT DIFFERENT STARCHES. WE CAN SEE A NUMBER THAT ARE ENRICHED IN THE HMP VERSUS FIJI AND THE NUMBER THAT ARE ENRICHED IN FIJI VERSUS HMP. SO, WE INITIALLY PUBLISHED THE PAPER ON HORIZONTAL GENE TRANSFER BACK IN 2012 AND GOT THIS E-MAIL FROM WHO I THOUGHT WAS A POSTDOC. SHE DEMANDED TO HAVE A SKYPE WITH ME. I SAID, OKAY. AND SHE TOLD ME HOW I GOTTEN EVERYTHING WRONG AND I HAD MISSED THE BULK OF THE SIGNAL IN MY DATA BECAUSE WE WANTED TO BE CONSERVATIVE ABOUT WHAT WE CALLED HORIZONTAL GENE TRANSFER. AND WE HAD 500 BASE PAIR CUT OFF. AND SHE SAID THAT CAUSED YOU TO MISS THE MOST EXCITING PART OF úPART IS THAT EVEN FOR GENES
THAT RARELY EVER GET HORIZONTALLY TRANSFERRED, THEIR UPSTREAM PROMOTOR REGIONS, THEIR REGULATORY INFORMATION OFTEN GETS TRANSFERRED BUT IT’S USUALLY LESS THAN 500 BASE PAIRS. SO SHE CAME UP TO MY LAB, FINISHED THE PROJECT WITH ME, AND COINED THIS TERM, HRT, WHICH IS HORIZONTAL REGULATORY TRANSFER. AND IDENTIFIED THAT AS A KEY TYPE OF REGULATORY SWITCHING THAT BUGS USE TO ADAPT THEIR ENVIRONMENT. SO HERE YOU CAN SEE, HERE IS THE GENE AND HERE IS THE REGULATOR. ALL THE E.COLI IS GROUPED TOGETHER. THE ENTER BACK TERIS GROUPED TOGETHER. HERE IS MET E. WE HAVE ENTER BACK TERAND THE E.COLIS WHEN WE LOOK AT THE PROMOTOR REGION BETWEEN MET E AND MET R, WE SEE THE ENTER BACK TORIS OVER HERE WITH THE E.COLIS. SO WHAT IT LOOKS LIKE IS IT LOOKS LIKE THE E.COLI PICKED UP HORIZONTALLY TRANSFERRED REGULATORY REGION FROM ENTER BACK TER. SHE WENT ON TO SHOW THAT IF YOU LOOK AT E.COLI STRAINS THAT PICKED UP THE — THAT SWITCHED THEIR REGULATION VERSUS IN TWO DIFFERENT STRAINS, IT EFFECTS THEIR FUNCTION. STOW EFFECTS THEIR GENE EXPRESSION. SO IF THEY PICKED UP A NEW REGULATORY REGION, THEY ARE MUCH MORE LIKELY TO HAVE DIVERGENT ACROSS THE TWO DIFFERENT STRAINS AND FOR THE MET R AND MET E EXAMPLE, SHE WAS ABLE TO SHOW IN THE LABORATORY THEY IT ACTUALLY HAD AN EFFECT ON GENE FITNESS. AND SHE ALSO SHOWED THAT THIS WAS PRETTY WIDESPREAD ACROSS THE TREE OF LIFE AND IT WAS ALSO SPECIES DEPENDENT. SO WE SEE VERY DIFFERENT RATES OF REGULATORY TRANSFER AND REGULATORY SWITCHING ACROSS DIFFERENT SPECIES. AND WE STILL DON’T REALLY UNDERSTAND WHAT THE RULES ARE THERE BECAUSE IT DOESN’T CORRELATE VERY OBVIOUSLY WITH THE OVER ALL AMOUNT OF RECOMBINATION OF THOSE SPECIES. SO GETTING BACK TO THE MAIN STORY. WE WANTED TO LOOK AND SO WHAT I SHOWEDY YOU THESE MAPS AND I’M SHOWING YOU THIS STUFF ABOUT HORIZONTAL REGULATORY TRANSFER, ALL OF THESE THINGS ARE HAPPENING OVER VAST TIME SCALES. AND SO, FOR DNA TO BE 1000 BASE PAIRS IN 99% IDENTICAL, WELL THAT MEANS THAT YOU COULD HAVE HAD A HORIZONTAL TRANSFER YESTERDAY OR LAST WEEK. YOU COULD HAVE ALSO HAD A HORIZONTAL TRANSFER 5000 YEARS AGO SORT OF THE DAWN OF MODERN CIVILIZATION. THOSE ARE BOTH GETTING YOU IN THAT 99% REGIME OVER A SINGLE GENE. SO, ONE OF THE KEY QUESTIONS TO ME WAS, WELL, WHEN WE GET AN OTU AND WE GET COLONIZED BY A NEW SPECIES, CAN THAT SPECIES PICK UP GENES THAT ARE MAYBE IN OTHER BUGS WITHIN OUR MICROBIOME? BECAUSE THAT WOULD MEAN THAT WE ARE MISSING A LOT WHEN WE GET A 16S AND CAN’T JUST LOOK AT THOSE AND GET THE LOCAL STORY. BECAUSE THE FUNDAMENTAL FUNCTIONAL PROPERTIES AND METABOLIC CAPABILITIES OF THESE BUGS ARE ADAPTING TO OUR OWN ENVIRONMENTS VE THIS VERY EFFICIENT PATH OF HORIZONTAL TRANSFER. AND IT’S BEEN A LONG TIME LOOKING AT SINGLE CELL GENOMICS AND A LOT OF THINGS ON TRY TO FIND EVIDENCE OF THIS TRANSFER AND I’LL WALK THROUGH — I THINK WE FINALLY FOUND IT AND I’LL WALK THROUGH SOME OF THE EVIDENCE-BASED ON THE ISOLATE GENOMES THAT WE NOW HAVE. AND SO THIS IS A PRO PHAGE. AND HERE WE CAN SEE THE DARK COLORS HERE ARE JUST SORT OF THE COVERAGE IN METAGENOMES THAT CORRESPOND TO THESE ISOLATES AND WHAT WE SEE IS THESE ISOLATES FORM A PLAGUE. ALL OF THESE ARE DESCENDED FROM A SINGLE BACTERIUM, PROBABLY NO MORE THAN A DICK AID A DECADE OR TWO AGO, AND THIS RIGHT HERE, THEY PRETTY MUCH ALL HAVE THIS PRO PHAGE EXCEPT FOR THIS ONE HAS LIKELY MISSED IT. SO TO ME, THAT IMPLIES AN ACQUISITION, ALTHOUGH YOU COULD ARGUE IT COULD BE PERHAPS MULTIPLE LOSSES. BUT IF WE GO BACK TO THE GENOMIC DATA, WHAT WE SEE IS THAT ON DAY ZERO, NONE OF OUR — SO WE HAVE ISOLATES FROM DAY ZERO. NONE OF OUR ISOLATES HAVE THE PRO PHAGE. BUT OUR METAGENOME HAS THE GENES. IF WE GO TO DAY 340, OUR ISOLATES HAVE ON AVERAGE ONE COPY OF THE PRO PHAGE AND THEN WE ALSO SEE IT IN THE METAGENOME AND WE HAVE DONE THIS FOR OTHER GENES AS WELL. AND SO, THE IMPORTANT THING TO NOTICE HERE IS WHEN WE LOOK AT THE ISOLATES AND WE SORT OF NORMALIZE EVERYTHING TO ONE, WE SEE IS THAT THERE ARE MORE COPIES OF THIS PHAGE IN THAT METAGENOME THAN WHAT WE WOULD EXPECT BASED ON THE ISOLATES. AND WE HAVE GONE BACK NOW AND WE HAVE CONFIRMED THAT WE CAN FIND SOME OF THESE ELEMENTS IN OTHER SPECIES WITHIN THAT MICROBIOME AND THOSE OTHER SPECIES KIND OF EXPLAIN THE DIFFERENCE HERE. SO WE THINK WE HAVE GOT A NUMBER OF CASES WHERE WE REALLY HAVE THAT SMOKING GUN OF MICROBES COMING INTO A GENOME AND THEN PICKING UP NEW FUNCTIONALITIES WITHIN THE COURSE OF A HUMAN LIFETIME. SO, I TALKED A LOT ABOUT B FRAG. OTHER BUGS MIGHT HAVE DIFFERENT DYNAMICS. HERE WE ARE LOOKING AT E.COLI AND THIS IS DAY ZERO TIME POINT. WE JUST HAVE ONE ISOLATE. WE LOOKED AT DAY ONE74. NOW WE SEE A FEW BUGS THAT LOOK LIKE THIS AND ALSO WE SEE IT SPLITTING HERE. WHEN WE GOAT DAY 372, ALL OF THESE BACTERIA, WE SAW ON DAY ONE74, ARE GONE. AND WE ONLY SEE BACTERIA FROM THIS PARTICULAR PLATE AND WE LOOKED AT DAY 709, ALL OF THOSE BUGS ARE GONE AND WE SEE THESE TWO NEW ONES. SO E FRAG, WHERE WE ARE ACCUMULATING GENETIC DIVERSITY OVER DECADES, WITH E.COLI THE STORY IS DIFFERENT AND YOU COME BACK A FEW MONTHS LATER AND A LOT OF THE PREVIOUS STANDING DIVERSITY IS LOST. AND SO, LIKELY HAS SOMETHING TO DO WITH THE PARTICULAR NICHE AND LIFESTYLE OF THAT ORGANISM. SO, THE LAST THING I WANT TO TALK ABOUT IS ENDOSPORES. AND THIS IS SOMETHING THAT WE ALL KIND OF KNOW IS GOING ON AND IT’S A SENSE WELL, WE JUST SAW THAT SPECIES CAN CHANGE THEIR FITNESS BY ACQUIRING POINT MUTATIONS AND DELETIONS. THEY CAN CHANGE THEIR FUNCTIONALITY BY ACQUIRING NEW GENES. AM, HERE IS A CASE WHERE THEY CAN CHANGE THEIR MORPHOLOGY JUST BY MAKING A SORT OF REGULATORY CHOICE. AND SO, WHAT A GRADUATE STUDENT IN MY LAB DID, HE TOOK WHOLE COMMUNITY AND THEN HE PROCESSED IT TO KILL EVERYTHING EXCEPT FOR ENDOSPORES, EXTRACTED SEQUENCE BOTH OF THOSE COMMUNITIES, JUST A STANDARD 16S SEQUENCING, AND THEN COMPARES THEM TO IDENTIFY WHICH ARE THE BUGS IN ANY PARTICULAR SAMPLE THAT ARE EN FLIPPED SPORES. HE DID THIS FOR DOZENS OF PEOPLE AND THEN ALSO THROUGH TIME SERIES SO WE CAN SEE OF THE POTENTIALLY SPORE-FORMING BUGS, HOW OFTEN DO THEY — WHAT PERCENTAGE OF THOSE BUGS ARE PRESENT AS VEGETATIVE CELLS VERSUS SPORES AT DIFFERENT POINTS IN TIME? SO HERE IS WHAT THOSE DATA LOOK LIKE. HERE IS THE BULK COMMUNITY AND AFTER ENRICHING FOR ENDOSPORES. SO YOU TAKE A LOT OF THIS DIVERSITY AND A LOT OF IT GOES AWAY AND YOU’RE LEFT WITH JUST A FEW CLAYEDS OF CLOSE TRADIA AND THIS GUY I WON’T TRY TO PRONOUNCE AND BACILL I, THOSE THINGS KNOWN TO FORM SPORES, WE AWLS ALWAYS SEE ACTING BACTERIA. SO EVEN THOUGH WE KNOW THEY DON’T MAKE CONVENTIONAL ENDOSPORTS, WE CAN ISOLATE THEM FROM STOOL AND THEY ARE AT LEAST AS HARDY AS NORMAL SPORES SO WE THINK THEY HAVE AN ALTERNATIVE DORMANT STATE THAT FUNCTIONS VERY MUCH LIKE A SPORE. I DON’T HAVE A TIMER SO LOOKS LIKE RYAN IS TELLING ME TO — OKAY. WE ARE ABOUT DONE. SO, WE LOOKED AT THESE SPORES AND WE WENT BACK AND WHEEL LOOKED AT THE DYNAMICS OVER TIME AND WHAT WE FOUND IS THAT IN MOST OF THE TIME SERIES WE HAVE, WE HAVE TWO DIFFERENT GROUPS. AT LEAST ONE OF THE GROUPS IS HIGHLY-CORRELATED AND ALSO HIGHLY-VARIABLE OVER TIME. WHAT WE FOUND IS THE VAST MAJORITY OF OUR ENDOSPORES WERE IN THIS HIGHLY VARIABLE COMPONENT ALONG WITH BILL OVLA. THAT WAS INTERESTING TO US BECAUSE WE KNOW THAT THEY ARE PROBABLY REQUIRED FOR SPORE GERM NATON SO WE TOOK A NUMBER OF OUR STRAINS AND KIND OF TESTED THIS AND RIGHT AT PHYSIOLOGIC CONCENTRATIONS IS WHEN WE START TO SEE THINGS MOVING FROM 100% SPORE TO MUCH LOWER FRACTIONS OF SPORES. SO MOSTLY VEGETATIVE CELLS. AND THE OTHER INTERESTING THING WE FOUND ABOUT THESE SPORES IS IF WE LOOKED AT HOW MANY DIFFERENT PEOPLE SHARE SPORES, FOR BACTERIA WE ARE ALMOST 24 OUT OF 24 PEOPLE SHARE THAT BACTERIA, THEY WERE GENERALLY SPORE-FORMING BACTERIA. WHEREAS FOR NON-SPORE FORMING BACTERIA, MOST OF THE TIME YOU WILL ONLY SEE THAT PARTICULAR OTN A SUBSET OF YOUR POPULATION. SO WHAT THIS LED US TO THINK IS MAYBE THERE IS SAY TRADE OFF BETWEEN BEING HIGHLY VARIABLE AND NOT VERY PERMANENT BUT ALSO BEING ABLE TO TRANSMIT REALLY WELL ACROSS MULTIPLE PEOPLE. AND SO WE GO BACK TO THE TIME SERIES THAT I SHOWED YOU INITIALLY. WE CAN LOOK AT SPORE FORMERS AND NON SPORE FORMERS THAT WERE ABUNDANT INITIALLY AND WE SEE THAT SWITCH POST INFECTION SO IN THAT POST INFECTION REGIME, I GET COLONIZED BY A LARGE NUMBER OF SPORE FORMERS. AND IN FACT, ALL OF THESE BUGS DOWN HERE THAT I NOTED AT THE BEGINNING OF THE TALK, THESE ARE EXACTLY THE SMORE FORMERS THAT WE ARE TALKING ABOUT. SO IT’S THE SPORE FORMERS THAT GOT WIPED OUT AS A RESULT OF MY SALMONELLA INFECTION AND SPORE FORMERS THAT VERY RAPIDLY REPLACED THEM. WE CAN LOOK AT IT IN THE CONTEXT OF SEEDA. AND THE RATIO OF SPORE FORMERS IN HEALTHY CONTROLS VERSUS FIRST-TIME C DIVIN FECKSES VERSUS — INFECTIONS IS LOWER AND LOWER. SO BACK TO FECAL TRANSPLANTS. SOMETIMES THE PREFMT RECIPIENT STRAINS WENT OUT AND SOMETIMES THE DONOR STRAINS WENT OUT AND A LOT OF THIS IS EXPLAINED BY SPORES. SO FOR SPORES, WHICH ARE RESISTANT OTUs, WE MOSTLY SEE DONOR STRAINS WHEN THIS HAPPENS. SO IF THE PATIENT AND THE DONOR BOTH HAVE A PARTICULAR STRAIN, FOOTS A SPORE FORMER, WE WILL ALMOST ALWAYS SEE THE DONOR STRAIN R AS IF IT’S NOTED, WE’LL OFTEN SEE THE PATIENT STRAINS. SO, I THINK I’LL END THERE AND JUST THANK YOU FOR THE INVITATIONS AND THANK YOU FOR YOUR ATTENTION. [ APPLAUSE ]>>DR. RANALLO: SO WE HAVE TIME FOR ONE OR TWO QUESTIONS FOR ERIC.>>AUDIENCE MEMBER: NICE TALK, ERIC. SO, MY QUESTION IS, GOES TO THE POINT THAT MANY OF US TRY TO DEFINE A HEALTHY MICROBIOME. AND WHAT I THINK YOUR WORK SUGGESTS IS MAYBE WE SHOULD& RETHINK HOW WE DO THIS, THAT IS MAYBE WE SHOULDN’T BE THINKING OF ALONG THE LINES OF SPECIES AND STRAINS, BUT WE SHOULD BE THINKING ALONG THE LINES OF ACTUALLY DEFINING FUNCTIONAL SUB SYSTEMS OR GENOMIC ELEMENTS THAT ARE ESSENTIAL FOR HEALTH. AND IN THAT REGARD, IN THINKING ABOUT WHAT WE CAN DO IN DEVELOPING TOOLS TO ACHIEVE THAT. I MEAN I FOUND YOUR PRO PHAGE FINDINGS VERY INTERESTING, AND THAT COULD POTENTIALLY BE A WAY OF INTRODUCING GENOMIC ELEMENTS IN A NON STOCHASTIC WAY. AND TRYING TO ACHIEVE THAT NIRVANA OF THE HEALTH MICROBIOME. I WAS WONDERING WHAT YOUR THOUGHTS WERE.>>DR. ALM: I THINK IT’S A GOOD POINT AND THERE ARE SOME FUNCTIONS THAT ARE HIGHLY VARIABLE AND MAYBE CAN BE ACQUIRED WHEN YOU GOAT A NEW HOST AND WHEN YOU NEED THEM AND I THINK THERE IS GOING TO BE — THEIR FUNCTIONS THAT ARE GOING TO BE MORE DEEPLY EMBEDDED IN METABOLISM AND MORE DIFFICULT TO TRANSFER. SO I THINK WHAT WE NEED TO DO IS JUST LOOK AT THESE AND IDENTIFY WHICH ARE THE FUNCTIONS WHERE IF I KNOW THE FILOLOGYNY LIKE MY PRESCRIPTION IS PROBABLY FAIRLY GOOD AND WHICH ARE THE ONES THAT ARE GOING TO BE VERY DIFFICULT TO DO THAT WAY. LOOKING AT B FRAG, WE ARE JUST STARTING TO LOOK AT OTHER GROUPS AND I THINK IT WILL BE INTERESTING TO SEE WHAT ARE THE SELECTEDDIVE PRESSURES WHEN AN ORGANISM ENTERS A NEW HOST. AND A LOT DON’T HAVE THE SUSFAMILY GENES SO THEY ARE DOING SOMETHING DIFFERENT. IS IT ALWAYS CARBOHYDRATE USAGE? IS IT SOMETHING WHERE MAYBE MUNDANE OR — NOT MUNDANE BUT LESS USEFUL, LIKE KNOWING THEY ARE USING PHAGE? I DON’T KNOW.>>AUDIENCE MEMBER: HI, ERIC. SO, THESE STRAINS YOU TERM, IS IT POSSIBLE THAT THEY ARE ACTUALLY IN RARE BIOSPHERE OF THE DONORS MICROBIOTA AND SECOND QUESTION IS HOW MANY STRAINS IN A PERSON GUT MICROBIOME CAN YOU ESTIMATE? ARE THERE ANY ROUGH NUMBERS?>>DR. ALM: YES. SO, IN TERMS OF HOW MANY STRAINS WE CAN ESTIMATE IN ANY ONE PERSON, IT MIGHT DEPEND A LITTLE BIT ON HOW DEEPLY YOU SEQUENCE, TO BE ABLE TO SEE THINGS THAT ARE VERY, VERY LOW ABUNDANCE BUT FOR THINGS THAT ARE AT LEAST A FEW PERCENT, IT’S GENERALLY NOT MORE THAN LIKE 5 OR SO. NOW I SHOWED YOU THE DATA ON B FRAG WHERE WE HAVE LIKE 30 DIFFERENT STRAINS BUT MOST OF THOSE DIFFER BY ONLY ONE SNP. SO IF YOU RUN STRAIN FINDER ON THOSE LIKE METAGENOMIC TIME SERIES AND SEE HOW IT PANS OUT, IT WILL SAY THERE ARE TWO STRAINS, ONE CORRESPONDING TO EACH OF THOSE GROUPS THAT ARE ABOUT 10 SNPS APART. AND SO THE ENVIRONMENTAL. I THINK IT’S UNLIKELY — ALTHOUGH TOTALLY POSSIBLE THAT THEY ARE LOW-LEVEL PRESENT IN THE DONOR. IT’S MORE LIKELY THAT THEY ARE LOW-LEVEL PRESENTED IN THE RECIPIENT. AND THE REASON I SAY THAT IS FOR MOST OF THESE, WE GO BACK AND LOOK AT THE DONOR AND THEN WE LOOK AT THE OTHER 11 PATIENTS THAT WERE TREATED BY THAT DONOR AND NONE OF THEM — IF THE DONOR DOESN’T HAVE A SINGLE READ THAT MATCHES IT AND NONE OF THE OTHER 11 PATIENTS A SINGLE READ THAT MATCHED IT, THEN IT SEEMS MORE LIKELY IT WAS IN THE PATIENT ALTHOUGH MAYBE THEY ARE BOTH JUST SO FAR BELOW OUR DETECTION LIMIT THAT YOU WOULDN’T SEE THEM. SO, I KNOW PEOPLE GET UPSET WHEN I SAY ENVIRONMENTAL BUT IT’S MORE OF A — LIKE FROM MY PERSPECTIVE IF I’M THINKING ABOUT DESIGNING A SYNTHETIC MICROBIAL THERAPEUTIC, I DON’T CARE THE ORIGIN, LIKE EVERYTHING CAME FROM SOMEWHERE. THE IMPORTANT THING IS, I’M GOING TO PUT THIS ISOLATE AND MAYBE IT’S A GENETICALLY ENGINEERED ORGANISM TO COMBAT INFLAMMATION OR SOMETHING LIKE INTO A PATIENT, AND ONCE IT IS THERE, IT MAY BE OUT COMPETED BY THINGS THAT WERE NEVER IN THAT PATIENT. AND I THINK THAT IS THE TAKE HOME MESSAGE FROM ME ON WHAT — THE IMPORTANT CONSIDERATION IS REGARDING THESE ENVIRONMENTAL STRAINS. AND ALSO THE FACT THAT WELL, WITH HORIZONTAL TRANSFER AND JUST ACCUMULATION OF SNPS, FUNCTION CAN CHANGE. SO, IT’S NOT ENOUGH TO LIKE — THE ONLY THING THAT SEEMS TO BE CONSTANT IS THE 16S AND SO, IF ALL OF THESE DIFFERENT STRAINS HAVE DIFFERENT FUNCTIONS THEN IT IS HARD TO KEEP THAT LOCKED DOWN TO THE PHENOTYPE THAT YOU WANT TO PUT IN THERE.>>AUDIENCE MEMBER: SOPHERIM STANFORD AND IT WAS A GREAT TALK AND YOU HIGHLIGHTED THE IMPORTANCE OF HORIZONTAL GENE TRANSFER WITHIN THE MICROBIOME. MY QUESTION DOES WHETHER OR NOT YOU LOOKED AT THIS EVIDENCED IN YOUR FMT! SO GENES THAT ARE TRAVELING FROM THE DONOR TO THE RECIPIENT MICROBIOME?>>DR. ALM: SO NOT YET. BUT NOW THAT WE HAVE ALL THE DONOR STRAINS — SO WE HAVE A STUDY GOING ON RIGHT NOW THAT USED THE DONOR WE CHARACTERIZED REALLY WELL WITH LIKE THE TWO YEARS AND ALL THE ISOLATES FROM DONOR 44, THAT DONOR WE HAVE USED IN A FECAL TRANSPLANT STUDY FOR INFLAMMATORY BOWEL DISEASE AND WE’LL GET SAMPLES BACK. SO WE WILL GO BACK AND THEN CULTURE THOSE AND SEE WHAT CAME UP. SO PRETTY EXCITED TO GET OUR HANDS ON THOSE SAMPLES. BUT YES, DON’T HAVE A STORY YET.>>AUDIENCE MEMBER: WE’LL STAY TUNED.>>DR. RANALLO: THANK YOU VERY [ APPLAUSE ]>>DR. MARUVADA: GOOD MORNING EVERYONE. MY NAME IS PADMA MARUVADA, A PROGRAM DIRECTOR IN NIDD. AND A MEMBER OF TRANS-NIH MICROBIOME WORKING GROUP. ON BEHALF OF OUR WORKING GROUP, I WOULD LIKE TO THANK ALL THE ATTENDEES AND THE SPEAKERS WHO HAVE AGREED TO ACCEPT OUR INVITATION AND ALSO PRESENT YOUR WORK. AND PARTICIPATE IN THIS 3-DAY EVENT WHICH IS NOT EASY CONSIDERING YOUR BUSY LIFE. AND I WOULD LIKE TO TAKE A MOMENT AND GIVE THEM A ROUND OF APPLAUSE AT THIS POINT. [ APPLAUSE ] SO, I WOULD LIKE TO TAKE A MOMENT TO RECOGNIZE RITA. IT’S A PLEASURE FOR HER EFFORT TO KEEP US ON TASK AND ALSO SPEARHEADING THE WHOLE EFFORT AND KEEPING THIS MOMENT AND GOING FOR LIKE MORE THAN A YEAR AND A HALF. SO I WOULD LIKE TO GIVE HER A ROUND OF APPLAUSE AS WELL. [ APPLAUSE ] SO THE NEXT SCIENTIFIC SESSIONS FOCUS FURTHER ON ASPECTS OF MICROBIOME AND FURTHER EXPLORE HOW THE KNOWLEDGE WE GAINED SO FAR CAN BE LIKE USED FOR IMPROVING HUMAN HEALTH AND ALSO FOR DISEASE PREVENTION AND TREATMENT. WE HAVE FOUR SPEAKERS IN THIS SESSION. PETER TURNBAUGH OF UCSF, SCOTT BULTMAN OF UNC, MARIA GLORIDA DOMINGUEZ-BELLO OF NYU AND VIJAY YAJNIK OF MD ANDERSON CANCER CENTER. — ROBERT JENQ SO EACH SPEAKER WILL GET 19 MINUTES AND I HOPE EVERYONE STICKS THEIR TIME SLOT? THE INTEREST OF KEEPING THESE SESSIONS GOING. WE WILL TAKE ALL THE QUESTIONS AT THE END OF THE SESSION AND ALL THE SPEAKERS HAVE COMPLETED THEIR TALKS. AND ALSO, I WANT THE SPEAKERS TO INDICATE IF IT IS OKAY FOR LIKE A TAKING PHOTOS OF THE SLIDES PRESENTATIONS AND ALSO REQUEST AUDIENCE TO RESPECT AND HONOR THEIR REQUEST. AND PETER WILL GIVE THE TALK, TOWARD METAGENOMIC BASIS OF THERAPEUTICS.>>DR. TURNBAUGH: SO IT’S REALLY A PLEASURE TO BE HERE. THANK YOU ALL FOR STICKING INTO THE BITTER END TODAY. AND IT’S BEEN A TWO DAYS OF REALLY INSPIRING AND EXCITING RESEARCH. IT’S VERY INTIMIDATING TO GO AFTER DR. ALM. SO I’M GOING TO TELL YOU ABOUT THE TOPIC WE REALLY HAVE BEEN FOCUSED ON FOR THE LAST FEW YEARS IN OUR LAB, WHICH IS THE IMPORTANT INTERACTIONS BETWEEN THE MICROBES THAT LIVE WITHIN OUR GUTS AND INTESTINAL TRACT AND XENOBIOTICS, INCLUDING DRUGS, AND DIETARY COMPOUNDS AND OTHER ENVIRONMENTAL CONTAMINANTS. AND SO, I WANT TO START BY POINTING OUT WE ARE NOT THE FIRST GROUP TO THINK ABOUT THIS. WE HAVE BEEN SCANNED BY ALMOST A CENTURY. IN 1939, GERHARD WAS AWARDED NOBEL PRIZE FOR THIS DISCOVERY THAT THESEAISEO DYES HAVE ANTIBACTERIAL PROPERTIES. AND THIS LED TO THE DEVELOPMENT OF PRONTO SILL HERE. WHAT HE DIDN’T REALIZE AT THE TIME DESPITE THE FACT THAT HE GOT A PRIZE FOR THIS, IS THAT PRONTO SILL IS NOT THE ACTIVE COMPOUND THAT KILLS BACTERIA. IT TURNS OUT RESEARCHERS AT THE PAS TOUR DISCOVERED THAT PRONTO SILL GETS CLEAVED INTO THE TWO DOWNSTREAM METABOLITES, ONE OF WHICH ANOTHER ACTIVE COMPOUND HAS THE ANTIBACTERIAL EFFECT. EVEN MORE INTERESTINGLY, THERE IS NO ENZYME IN THE HUMAN GENOME THAT PERFORMANCE THIS BIOTRANSFORMATION. IT’S ONLY PERFORMED BY BACTERIA. SO YOU EITHER NEED THE PATHOGEN ITSELF OR THE MICROBIOME TO ACTIVATOR THIS PRO DRUG OR INERT COMPOUND FORMING THE ANTIBIOTIC. SO I THINK THIS IS EXCITING IN THE SENSE THAT IT SORT OF LED TO THE DAWN OF ANTIBIOTICS BUT ALSO WAS AN EARLY LESSON OF DRUGS WE USE IN PATIENTS ARE REALLY IMPORTANTLY INFLUENCED BY THE MICROBIOME. IF WE FAST FORWARD TO TODAY, WE NOW KNOW THAT AT LEAST 50 DIFFERENT WELL DRUGS ARE METABOLIZED BY GUT BACTERIA AS WELL AS BACTERIA AND OTHER BODY SITES. AND THIS LIST CONTINUES TO GROW ALTHOUGH RELATIVELY SLOW PACE YEAR BY YEAR. ONE OF THE THINGS THAT IS REALLY I THINK INTERESTING ABOUT THIS IS THAT THESE DRUGS ARE VERY DISTINCT FROM EACH OTHER IN THEIR STRUCTURE AS YOU’LL SEE IN THESE FEW EXAMPLES ON THE SLIDE. BUT THEY ARE ALSO USED FOR MANY DIFFERENT DISEASES. SO THIS IS NOT JUST RESTRICTED TO ANTIBIOTICS LIKE WE TALKED ABOUT. IT INCLUDES REALLY A KEY COMPOUND THAT ARE USED FOR THE TREATMENT OF CANCER, PARKINSON’S, RHEUMATOID ARTHRITIS AND, AND MANY OF THESE DRUGS ARE THE MAINSTAYS OF UPON CHEMOTHERAPIES FOR THESE INDICATIONS EVEN TODAY. AND SO, UNFORTUNATELY, DESPITE THE FACT THAT MANY OF THESE BIOTRANSFORMATIONS HAVE BEEN KNOWN FOR DECADES, WE STILL KNOW VERY LITTLE ABOUT THE ENZYMES THAT ARE RESPONSIBLE. AND SO IS THAT MEANS IF WE WERE TO SEQUENCE A MICROBIOME IT WOULD BE DIFFICULT PREDICT WHETHER OR NOT IT IS CAPABLE OF METABOLIZING ANY OF THESE DRUGS. AND SO, SOME OF YOU MAY HAVE HEARD THE PIONEERING WORK IN THIS AREA FROM THIS YOUNG SCIENTIST AT POSTER 36 YESTERDAY. AND MATT REALLY DID AMAZING STUDIES ON RENO T CAN IN THE WAY IN WHICH THE DOWNSTREAM METABOLITE IS LIBERATED BY IN THE GUT. OUR LAB ALSO WORKED ON DIGOXIN. WE PUBLISHED THE FIRST PAPER A FEW YEARS AGO NOW. HOPEFULLY MORE TO COME SOON. AND SINCE MOVING TO UCSF THREE YEARS AGO WE EXPANDED OUT TO LOOK AT OTHER MEDICATIONS, OTHERS IN THE LAB STUDYING DIJOCKS IN AS WELL AS MANY OF THE OTHER TYPES OF COMPOUNDS WE SEE ON THIS SLIDE. AND ALL OF THESE PEOPLE ARE FINDING INTERESTING THINGS AND I HOPE TO SHARE THE DATA WITH YOU GUYS SOON IN THE NEAR FUTURE. BUT I KNOW THAT PADMA IS THINKING WHY IS PETER TALKING ABOUT THERAPY? HE WAS SUPPOSED TO TALK ABOUT PREVENTION OF DISEASE. SO I WANTED TO SWITCH FOR THE REST OF THE TAKE TODAY TO AN AREA RELATED TO XENOBIOTIC METABOLISM THAT COULD HAVE IMPLICATIONS PRIOR TO THE DEVELOPMENT OF DISEASE. AND SO FIRST I WANT TO REMIND YOU THAT WE ARE NOT ONLY EXPOSED TO XENOBIOTICS THROUGH DRUGS. OUR DIET IS A RICH SOURCE OF SMALL MOLECULES. WE ALL KNOW THE DIET IS A MAJOR RISK FACTOR FOR DISEASE. BUT MOST OF US THINK ABOUT DIET AS A SORT OF MACRO LEVEL WHETHER OR NOT IT’S A FOOD LIKE A BROCCOLI OR A BREAD WHEREAS WE SHOULD THINK ABOUT OUR FOOD IN THIS WAY, WHICH IS THAT THEY ARE A COMPLEX MIXTURE OF SMALL MOLECULES THAT ARE NOT ONLY THE MACRO NUTRIENTS EVERYBODY TALKS ABOUT ALL THE TIME LIKE CARBS AND PROTEIN AND LIPIDS, BUT ALSO A RICH ARRAY OF COMPOUNDS ENTER OUR BODY ON A DAILY BASIS AND ARE THEN MODIFIED BY BACTERIA IN WAY THAT IS CHANGE THEIR BIOACTIVITIES. AND SO, OUR LAB IS REALLY INTERESTED IN APPLYING THE LESSONS WE LEARNED FROM DRUG METABOLISM TO BETTER UNDERSTAND THE PATHWAYS THROUGH WHICH GUT BACTERIA BIOTRANSFORM DIETARY SMALL MOLECULES. AND SO I’M GOING TO FOCUS ON ONE CLASS OF COMPOUNDS. THIS IS WORK DONE BY ELIZABETH BEST WHO IS A CHEMIST THAT JOINED OUR LAB A COUPLE OF YEARS AGO. AND SHE, LIKE MYSELF IS OBSESSED WITH COFFEE AND CD BREADS AND INTERESTINGLY, THESE ARE THE TWO MAIN SOURCES OF THESE POLYPHENOLS, AND THEY ARE ALSO FOUND IN VEGETABLES AND UBIQUITOUS THROUGHOUT OUR DIET. SO ALL OF US CONSUME LIGNANS EVERY DAY BUT THE CONCENTRATION VARIES DEPENDING ON OUR DIET. SO THE REASON WHY WE ARE INTERESTED IN LIGNANS AS MICROBIOLOGIST IS THE LIGNAN ITSELF IS THOUGHT TO BE AN INERT COMPOUND DELIVERED THROUGH OUR DIET BUT HAS LITTLE EFFECT ON THE BODY. WHAT HAPPENS IS THAT EVER WE CONSUME LIGNANS AS WE HEARD ABOUT FROM JOANNA YESTERDAY ETHEY GET MODIFIED BY A SERIES OF REACTIONS CALLALIZED ONLY BY GUT BACTERIA TO FORM THESE DOWNSTREAM PRODUCTS CALLED PHYTOESTROGENS. SO THE IMPACT OF THESE DIETARY COMPOUNDS ON DISEASE DEPENDS ON THE DEGREE TO WHICH THE MICROBIOME CAN ACTIVATE THEM. THE AREA IN WHICH LIGENANCE HAVE BEEN STUDIED IS BREAST CANCER ALTHOUGH IMPLICATED IN MANY OTHER DISEASES AND THIS COMES FROM WORK BY JOANNA AS WELL AS OTHERS TO SHOW THAT IN HUMANS IF YOU LOOK AT PEOPLE WITH THE HIGHEST QUARTILE OF PLASMA, THERE IS A 45% REDUCTION IN BREAST CANCER. AND IN RODENTS YOU CAN ADMINISTER THE COMPOUND ITSELF OR BACTERIA THAT PRODUCE THE COMPOUND ANDED THAT IS SOFT REDUCE TUMOR GROWTH IN ANIMAL MODELS. HOW DO WE GO FROM THE DIETARY COMPOUND TO THE PHYTOESTROGEN. SO THIS IS A SIMPLE MODEL OF WHAT LIFE MIGHT LOOK LIKE IN THE GUT IF YOUR BACTERIA LOOKING FOR THESE COMPOUNDS IN THE FOOD. AND SO, WE CONSUME THE INITIAL SUBSTRATE, AND OUR FAVORITE GUT BACTERIA WIDESPREAD IN HUMANS, PERFORMANCE THE FIRST TWO REACTIONS, THE SMITTLE NOT SHOWN HERE. SEIKO GETS PASSED OFF TO THE NEXT WHICH DOES THE NEXT REACTION AND THEN GOES BACK TO ELENTA OR POTENTIALLY OTHER MEMBERS AND THEN THAT GOES ON TO AN EXAMPLE OF A MULTI-STEP PATHWAY THAT CREATES THESE ACTIVE COMPOUND FROM DIETARY SUBSTRATES BUT ALSO REQUIRES THE PARTICIPATION. MANY DIFFERENT BACTERIA FOR THE FULL PATHWAY TO BE PERFORMED. THEY GO IN AND SO UNFORTUNATELY FOR ALL OF THESE SNIPPS THIS PATHWAY, WE DON’T KNOW THE GENES THAT ARE RESPONSIBLE. SO IF YOU GO TO ANY OF THESE DATABASES, YOU WON’T FIND ANY ANNOTATIONS OR LIGNAN METABOLISM. AND SO, WE WOULD LIKE TO KNOW HOW EACH OF THESE BACTERIA PERFORM SYSTEM PERFORMS THEIR STUFF. SO OUR LAB HAS BEEN COLLECTING UNIQUE STRAINS OF ELENTA FROM AROUND THE WORLD. WE HAVE 27 LENTA STRAINS NOW THAT COME FROM THREE DIFFERENT CONTINENTS. AND WHAT SHE DID IS DEVELOP AN ASSAY WHERE SHE CAN QUANTIFY IS IT THESE STRAINS. BECAUSE WE ARE NOT ADDING THE NEXT BACTERIA IN THE PATHWAY IT WILL STOP WHEN WE GET TO SECO. AND SHE QUANTIFIED THE CONVERSION FOR EACH STRAIN. SO YOU CAN SEE THAT 18 OF THE 27 MAKE SECO IN GREEN AND THE OTHER 9 LEAVE THE PINO INTACT. WE THEN SEQUENCE THE GENOMES OF THESE 27 STRAINS AND ANNOTATED ORTHOLOGOUS GENES OR GENE FAMILIES. SO EACH ROW IS SAY GENE FAMILY AND WE ARE LOOKING AT THE PRESENCE OR ABSENCE OF THE BLUE. AND WE JUST ORGANIZED BY THE NON METABOLIZERS ON THE LEFT AND METABOLIZERS IN THE MIDDLE AND THEN ON THE RIGHT HERE THIS IS A RANDOM FORREST ANALYSIS TO TRY TO FIND GENES THAT PREDICT METABOLISM. YOU CAN PROBABLY FIND THE SIGNAL WITHOUT ANY SORT OF STATS BECAUSE OF THE TOP YOU CAN SEE THERE ARE TWO GENES THAT PERFECTLY MATCH THE PATTERN OF METAP LIMP. SO THEY ARE FOUND IN THE REDUCING STRAINS AND MISSING IN ALL THE STRAINS. BOTH OF THESE GENES FALL TOGETHER IN THE ELENTA GENOME AND IS THERE ONLY ONE ENZYME THAT WE ARE CALLING BER AND THEN A TRANSCRIPTIONAL REGULATOR THAT IS NEXT TO IT THAT RECALL BERR. AND SO IS THIS IS SORT OF THE FIRST MYSTERY IS WE WENT IN LOOKING FOR TWO STEPS PERFORMED BY ELENTA AND WE ONLY HAVE ONE ENZYME. AND SO BECAUSE WE ARE SIMPLE-MINDED PEOPLE WE THOUGHT THE ONE ENZYME JUST DOES BOTH STEPS AND THEN THAT KIND OF MAKES SENSE IF YOU LOOK AT THE SYMMETRY AND REACTIONS. CONSIDERING THE ROLE OF BER IN THIS REACTION, IF WE ADD. INO, WE SEE IS THERE ONE THOUSANDFOLD UP REGULATION OF EXPRESSION OF BER AND WHAT IS MORE STRIKING IF WE LOOK GENOME-WIDE WE FIND THAT BER IS THE MOST HIGHLY UP REGULATED TRANSCRIPT. SHOW IS RNA-SEQ DATA. EACH DOT IS A TRANSCRIPT AND THEN THEY ARE ORDERED BY THE EXPRESSION LEVEL ON THE X AXIS. AND WHAT YOU CAN SEE IS THAT THERE IS A LOT OF SIGNIFICANT GENE THAT IS GO UP AND DOWN IN RED BUT THERE IS THE ONE LONELIY DOT AT THE TOP. SO IS THIS IS BER. SO ORDERS OF MAGNITUDE IS MORE EXPRESSED THAN ANY OTHER. WE ALSO SEE UPREGULATION OF REGULATOR ALTHOUGH TO A LESSER EXTENT. AND SO ELIZABETH WAS ABLE TO GO ON TO CLONE BER INTO A BACTERIUM THAT DOESN’T NORMALLY METABOLIZE LIGNANS. SO IS THIS IS E.COLI. THIS IS AN ANTIBACTERIA SHOWN HERE. WE ONLY SEE PIN-O AND DON’T SEE THE DOWNSTREAM PRODUCTS. WHEN WE CLONE IN BER, WE SEE 80% CONVERSION OF SECO AND THE 20% IS INTERMEDIATE COMPOUND. IN ADDITION TO THAT, SHE WAS ABLE TOUTE STRUCTURAL MODELING TO PREDICT RESIDUES THAT ARE IN THE ACTIVE SITE OF BER. SO SHE FOUND THESE TWO TYROSINES WE PREDICTEDDED WOULD BE INVOLVED IN SUBSTRATES. MUTATED IN THE ALLAH 13 AND THEN REPEATED THE ASSAY AND YOU CAN SEE AGAIN THE WILDTYPE EFFICIENT. THE CONTROL DOESN’T DO ANYTHING. AND THEN THE DOUBLE MUTANT HAS IMPAIRED ACTIVITY. SO IT IS STILL CAPABLE OF GOING TO SECO BUT TO A LESSER EXTENT THAN THE WILDTYPE ENZYME. SO THE CHALLENGE NOW IS THAT WE WANT TO KNOW ALL THE STEPS IN THIS PATHS WAY BUT WE HAVE A LOT OF TOOLS FOR RELIANT BUT DON’T HAVE ANY FOR — ELENTA — AND I’M NOT GOING INTO IT BUT WE DON’T THINK THIS STUFF IS PERFORMED BY ELENTA, POTENTIALLY FORMED BY OTHER RELATED BACTERIA. SO HOW DO WE NOW IDENTIFY THE STEPS IN THIS PATHWAY WITHOUT NEEDING TO DEVELOP THE STRAIN SELECTION FOR EACH OF THESE AND SO, SORT OF INSPIRED BY THE RNA-SEQ RESULTS FOR OTHER COMPOUNDS WE LOOKED AT, WE HAVE BEEN DOING JUST INCUBATIONS OF EACH OF THESE BACTERIA WITH THE SUBSTRATE THAT ARE METABOLIZED AND LOOKING FOR UPREGULATED TRANSCRIPTS A QUICK WAY TO LOOK AT CANDIDATE GENES. AND SO, WHAT WE FIND IS THAT THIS IS SECO INCUBATION AND YOU CAN SEE IT IS MESSIER THAN PINO BUT THERE ARE TWO GENES IN THE TOP RIGHT THAT ARE ALSO IN A SINGLE GENOMIC LOCI. THEY REPRESENT TRANSPORTER AND METHYL TRANSFERASE SO IS THIS IS A GOOD CANDIDATE FOR THAT ACTIVITY. AND THEN THE SAME THING HERE. YOU CAN SEE THERE ARE THREE GENES THAT ARE REALLY FAR REMOVED FROM THE CLOUD AND THOSE ARE ALSO WITHIN A SINGLE GENOMIC LOCI AND THEY REPRESENT TWO ENZYMES AND A TRANSPORTER. SO WE ARE CURRENTLY VALIDATING THESE IN E.COLI AS WELL AS THE ENZYME FOR THE REMAINING. SO JUST TO WRAP UP THIS PROJECT I WANTED TO EXPLAIN TO YOU WHY WE THINK IT IS WORTH GOING TO THE TROUBLE OF IDENTIFYING THESE NOVEL GENES THAT ARE INVOLVED IN XENOBIOTIC METABOLISM. AND SO THE FIRST THING YOU COULD MANAGE SIN ONCE WE SUCCEED AND IDENTIFYING ALL THE STENS OF THIS PATH I WAXER THAT PROVIDES A TOOL IN WHICH WE CAN NOW ENGINEER BACTERIA THAT PERFORM THE FULL PATHWAY, AND SO, WHAT WE ARE STARTING WITH IS A COMPLICATED SYSTEM. YOU HAVE CHANGES IN DIET, MANY DIFFERENT BACTERIA INVOLVED, AND CHANGES IN THE COMPOUNDS AND THEN ULTIMATELY PHENOTYPES PEOPLE CARE ABOUT WHICH IS REDUCTION IN BREAST CANCER OR OTHER DISEASES. SO WE’D LIKE TO EMERGE ALL OF THESE INTO A SINGLE ORGANISM THAT PERFORMANCE ALL THE STEPS IN THE PATHWAY IN WHICH WE CAN REGULATE THE ACTIVITY OF EACH. WE ALSO NOW HAVE THE ABILITY TO PERFORM GERM-FREE MOUSE EXPERIMENTS IN MODELS OF BREAST CANCER. SO TOGETHER WITH UCSF, WE HAVE DEVELOPED MOUSE MODELS OF BREAST CANCER AND HOPE TO COLONIZE THEM WITH CONTROLLED STRAINS REPRESENTING DIFFERENT STEPS IN THE LIGNAN WELL PATHWAY. AND SEE WHETHER OR NOT THAT RESULTS IN A CHANGE IN TUMOR BURDEN. AND SO I WANTED TO END WITH A TOP TAKE I THINK HAS COME UP THROUGHOUT MANY TALKS THROUGHOUT THE LAST COUPLE OF DAYS AND THAT IS I THINK IN ORDER TO UNDERSTAND WHAT IS GOING ON IN THE MICROBIOME AND IN GENERAL IN HOST MICROBIAL INTERACTIONS IT WILL REQUIRE A LOT OF US THAT ARE BIOLOGIST AND METAGENOME CYSTS AND COMFORTABLE WITH MICROBES TO START THINKING ABOUT THE CHEMISTRY THAT IS PERFORMED BY THESE MICROBIAL COMMUNITIES. SO JUST LIKE WALTER WAS INSPIRED BY HIS BATTLES WITH CANCER TO BECOME A CHEMIST, WE AS MICROBIOME RESEARCHERS NEED TO LEARN AND GO BACK TO CHEMISTRY, BIOCHEMISTRY, STRUCTURAL BIOLOGY AND ENZYMOLOGY TO BETTER UNDERSTAND HOW THESE MICROBIAL FUNCTION AT A MOLECULAR LEVEL. IF YOU’RE INTERESTED IN SORT OF MEETING CHEMISTS OR HANGING OUT WITH CHEMISTS, MAYBE BECOMING ONE, TOGETHER WITH EMILY AND DENNIS WE ARE ORGANIZING A KEYSTONE CONFERENCE FOR THE NEXT SESSION AND SOMETIME IN 2018-2019. SO STAY TUNED. AND SO I JUST WANT TO ACKNOWLEDGE ALL OUR WONDERFUL MEMBERS OF THE LAB: [ READING ] ELIZABETH IS THE POSTDOC LEADING THE LIGNAN PROJECT. AND DAVID GUTTEENBURG IS HERE AT THE MEETING. HOPEFULLY HE IS STILL AROUND. THE FIRST PERSON TO JOIN MY LAB WHEN I WAS A FELLOW IN BOSTON AND HAD A TRANSFORMATIVE EFFECTED ON GETTING US STARTED AND ALL OF THE EARLY WORK WE DID WHEN WE WERE ON THE EAST COAST. SO THANK YOU AND THANK YOU FOR HAVING ME. [ APPLAUSE ]>>DR. MARUVADA: THANK YOU, PETER. SO THE NEXT SPEAKER IS SCOTT BULTMAN AND HE IS GOING TO TALK ON GUT MICROBIAL METABOLITES AND CANCER PREVENTION.>>DR. BULTMAN: SO THANK YOU TO THE ORGANIZERS FOR THIS OPPORTUNITY. I’M HAVING A GREAT TIME. OUR LAB IS INTERESTED IN THE IDEA THAT DIETARY FACT EXPOSE DIGESTIVE COMPONENTS GET METABOLIZED BY GUT MICROBIOTA INTO METABOLITES THAT INFLUENCE THE RISK OF VARIOUS DISEASES INCLUDING CANCER. SO, THIS CAN IMPINGE A NUMBER OF DIFFERENT CANCER MECHANISMS. SO CERTAIN THINGS LIKE BIOACIDS CAN GET CONVERTED TO CONVERTED ONCOMETABOLITES WHEREAS OTHER THINGS LIKE PLANT-BASED FIBERS AND POLYPHENOLS CAN GET CONVERTED TO TUMOR SUPPRESSIVE METABOLITES. THEY CAN HAVE DIRECT EFFECT ON THE INTESTINAL EPITHELIAL CELLS. THEY CAN ALSO EFFECT THE IMMUNE CELLS TO MODULATE THE IMMUNE RESPONSE AND INFLAMMATION. SO, I SHOULD GO BACK ONE. WE ARE ESPECIALLY INTERESTED IN THIS GUY HERE, BUTYRATE IT’S A SHORT-CHAIN FATTY ACID. AND IF YOU LOOK ATS STRUCTURE, YOU CAN REALLY SEE FOR YOURSELF IT IS A SHORT CHAIN WITH ONLY FOUR CARBONS AND I DO KNOW THAT THERE IS A HANDFUL OF SHORT-CHAIN FATTY ACID AND BUTTERIATED AFFICIONADOS IN THE AUDIENCE. FOR THOSE WHO AREN’T, THE STORY BEGINS UP HERE WITH DIETARY FIBER. SO IS THIS IS THE COMPLEX CARBOHYDRATE THAT IS NOT DIGESTED OR ABSORBED IN THE UPPER GI TRACT AND REACHES THE COLON AND HERE IS BACTERIA THAT FERMENT INTO SHORT-CHAIN FATTY ACIDS. THESE ARE THE THREE MOST ABUNDANT. EACH PRESENT AT THE LUMEN AT MOLAR LEVELS. WHAT MAKES BUELLERATE INTERESTING TO SHE IT IS UTILIZED — BUTYRATE — IN THE EPITHELIAL CELLS THEMSELVES. IT GETS TRANSPORTED IN AND CAN GO TO TWO DIFFERENT COMPARTMENTS. FIRST TO THE MITOCHONDRIA WHERE IT IS IMPORTANT FOR ENESH JET I. SO UNLIKE MOST CELL TYPES IN OUR BODY THAT USE GLUCOSE AS PRIMARY ENERGY SOURCE. THESE ARE DIFFERENT. THEY GET 60-TENT 70% OF THEIR ENERGY FROM BEAUTY 8. THERE IS SAY LOT OF IT AND AS A FATTY ACID, IT IS OXIDIZED READILY. NOW SECONDLY, BUTYRATE CAN GO TO THE NUCLEUS WHERE IT IS IMPORTANT FOR EPIGENETICS. IT’S A NATURALLY-OCCURRING HISTONE DEACETYLASE INHIBITOR OR HDAC INHIBITOR. THE FIRST ONE EVER CHARACTERIZED. SO THERE IS SAY COUPLE OF LINES OF EVIDENCE THAT IMPLICATE BUTYRATE IN CANCER PREVENTION. FIRST, IS IF YOU ADD BUTYRATE TO TUMOR DERIVED CELL LINES INCLUDING COLORECTAL CANCER CELLS, IT DEES COUNTRIES PROLIFERATION AND INCREASES APOPTOSIS AND/OR DIFFERENTIATION. THIS IS A GREAT RESULT BUT WE ARE ALL AWARE OF THE CAVEATS OF TUMOR-DERIVED CELL LINES AND I’M NOT GOING TO GET INTO. SO IS THERE IS SAY SECOND LINE OF EVIDENCE COMING FROM 16S SEQUENCING STUDIES. THESE ARE ALL WORKING WITH HUMAN FECAL SAMPLES. AND THEY ALL REACH THE SAME CONCLUSION AND THAT IS FOR BUTTE RATE PRODUCERS, THERE ARE A NUMBER OF ABUNDANCES THAT DIMINISH IN COLORECTAL CANCER CASES COMPARED TO CONTROLLED. AND SO IS THIS IS ALSO AID GOOD RESULT BUT THERE IS A LIMITATION HERE TOO AND THIS IS REOCCURRING THEME AT THIS MEETING IT’S REALLY DIFFICULT OR IMPOSSIBLE TO KNOW WHETHER A PARTICULAR CHANGE IN THE MICROBIESOME A CAUSE OR CONSEQUENCE OF DISEASE. AND THAT LIMITATION HOLDS HERE FOR SURE. SO WE HAVE TAKEN A DIFFERENT APPROACH TO FURTHER INTERROGATE BUTTURE 8 FUNCTION AND WHAT WE ARE DOING HERE — BUTYRATE — WE ARE USING MOUSE MODELS. I’M DEPICTING TWO ISOLATORS HERE. I’LL START ON THE LEFT. THESE MICE WERE GERM-FREE AND NOW WE COLONIZED THEM WITH FOUR COMMENSAL BACTERIA REFERRED TO AS THE [ INAUDIBLE ] SO THESE ARE COMMENSALS THAT OCCUPY DIFFERENT GI NICHES AND THEY RESTORE SOME DEGREE OF NORMALCY TO THE GUT WHICH IS ABNORMAL IN A GERM-FREE STATE BUT IT DOES THIS IN A CONTROLLED MANNER. AND WE PROVIDE THE MICE WITH CONTROL OR HIGH-FIBER DIETS THAT ARE CALOREICALLY MATCHED AND VIRTUALLY IDENTICAL. AND THE HIGH-FIBER DIET IN THIS CASE IS 6% FUKETOWAL GO SACCHARIDES AND IMLIN BECAUSE IT’S FERMENTED EFFICIENTLY INTO BUTYRATE AND THEN WE INDUCE TUMORIGENESIS. WE ARE USING THE PRO CARCINOGEN, AOM, AND THIS ONLY INDUCES COLORECTAL TUMORS AND THERE ARE A LOT OF SIMILARITIES WITH HUMANS SPORE ADDIC COLORECTAL CANCER. FOR EXAMPLE, IT MUTATES EITHER APC OR BETA CATENIN LEADING TO DEREGULATED WNT SIGNALING. OVER HERE THE SAME SCHEME. THESE MICE HAVE BEEN COLONIZED WITH THE FOUR ASF BUGS PLUS THIS GUY HERE, THIS IS A BUTYRATE PRODUCER. OTHER THAN THAT, CONTROL DIET, HIGH-FIBER DIET, INDUCED TUMORIGENESIS. THE IDEA IS CONTROL CONTROL CONTROL, EXPERIMENTAL. IT’S THE COMBINATION OF THE HIGH-FIBER DIET WITH THE BUTYRATE-PRODUCING BACTERIA NA YIELDS HIGH LEVELS OF BUTYRATE IN THE LUMEN OF THE GUT IN THE FIRST PLACE. AND WE KNOW THIS BASED ON LC MASS SPEC MEASUREMENTS. THE HYPOTHESIS IS AS A RESULT, THE EXPERIMENTALS WILL HAVE DIMINISHED BURDEN. SO THIS IS THE FACT BASED ON A NUMBER OF EXPERIMENTS. SO, WHEN WE LOOK THAT THE GRAPH, FIRST THE HIGH-FIBER DIE OAT ITS OWN IN THE ABSENCE OF BUTTE RATE PRODUCING BACTERIA DOES NOT HAVE A PROTECTIVE EFFECT. AND SIMILARLY, THE BUTTED RATE PRODUCE OR ITS OWN WHEN MATCHED WITH A LOW-FIBER DIET ALSO DOES NOT HAVE A PROTECTIVE EFFECT. INSTEAD IT IS THE COMBINATION OF THE HIGH-FIBER DIET WITH THE BUTYRATE-PRODUCING BACTERIA IN THESE EXPERIMENTAL ANIMALS THAT GIVES RISE TO SIGNIFICANTLY FEWER TUMORS. IN ADDITION THESE TUMORS ARE SMALLER AND WHEN WE DOLL H&E-BASED HISTOPATHOLOGY, THEY ARE LESS PROGRESSED. SO WE NEEDED TO DOD ANOTHER EXPERIMENT TO REALLY SHOW THAT BUTYRATE IS A CAUSAL FACTOR. AND STOW I’M SHOWING HERE ON THE LEFT IS RESHOWING WHAT I JUST SHOWED YOU. THE THREE CONTROL GROUPS AND THE EXPERIMENTAL WITH THE WILDTYPE BUTYRATE PRODUCER AND THE LOWER TUMOR BURDEN. NOW OVER HERE, IN THIS ISOLATER, IT WAS THE SAME EXPERIMENT THAT WE ARE WORKING WITH A MUTANT STRAIN OF B FIB. SO SAME BACTERIA, DIFFERENT STRAIN, 0.8KB DELETION IN THE MIDDLE OF THE BUTTERAL — AND THESE BUGS HAVE DECREASED DIMINISHED BUTYRATE PRODUCTION. SO WHEN WE DO OR MATCH THIS WITH THE HIGH-FIBER DIET, THERE IS TUMOR SUPPRESSIVE EFFECT BUT IS SIGNIFICANTLY ATTENUATED COMPARED TO THE WILDTYPE. SO IN OTHER WORDS, THE TUMOR SUPPRESSOR EFFECT IS COMMENSURATE WITH THE BUTYRATE-PRODUCING CAPACITY OF THE BACTERIA. WE DID ONE OTHER IMPORTANT CONTROL EXPERIMENT AND THAT IS SHOWN ON THE RIGHT SIDE HERE. SO THESE MICE ONLY GOT THE AS IS F BACTERIA, NO BUTTE RATE PRODUCER AND INSTEAD OF BEING GIVEN HIGH-FIBER DIET, THEY WERE GIVEN CONTROL DIET BUT FORTIFIED WITH BUTYRATE. THIS HAD STRONG OR STRONGER OF A TUMOR SUPPRESSER EFFECT. WE CAN RECAPITULATE THE HIGH-FIBER DIET BY WILDTYPE BUTYRATE BY SUPPLYING THE BYES EXOGENOUS BUTYRATE. SO WE HAVE DONE A LOT TO DEVELOP A WORKING MODEL. THERE IS ASPECTS THAT I WON’T BE ABLE TO GET INTO DETAIL TODAY BUT IT IS FIBER, BACTERIAL FERMENTATION INTO BUTYRATE T IS IMPORTANT FOR NORMAL COLONIC HOMEOSTASIS N LARGE PART BECAUSE IT IS METABOLIZED IN THE MITOCHONDRIA HAS MORE TO DO WITH ENERGETICS. IT IS IMPORTANT FOREVER TUMOR SUE PRUSSIAN. IN THE TUMOR CELL, THESE CELLS DUE TO THE WAR BRED EFFECT SWITCH THEIR METABOLISM SUCH GLUCOSE METABOLISM.RELIANT ON THE BUTYRATE TRANSPORTERS ARE STILL EXPRESSED. BUTYRATE STILL TRANSPORTED IN BUT NOW BECAUSE IT IS NOT METABOLIZED TO THE SAME EXTENT IN THE MITOCHONDRIA, IT ACCUMULATES TO HIGHER LEVELS, GOES TO THE NUCLEUS, AND ACTS AS AN HDAC INHIBITOR TO EPIGENETICALLY REGULATE GENE EXPRESSION THAT DO THESE THINGS. THERE IS SAY NUMBER OF THINGS STILL NEED TO BE DONE WITH THIS MODEL TO FLUSH IT OUT FURTHER. ONE IS TO GET AT THE IDEA OF BUTYRATE TARGET GENES AND THE WAY THAT WE ARE DOING THIS IS CHIP STEEK LOOK AT H3K9 AND H3K27 ACETYLATION. THESE MARKS ARE ENRICHED AT PROMOTORS AND ENHANCERS RESPECTIVELY ALONG WITH RNA-SEQ AND TO GIVE AN EXAMPLE, WE ARE SEEING ENRICHMENT AT A LOT OF CELL CYCLE AND PRO APOPTOTIC GENES SHOWING A TRACE WITH FASLOOKING AT H3K9 ACETYLATION IN THE PROMOTOR WHERE YOU CAN SEE TUMORS FROM THE EXPERIMENTAL MICE THAN THE CONTROL MICE. THE OTHER THING THAT WE ARE LOOKING AT TO TRY TO GET AN IDEA OF WHERE THE SPECIFICITY COMES IN, IS OCCUPANCY WITH 3 HDACS THAT ARE OVER EXPRESSED IN COLORECTAL CANCER. SO WE ARE DOING THIS NOW. THE MODEL THAT WE HAVE IS THAT DURING TUMORIGENESIS THE H DAX ARE UP REGULATED AND THEY ARE PLAYING A ROLE IN DRIVING CANCER AND THEY ARE DIMINISHING THE EXPRESSION OF CERTAIN PRO APOPTOTIC GENES LIKE FAAS AND NOW IF THEIR IS SUFFICIENT& LEVELS OF BUTTE RATE, IT CAN ACT AS A BRAKE PEDAL ON THE DRIVER TO ALLOW HIGHER LEVELS OF EXPRESSION TO BE REESTABLISHED. THERE IS OTHER THINGS THAT HAVE TO BE DONE AS WELL. WE NEED TO INVESTIGATE MORE THROUGHLY THE ROLE OF BUTYRATE IN INFLAMMATION. WE ARE DOING THIS A COUPLE OF DIFFERENT WAYS. LOOKING AT OTHER DIETARY FACTORS AND THEN THE OTHER IMPORTANT THING WITH MOST MODELS AND THIS HAS COME UP EARLIER TOO, IT IS HUMAN RELEVANCE. WE HAVE A LITTLE BIT OF DATA ON THAT. SO LOOKING AT A NEARLY A DOZEN ADENOCARCINOMAS ALONG WITH NORMAL-MATCHED COLON SAMPLES, WE SEE JUST LIKE OUR MOUSE MODEL, WE SEE HIGHER LEVELS OF BUTYRATE ACCUMULATING IN THE TUMORS COMPARED TO THE NORMAL. AND ALSO JUST LIKE OUR MOUSE MODELS, WE SEE HIGHER LEVELS OF GLOBAL HISTONE ACETYLATION IN THE TUMORS COMPARED TO NORMAL. SO, WE THINK THAT THIS IS ENCOURAGING. NOW, SHIFTING OVER TO CHALLENGES. I HAVE A COUPLE. CHALLENGE NUMBER 1 IS THE NEED TO DO HIGH-THROUGHPUT FUNCTIONAL ANALYSIS OF MICROBES. I THINK THIS PROBLEM IS BECOMING MORE ACUTE BECAUSE THIS NOTION THAT MOST OF THE MICROBIOTA ARE UNCULTIVATABLE SEEMS TO BE THE IDEA IS DIMINISHED DAY-BY-DAY. WE ARE GETTING MORE AND MORE MICROBIAL ISOLATES AND WE WILL NEED A WAY TO INTERROGATE THEIR FUNCTION. SO I’M OBVIOUSLY A FAN OF MOUSE MODELS BUT THERE ARE LIMITATIONS AND I HAVE A FEW LISTED HERE INCLUDING THE FACT THAT THEY ARE EXPENSIVE AND LOW THROUGH PUT. SO THERE IS SAY NEED TO MAYBE DEVELOP CELL CULTURE MODELS THAT WILL ALLOW OR BE AMEN TO BELIEVE COCULTURES WITH MICROBIOTA. I’M NOT TALKING ABOUT KPO2 CELLS. I’M GOING IN THE WAY OF ORGANOID TECHNOLOGY. THIS IS A HUGE ADVANTAGE BUT THIS ALSO HAS LIMITATIONS. THIS IS THE TYPICAL STATE OF THE TECHNOLOGY AND THEY DO GROW AS STARED STRUCTURES. SO THE PSEUDOLUMEN IS ENCLOSED IN THE MIDDLE HERE AND IT IS VERY DIFFICULT TO CONTROL THE CONDITIONS AND THIS WHERE THE BACTERIA WOULD BE. SO THE BACTERIA NEED TO BE PHYSICALLY MICROINJECTED INSIDE. SO IS THIS ISN’T IDEAL. THERE IS ROOM FOR NEW APPROACHES AND MY COLLEAGUES AND I ARE WORKING ON THIS. AND SO WHAT WE HAVE, WE HAVE A SCAFFOLD AND IT IS SHAPED, THE SAME SIZE AND DIMENSION OF A HUMAN CRYPT. AND IT IS CODED WITH HYDROGEL SHOWN IN PINK HERE. AND THEN SEEDED WITH HUMAN LGR5 INTESTINAL STEM CELLS. AND ONE OF THE ADVANTAGES OF HAVING THIS IN AN OPEN FORMAT WHERE IT IS NOT ENCLOSED IS A SPHEROID AND WE CAN APPLY CHEMICAL GRADIENTS AND GROWTH FACTOR GRADIENTS, INCLUDING WNT AND THIS ALLOWS THE CRYPT TOP POLARIZED SUCH THAT THE STEM AND THE PROGENITOR CELLS THAT ARE PROLIFERATIVE, SHOWN IN GREEN, ARE AT THE BASE OF THE CRYPT AND THE POST MITOTIC DIFFERENTIATED CELLS SHOWN IN BLUE ARE NEARLY THE LUMEN. AND TO SHOW YOU THIS, HERE IS AN IN-VIVO HUMAN CRYPT AND SHEAR ONE OF OUR IN-VITRO CRYPTS ON THE DEVICE. SO IF WE LOOK AT THE GREEN MARKER, WE HAVE THE PROGENITORS AND THE STEM CELLS AT THE BASE AND IF WE LOOK AT THE RED MARKER, WE HAVE THE DIFFERENTIATED CELLS NEAR THE LUMEN. WE CAN COCULTURE THESE WITH MICROBIOTA. WHAT WE ARE DOING FIRST AND IS TRYING TO DELIVER A SHARP OXYGEN GRADIENT, DEPICTED HERE, AND WE HAVEN’T DONE THIS YET. IT’S STILL ONGOING. BUT THE HOPE IS TO KEEP THE CRYPT IN A NOR MOCKSIC STATE THAT WILL KEEP THE COLONIC EPITHELIAL CELLS HAPPY. BUT KEEP — IT WOULD HAVE TO BE SHARP GRADIENT OF COURSE AND KEEP THE LUMINAL COMPARTMENT AN AEROBIC TO ALLOW FOR CO-CULTURE OF OB I WILL GAT ANNA ROBES GETTING US AT HOST MICROBE INTERACTIONS THAT ARE PHYSIOLOGICALLY RELEVANT. ANOTHER CHALLENGE IS KIND OF MOVING FROM IDENTIFYING METABOLITES TO REALLY UNDERSTANDING THAT FUNCTION. SO THE FIRST PHASES OF THE HUMAN MICROBIOME PROJECT MAKES SENSE. PERFECTLY APPROPRIATE TO TAKE DISCOVERY-DRIVEN, MULTIPLE-OMICS APPROACHES AND YIELDED A LOT OF INFORMATION. I LIKE THIS APPROACH OBVIOUSLY BECAUSE IT’S UNBIASED IT COVERS A LOT OF GROUND KIND OF LIKE PLOWING TO USE A FARMING ANALOGY. BUT THE LIMITATION IS IT ONLY SCRATCHES THE SURFACE. AND SO, HOPEFULLY AT SOME POINT, WE ARE GOING TO BE AT A POINT WHERE WE HAVE A LIST OF INTERESTING CANDIDATES AND THE CHALLENGE OF HOW THAT IS VETTED AND HOW WE MOVE INTO THE NEXT PHASE, WHICH IS MORE HYPOTHESIS-DRIVEN WHERE WE LOOK AT SPECIFIC CANDIDATES AND STICK WITH A DRILLING, FARMING ANALOGY, WHERE WE DRILL DOWN AND PROBE FUNCTION MORE. BUT THIS TAKES A LOT OF TIME AND SOMETHING WE’LL NEED TO DISCUSS. ONE IDEA ON THAT IS THAT THERE COULD BE SOME CHALLENGES ON THIS. A CAUTIONARY NOTE COMES FROM BUTYRATE. THE MEITABLE LIGHT WE KNOW RELATIVELY A LOT ABOUT. — METABOLITE — AND PROBABLY A LOT OF THESE METABOLITES WILL BE PLEAO TROPEIC. IT’S A LIGAND FOR G PROTEIN COUPLED RECEPTORS AND CAN ACT ON CELL AUTONOMOUSLY ON THE CANCER CELL ITSELF, BUT IT CAN ALSO ACT NON-CELL AUTONOMOUSLY VIA THE IMMUNE SYSTEM EITHER THROUGH BARRIER FUNCTION OR THROUGH DIRECT BY INDUCING THE REGULATION OF T-REG CELLS. SO TRYING TO FIGURE OUT THE RELATIVE IMPORTANCE OF ALL THESE DIFFERENT MECHANISMS IS NOT TRIVIAL. AND THEN MY LAST THING, CHALLENGE NUMBER 3, TRYING TO IMPROVE OR MOVE THINGS INTO THE PRO BIOTIC AND PREBIOTIC REALM IN HAN ACCELERATED MANNER. THIS CAN TAKE A LOT OF FORMS. ONE OF THE THINGS IS TO INTEGRATE MICROBIOME STUDIES A LITTLE BIT BETTER WITH EPIDEMIOLOGY AND GWAS OR EXOME SEQUENCING. AND SO I’M OVER. JUST ACKNOWLEDGE FOLKS MY LAB: [ READING ] WITH THAT I’LL STOP. THANKS. [ APPLAUSE ]>>DR. MARUVADA: SO THE NEXT SPEAKER IS MARIA GLORIDA DOMINGUEZ-BELLO FROM NYU. SHE WILL BE TALKING ON MIKE CROW BIOMES AND PHENOTYPES: IMPACT, RESTORATION AND TRANSFER.>>DR. BELLO: SYSTEM>>DR. BELLO: THANK YOU PADMA AND LETTA AND THE ORGANIZERS OF THIS WONDERFUL SYMPOSIUM. HUMANS STARTED AN USH ANIZATION PROCESS THAT HAS LASTED AND IS CONTINUING THROUGH THE LAST FEW THOUSAND YEARS. AND WE KNOW THAT THE WORLD IS BECOMING MORE URBAN EVERY TIME. AND WITH URBANIZATION, WE HAVE THE WELL-KNOWN IMMUNE ASSOCIATED DISORDERS. SO, THERE ARE TWO HYPOTHESIS. WE DON’T KNOW WHY THIS IS HAPPENING. AND THERE ARE TWO HYPOTHESIS THAT DEAL WITH MICROBIAL ETIOLOGY. ONE IS THE HYGIENE HYPOTHESIS WHICH DEALS WITH THE EFFECT OF EXPOSURE TO ENVIRONMENTAL BACTERIA. AND THE OTHER IS THE DISAPPEARING MICROBIOTA HYPOTHESIS WHICH POSTULATES THAT IT IS HUMAN BACTERIA FROM THE MICOBIOME. THE FACT IS THAT AS MAMMALS, HUMANS START LIFE WITH HEAVY EXPOSURE TO HUMAN BACTERIA, MATERNAL. WE ARE ALL BORN — IF WE ARE BORN NATURALLY, ALREADY SEEDED, ALREADY INOCULATED BY THE TIME OF BIRTH, PICKING UP THE COLONIZATION BOX FROM OUR MOTHER’S VAGINAS AND THEN THE BABIES WILL NOT EAT BUT A LIQUID PRODUCED BY THE MOTHERS. WHICH IS MILK. AND THAT WILL SELECT FOR SOME OF THE VAGINAL PERINEIL BACTERIA THAT WERE PICKED AT BIRTH. AND THEN MOM IS STILL THERE AND UNTIL THE BABY REALLY DEVELOPS ENOUGH SENSORIAL, BRAIN, LOCOMOTION, TO BE ABLE TO EXPLORE THE ENVIRONMENT. AND THERE COMES A VERY BIG EXPLORATION OF THE ENVIRONMENT AFTER THAT. AND IN URBAN SOCIETIES, BECAUSE WE HAVE TECHNOLOGIES THAT HAVE BEEN VERY EFFICIENT FOR EXTENDING LIFESPAN AND — BUT WE PERTURB AND ABUSE PRACTICES THAT REALLY IMPAIR TRANSMISSION AND COLONIZATION OF MOST MICROBES. ON THE HUMAN SIDE WE HAVE C-SECTIONS AND ANTIBIOTICS, FORMULA FEEDING. WE USE TECHNOLOGY TO KEEP THE BABY FAR FROM THE MOTHERS TO TRANSPORT OR MONITOR THEM IN THEIR OWN, VERY CLEAN ROOMS WHERE THEY ARE RAISED. AND THE FIRST BIG IMPACT AT BIRTH, DURING LABOR AT BIRTH IS C-SECTION. C-SECTION IS A COMPLISIDE BECAUSE ITSELF REQUIRES ALSO ANTIBIOTICS. SO IT IS BY PASSING THE BIRTH CANAL AND ANTIBIOTICS. C-SECTION HAS BEEN RELATED WITH THE MODERN DISEASES AS HAVE EARLY ANTIBIOTICS. IT’S THE SAME DISEASES THAT ARE INCREASED IN RISK. WE SHOWED EARLIER HOW C-SECTION IMPACTS THE NEONATAL MICROBIOTA IF WE COMPARE WITH MATERNAL SITES, ORAL, VAGINAL OR SKIN, THE BABIES WILL CLUSTER ANTIBODY NEONATE WITHIN THE FIRST 24 HOURS, WILL CLUSTER WITH THE VAGINA, IF THE BABY WERE DELIVERED VAGINALLY OR WITH SKIN IF THEY WERE BY C-SECTION. THIS IS A VIEW OF THE VAGINAL MICROBIOTA. THIS IS WORK BY MY GRADUATE STUDENT, KEITH MARTINEZ AND AMANDA BIRMINGHAM HELPED US WITH THE ANALYSIS. SO WE CAN SEE MOSTLY LACK TOW BACILLUS AND FIRM CUTE AND BACTERIA BEADS. THIS IS THE VAGINAL KNOCKULOUS THAT IS MASSIVELY TRANSFERRED TO BABIES. NOWED LET’S LOOK HOW THE GUT SELECTS AFTER TWO DAYS OF GETTING THIS KNOCK LA. WHAT WE SEE IS AT THE EXPENSE OF THE FIRM I CUTES, THEY REALLY EXPAND. HOW DOES A C SECOND-BORN BABY LOOK AT TWO DAYS? THEY REALLY LACK THE BACTER IDENTITIES AND BACTERIA COMPONENT. WE ARE USING THESE TO HUMAN ICE MICE. BUT WE KNOW THAT THERE ARE LONGER-TERM EFFECTS. THE COMMUNITIES BETWEEN THE BABIES CONVERGING BUT THERE ARE POPULATIONS THAT NEVER DO Y SECONDS BABIES SUSTAIN A LOW BACK TERIDENTITYETS IN THEIR GUT. THERE ARE DIFFERENCES THAT EMERGE AFTER THE EIGHTH MONTH. SO WE SEE CONVERGENCE AND DIVERSITY BUT EVENTUALLY THOSE BABIES AROUND 1-2 YEARS OF AGE, THEY WILL HAVE LOWER ALPHA DIVERSITY THAN THE VAGINALLY-BORN AND THEY ARE SUSTAINED DIVERSITY DIFFERENCES. SO C-SECTION IS A BIG PART. NO WONDER IT’S EXPECTED. BUT HOW ABOUT SMALLER IMPACTS? FOR EXAMPLE, GOING TO THE HOSPITAL TO GIVE BIRTH. SO, A SUANT INSISTS THAT SHE IS A MID WIFE AND WAS DOING A PIECE IN NURSING AND INSISTED SHE WANTED TO DO THUNDERSTORM BIRTH. I WARNED HER THAT — HOME BIRTH. I WARNED HER WITH THE BABIES WE COULD HANDLE. SO WE TOOK WHAT WE CALLED GREEN BABIES. GREEN BABIES ARE VAGINALLY DELIVERED WITHOUT ANTIBIOTICS AND EXCLUSIVELY BREAST-FED. SHE FOLLOWED THE NEONATES FOR THE FIRST MONTH. AND TO OUR SURPRISE, ALTHOUGH NO DIFFERENCES WERE SEEN IN ALPH DIVERSITY, THEY WERE IN DIVERSITY WITH HOSPITAL BABIES HAVING SIGNIFICANTLY HIGHER [ INAUDIBLE ] AND HOME BABIES HAVING HIGHER HIGHER BACK TORE IDENTITIES AND STREPTOCOCCUS. IT IS A VERY SOFT IMPACT IF YOU WANT A STRESSOR. WE THINK WHAT HAPPENS IN THE HOSPITAL, IT’S NOT THE HOSPITAL AIR, WU DON’T KNOW. BUT MOST LIKELY, HOSPITAL DELIVERIES HAVE ALWAYS INTERVENTIONS. MAYBE LABOR INDUCTION OR ANESTHESIA OR THEY — AND THE FACT THAT ALL BABIES IN THIS COUNTRY BY PROTOCOL RECEIVE ANTIBIOTICS EVEN IF THEY ARE BORN BY C-SECTION. SO INTERVENTIONS AT BIRTH DO CHANGE THE NEONATAL MICROBIOTA AND THIS MAY LEAD TO DEVELOPMENTAL CHANGES. SO, THE FIRST THING WE THOUGHT IS OKAY, CAN WE RESTORE THIS IN SOME WAYS? ONE WAY WE CAN RESTORE IS EXPOSING THE NEWBORNS TO MICROBES OF THE VAGINAL TRACT. SO, WE DID A PILOT STUDY AND WE ARE NOW ANALYZING THE BIGGER STUDY DATA. IN WHICH HEALTHY MOTHERS WITH HEALTHY PREGNANCIES NEGATIVE TO INFECTIONS THAT HAD TO HAVE A SCHEDULED C-SECTION DUE TO MALL POSITION PRESENTATION OR REPEATED C-SECTIONS, WHERE THEY WERE INSERTED IN THE VAGINAL CANAL ONE HOUR BEFORE BIRTH AND THEN WE USED THAT TO IMMEDIATELY AFTER THEY CUT THE UMBILICAL, AS SOON AS WE COULD EXPOSE THE BABY IN ALL BODY SITES, STARTING WITH THE MOUTH. AND WE SHOWED IN THAT PILOT PAPER PUBLICATION HOW THE BACTERIAL SOURCES REFLECTED IN THE DIFFERENT BABIES BORN VAGINALLY OR BY C-SECTION, SEE THREE BODY SITES AND THESE ARE THE SOURCES. SO THE FIRST THING TO NOTE IS HOW RAPIDLY, WITHIN ONE WEEK THE ANAL SITE BECOMES TYPICAL. THE ORAL SITE OR THE SKIN. AND IN THE VAGINALLY BORN BABIES WE HAVE THE PURPLE SOURCE OF VAGINAL BUGS. NOT IN THE C-SECTION THROUGHOUT THE FIRST MONTH. AND EXPOSING THEM THIS RESTORE AT LEAST PARTIALLY THAT SIGNAL THAT WAS LACKING IN THE C-SECTION. AND WE CAN SEE WHAT POPULATIONS, ANAL AND SKIN AND SO IF YOU EXPOSE A BABY THAT IS TAKEN OUT THROUGH A ORIFICE ARTIFICIALLY, TO THE WORLD AND EXPOSE THAT BABY TO VAGINAL BACTERIA, THEY WILL PICK UP VAGINAL BACTERIA. SO THAT IS MICROBIAL RESTORATION. BUT SO WHAT? MANY MOTHERS ASKED THAT. WE DON’T KNOW YET — IT HASN’T BEEN PROVED THAT THERE IS DIRECT DISEASE CAUSATION BY THE C-SECTION OR WHETHER THESE MICROBIAL RESTORATION PROTECTS. SO HERE IN THE GUT. TO DO THE — TO TEST WHETHER MICROBIAL RESTORATION PROTECTS AGAINST THE DISEASES, WE NEED RANDOMIZED CLINICAL TRIALS TO ASSESS DIFFERENT DISEASES THAT REQUIRE TO FOLLOW BABIES FOR FIVE YEARS AND IS EXPENSIVE WITH A LOT OF BABIES. ALSO WE NEED TO KNOW WHICH ARE THE TAXA THAT ARE NORMALIZING IF IT WORKS. SO WE NEED ANIMAL MODELS AND MEAT GENOMICS STRAIN DISCRIMINATION APPROACHES IT’S EXPENSIVE. WE ALL LACK THE APPROPRIATE TECHNICAL CULTURE CAPABILITY. SOY, ONE QUESTION WE CAN ASK IS, GIVEN THE MULTIPLE COMMONLY-USED PERINATAL STRESSORS THAT FOLLOW IN ADDITION TO THE ONES I MENTIONED, THERE IS PROCESSED FOOD AFTERWARDS. CAN WE ASK THE QUESTION, ARE WE IMPACTED? AND THAT WE CAN COMPARE OURSELVES WITH PEOPLES, TRIBAL PEOPLES, WHO HAVE NOT BEEN EXPOSED TO MEDICAL TECHNOLOGY. WE DID THAT INITIALLY COLLABORATION WITH JEFF GORDON AND LATER WITH ROB ASK JOSE. WE FIRST SHOWED THE U.S. HAS THE LOWEST DIVERSITY GUT MICROBIOME IN RELATION TO AFRICANS FROM MALAWI OR GUAHIBO. THEY WERE TRANSCULTRATED RULE PEOPLE AND THEN WE PUBLISHED THE HIGHEST DIVERSITY MICROBIOME SO FAR FROM A CONTACT AT YANOMAMI INDIANS. WE COULD FOLLOW THE OTUs AND THE PREVALENCE ABUNDANCE CURVES SHOW THAT IN RELATION TO THE GREEN INDIANS TOWARDS THE YELLOW U.S., WE LOSE ABUNDANCE AND LOSE OR DECREASE PREVALENCE. IN A RECENT STUDY THAT WILL BE PUBLISHED VERY SOON IN SCIENCE, ON THE TANZANIA, WE SHOW HOW THE FECAL MICROBIOTA MOVES ALONG THE PC0A, AND THE TRAJECTORY OF THE MICROBIOTA ORDERS IN FUNCTION OF LIFESTYLE FROM JUNGLE TO RURAL TO URBAN, CONFIRMING THAT URBANIZATION IS INDEED ASSOCIATED WITH CHANGES IN THE GUT MICROBIOTA AND LOSINGS DIVERSITY. SO, THE HMP MICROBITEOA IS IMPACTED AND ANOTHER IS WE NEED TO STUDY IMPACTED MICROBIOTA AND UNDERSTAND WHAT IS THE LOST MICROBES? AND WHAT ARE THE FUNCTIONS WE ARE LOSING? IN COLLABORATION WITH PETER, WE DID URINE METABOLITES ACROSS URBANIZATION FROM RED LOW URBAN LEVELS TO HIGHER RURAL LEVELS IN ORANGE. AND A CONTROL. SO WE SEE THE GRADIENT OF URBANIZATION IN THE URINE IN METABOLITES. SO PEOPLE DO CHANGE. IN ANOTHER GRADIENT OF URBANIZATION, WE DECIDED TO STUDY HOMES TO ADDRESS THE ENVIRONMENTAL DIFFERENCES. AND WE COULD TELL IN A PAPER WITH MY STUDENT, WE COULD TEAR APART THE WALLS OF THE HOUSES BY THE URBAN SITE AND SO WITH INCREASED URBANIZATION, INCREASED HUMAN BACTERIA IN THE HOUSES AND REDUCED SOIL, WE DID METABOLOMICS IN COLLABORATION WALLS PETER AND AGAIN, WE SEE THAT FLOORS AND WALLS ARE GRADIENT OF URBANIZATION IN THE CHEMICAL SIMILARITIES BETWEEN THE SURFACES OF HOMES AND OUR SKIN. AND THE REASON WHERE MOSTLY OUR PRACTICES. SO IN THE JUNGLE TOWN WE SEE A LOT OF BREAKDOWN OF CHLOROPHYLL AND OTHER NATURAL PRODUCTS. IN THE CITY, WE SEE SWEETENERS AND ANALGESICS AND ANTIFUNGAL AND MEDICINE FOR HIGH BLOOD PRESSURE, EPILEPSY, REFLECTING THE DISEASES BEING TREATED. SO URBANIZATION IS ASSOCIATED WITH REDUCED SOIL AND PLANT EXPOSURE AND INCREASED EXPOSURE TO SYNTHETIC CHEMICALS. SO MY LAST TWO GAPS. GAP 4, WE NEED MORE EVOLUTIONARY APPROACHES TO STUDY THE MICROBIOME. THE IMPACTS AND CONSEQUENCES. WE NEED TO MAKE UP THE MYCOBIOME AS AN ANTH POE LOGICAL DISCIPLINE. HOW DO WE COME WITH RESTORATION? WHICH TAXA? AND WHAT ABOUT IF IT HAS BEEN LOST? SO TO PROTECT FUTURE GENERATIONS OF THESE DISEASES, THE SAME WAY WE ARE CONSERVING, WE HAVE A LIST OF ENDANGERED SPECIES OF ANIMALS, AND THERE IS GLOBAL IN THE PERMA FROST IN NORWAY. WE SHOULD DEFINITELY BE CONSTRUCTING FOR THE FUTURE OF HUMAN MICROBIOME EVALUATE. THE FUTURE, WE DON’T KNOW THE FUNCTIONS YET. WE DON’T KNOW THE UTILITY BUT HOPEFULLY FUTURE GENERATIONS SCIENCE WILL HAVE THESE RESOURCES TO APPLY FOR HUMAN HEALTH. AND WITH THAT, I ACKNOWLEDGE THE FUNDING OF THE PEOPLE IN MY LAB AT NYU, MY STUDENTS AT UPR AND MY VERY VALUABLE COLLABORATIONS AND THANK YOU FOR YOUR ATTENTION [ APPLAUSE ]>>DR. MARUVADA: FINAL PRESENTATION FOR SESSION IS BY DR. XI JINPING TALKING ON ALLOGENIC HEMATOPOIETIC STEM CELL TRANSPLANTATION CLINICAL OUTCOMES AND UNDERSTANDING BACTERIA AND POTENTIAL MECHANISMS. — ROBERT JENQ.>>DR. JENQ: HI. GOOD MORNING. SO I’M ROBERT JENQ AND WORK AT MD ANDERSON CANCER CENTER. I MOVED THERE RECENTLY FROM MEMORIAL SLOAN-KETTERING WHERE I WAS DOING MY TRAINING AND WORKED AS JUNIOR FACULTY FOR MANY YEARS. THE TITLE OF MY TALK IS ALLOJENAIC BONE MARROW TRANSPLANT, CLINICAL OUTCOMES AND POTENTIAL MECHANISMS. I SHOULD SAY I’M A CLINICIAN. I AM NOT A MICROBIOLOGIST ALTHOUGH I HAVE TRIED TO PICK UP SOME STUFF OVER THE YEARS, I GUESS. I WANT TO START WITH MY UNMET NEED. AND I THINK THIS IS TIEING INTO WHAT OTHER PEOPLE SAID DURING THE MEETING. THERE IS A LOT OF VERY INTERESTING AND FASCINATING ASSOCIATIONS THAT WE HAVE SEEN. VERY, VERY GOOD PRE-CLINICAL MODELING THAT HAS BEEN DONE TO ADDRESS THE QUESTION OF CAUSALITY BUT ONE UNMET NEED I THINK IS CLINICAL TRIALS. WELL DONE RANDOMIZED CLINICAL TRIALS TO HELP SPUR 50S BIOTECH TO DECIDE WHICH DISEASES TO FOCUS THEIR EFFORTS ON. AND A LOT OF THESE STUDIES CANNOT BE DONE WITHOUT EITHER FEDERAL FUNDS OR PHILANTHROPY FUNDS BECAUSE THESE ARE AGENTS THAT CAN’T BE PATENTED. THESE ARE ANTIBIOTICS OR PREBIOTICS OR PROBIOTICS OR FECAL TRANSPLANTS. YOU CAN’T PATENT THESE THINGS. AT LEAST NOT VERY EASILY. I FOUND THIS PICTURE LAST NIGHT OF DR. BENIZE MAN, A SURGEON WHO WAS AT DENVER IN COLORADO FOR MANY YEARS AND IN 1958, HE REPORTED IN THE JOURNAL OF SURGERY, FOUR PATIENTS WITH PSEUDOMEMBRANEOUS COLITIS. THIS PRECEDED THE IDENTIFICATION OF C DIF. AND THEY REPORTED THAT THEY TREATED THESE PATIENTS WITH FECAL EN MAS AND ALL FOUR PATIENTS RESPONDED WITHIN DAYS AND WERE DISCHARGED FROM THE HOSPITAL. SO IS THIS IS 1958. AND THEN I SHOULD MENTION FECAL TRANSPLANT WAS CHAMPIONED BY TOM BRODIE, GASTROENTEROLOGIST IN AUSTRALIA. BUT IT WASN’T UNTIL 55 YEARS LATER WHEN A RANDOMIZED TRIAL IN THE NEW ENGLAND JOURNAL DONE BY SOME DUTCH INVESTIGATORS, NOT AMERICANS, AND THIS REALLY LED TO THE IDEA THAT THE MICROBIOME COULD BE A THERAPY. SO, THAT’S MY SOAPBOX TO HIGHLIGHT. SO A LITTLE BIT ABOUT BONE MARROW TRANSPLANT. THIS WAS ORIGINALLY DEVELOPED AS A MEANS OF RESCUING PATIENTS AFTER HIGH-DOSE CYTOTOXIC THERAPY. THE CONCEPT WAS IF YOU CAN GIVE PATIENTS BIGGER AND MORE TOXIC DOSES OF CHEMOTHERAPY OR RADIATION, CAN YOU CURE MORE PATIENTS? AND IT TURNS OUT YOU CAN. EVENTUALLY YOU START TO HIT A WALL OF TOXICITY AND ONE OF THOSE WALLS WAS MARROW FAILURE. AND SOME CLEVER SCIENTISTS WERE ABLE TO FIGURE OUT THAT YOU COULD RESCUE PATIENTS BY TAKING OUT THEIR MARROW, GIVING THEM THE KIEMY AND RADIATION AND THEN REINTRODUCING THE MARROW AND SUDDENLY THAT WALL AT LEAST, IS ELIMINATED AND YOU CAN GIVE HIGHER DOSES. LATER ON, SOME OTHER CLINICIANS WERE TRYING TO USE BONE MARROW GRAPHS THAT WERE CANCER FREE. SO THEY WENT ON TO USE A BONE MARROW FROM A DIFFERENT INDIVIDUAL, ALLOGENEIC BONE MARROW TRANSPLANT. THIS LED TO HIGHER CURE RATES BUT AT THE SAME TIME, WITH THE INVESTIGATORS FOUND IS THERE WAS A DRAMATIC INFLAMMATORY IMMUNE RESPONSE THAT WAS MEDIATED BY THE DONOR IMMUNE CELLS AND THAT SYNDROME WAS CALLED GRAPH VERSUS HOST DISEASE. AND THAT CONTINUES TO BE A PROBLEM. THIS IS CIBMTR REGISTRY DATA SHOWING HOW WE FAIL OUR ALLOGENEIC BONE TRANSPLANT RECIPIENT PATIENTS. THE BIGGEST SLICE OF THE SPY DISEASE RELAPSE SO THAT IS THEIR MALIGNANCY COMING BACK. BUT THE SECOND BIGGEST PIECE OF THE PIE IS GVHD. THIS IS WHAT IS GENERALLY KNOWN ABOUT THE PATH OF PHYSIOLOGY. YOU START OUT WITH THE PATIENT WHO UNDERGOES HOST CONDITIONING SO THEY UNDERGO CHEMOTHERAPY, RADIATION, THEY GET THE CELLS INFUSED AND EARLY ON, IN THE PROCESS, BACTERIAL PRODUCTS, SO PRIMARILY BACTERIA IN OUR INTESTINAL TRACKS, THEY RELEASE ALL KINDS OF INFLAMMATORY MEDIATORS AND THESE ARE THOUGHT TO ACTIVATE HOST ANTIGEN PRESENTING CELLS, WHICH IN TURN ACTIVATE DONOR T-CELLS THAT ARE GRAFT DERIVED AND THEN THIS LEADS TO A WHOLE INFLAMMATORY TESTING. EVENTUALLY THIS LEADS TO INFLAMMATION OF THE CLASSIC AFFLICTED TARGET ORGANS, SKIN, GI TRACT, LIVER, HEMATOPOIETIC SYSTEM. AND YOU CAN ALSO HAVE A BENEFICIAL IMMUNE EFFECT AGAINST THE TUMOR AS WELL. SO I HIGHLIGHTED IN THE PATHOPHYSIOLOGY THE BACTERIAL PRODUCTS. AND SO THESE EARLY BONE MARROW TRANSPLANTERS, THEY WERE ABLE TO SHOW IN VERY EARLY TIME PERIOD, THAT THE MICROBIOME IS INFLUENCING THIS DISEASE PROCESS. AND SO THEY DID THIS IN TWO WAYS. ONE WAS WITH GERM-FREE MICE IN THE 1970s. THEY SHOWED THAT MICE THAT WERE ERADIATED AND TRANSPLANTED IN THE GERM-FREE SETTING HAD MINIMAL GRAPH VERSUS HOST DISEASE AND THEN ANOTHER GROUP THAT SHOWED THAT YOU CAN GET A SIMILAR BENEFIT BY ADMINISTERING GUT DECONTAMINATING ANTIBIOTICS. SO THIS LED TO CLINICAL TRIALS OF GUT DECONTAMINATION IN PATIENTS, SOMETIMES WITH POSITIVE RESULTS, OTHER TIMES WITH MIXED RESULTS AND AS A RESULT, THED PRACTICE SORT OF FELL OUT OF FAVOR AND THE FIELD DOESN’T REALLY KNOW EXACTLY WHAT TO DO IN TERMS OF MICROBIOME. SO THIS IS OUR SCHEME. WE HAVE BEEN COLLECTING STOOL SAMPLES FROM PATIENTS UNDERGOING BONE MARROW TRANSPLANTATION, SEQUENCING THEM BY 16S AND THEN TRYING TO ASSOCIATE WITH VARIOUS CLINICAL OUTCOMES THAT WE ARE INTERESTED IN, BLOODSTREAM INFECTIONS, SURVIVAL OF GVHD AND RELAPSE. WE STARTED IN 2009. THIS IS A WONDERFUL COLLABORATION BETWEEN TWO PHYSICIAN-SCIENTISTS AT SLOAN-KETTERING. MY FORMER MENTOR IS THE BONE MARROW TRANSPLANTER PHYSICIAN SCIENTIST AND ERIC, WHO IS IN THE AUDIENCE AND SPEAKING LATER, WAS THE INFECTIOUS DISEASE PHYSICIAN SCIENTIST. AND THE TWO HEAD OFTENOS GOT TOGETHER AND SET UP THIS COLLABORATION. AND WHEN I LEFT SLOAN-KETTERING, WE HAD COLLECTED 3000 STOOL SPECIMENS FROM OVER 800 PATIENTS AND THAT IS BEEN ONGOING SINCE AND I’M SURE SELL MUCH HIGHER NOW. SO, THIS IS WHAT THE DATA LOOKS LIKE. EACH SAMPLE HERE IS A STOOL SAMPLE COLLECTED FROM A SINGLE PATIENT DURING HIS TRANSPLANT HOSPITALIZATION. AND WITH THE COLORS WE ARE SHOWING YOU THE COMPOSITION. SO, YOU CAN SEE THAT THE PATIENTS STARTED OUT PRETTY DESSERTS LOTS OF CLOSE TRADE ALLEYS, AND WAS ABLE TO MAINTAIN THAT DESPITE SOME ANTIBIOTICS HE RECEIVED, AND THEN AROUND DAY 30 SOMETHING HAPPENS AND SUDDENLY THERE IS A BLOOM OF GREENBACKTERIA WHICH IS INTERCAUCUS AND IT TURNS OUT THAT WAS VEERY WHICH WE HEARD ABOUT YESTERDAY. AND THAT COINCIDED WITH A DIAGNOSIS OF C DIVIN FECKS AND TREATMENT WITH METRO NIDE ZOL. SO THIS IS INTERESTING. IT WAS INTERESTING THAT CERTAIN ANTIBIOTICS IMPACT ON THE MICROBIOME MORE THAN OTHERS AND THAT THERE IS HETEROGENERATE NETHESE PATIENTS IN TERMS OF HOW WELL THEY ARE ABLE TO MAINTAIN THEIR BASELINE GENERALLY HEALTHY MICROBIOME COMPOSITION. SO WE ASKED THE QUESTION, IS THERE ANY ASSOCIATION OF CERTAIN BACTERIAL DYING FROM GOVERNMENT VHD? WE ASKED THIS QUESTION IN A COHORT OF 64 PATIENTS. HERE ARE THE RESULTS USING A TOOL AND I HAVE DEPICTED THE P-VALUE ON THE Y AXIS AND ITS IT INVERTED ON THE LOG SCALE. SO BETTER P-VALUE HIGHER UP. AND HITS TO THE LEFT ARE ASSOCIATED WITH LESS GVH. AND HITS TO THE RIGHT ARE ASSOCIATED WITH MORE. SO OUR TOP HIT WAS A JEAN US CALLED BLAUTIA ASSOCIATED WITH LESS GVHD. SO WE STRATIFIED THE PATIENTS BASED ON THEIR BLA. TIA ABUNDANCE IN TWO HALVES. THE PATIENTS WITH MORE ARE IN BLUE AND THEY DID VANISH WELL. LOW INCIDENCE OF MORTALITY FROM GOVERNMENT VHD. THOSE WHO HAD LESS DID VERY POORLY. – OL GVHD. WE WERE LUCKY TO HAVE A SECOND COHORT OF PATIENTS TO TRY TO VALIDATE OR REPRODUCE THIS FINDING AND REPRODUCED VERY NICELY. AND THEN HERE IS THE COMBINED CURVES WITH OVERALL SURVIVAL. SO WE THOUGHT THIS WAS INTERESTING. THERE WERE OTHER GROUPS IN THE FIELD THAT WERE ALSO ASKING SIMILAR QUESTIONS. THIS IS A STUDY FROM A GROUP IN REAGANSBURG AND THEY WERE ABLE TO IDENTIFY A URINARY METABOLITE OF MICROBIOME HEALTH, URINARY IN DOCKSIL SULPHATE IS ORAL TRYPTOPHAN METABOLIZED BY YOUR GUT MICROBIOME INTO IN DOLL. AND HE WAS ABLE TO SHOW AN ASSOCIATION WITH LOST RIDDIA MEDIATING THAT FERMENTATION. SO THEY ARE MEASURING THESE URINARY METABOLITE LEVELS WHICH IS POTENTIALLY A WAY, A QUICK MEASURE OF MICROBIOME HEALTH THAT DOESN’T RELY ON 16S SEQUENCING. SEWED THEY WERE ABLE TO SHOW THIS WAS PROGNOSTIC FOR TREATMENT TRANSPLANT RELATED MORTALITY. AND THEN THERE IS A FRIEND OF MINE, ANDY COAT UT SOUTHWESTERN, A PEDIATRIC TRANSPLANTER AND HIS GROUP WAS ABLE TO FIND A SIMILAR FINDING IN THAT PATIENT POPULATION. SO THEN WE WENT ON TO ASK, IT LOOKS LIKE ANTIBIOTICS ARE A MAJOR MEDIATOR OF THIS HETEROGENEITY WE SEE IN THIS PATIENT POPULATION. SO WHAT ARE THE EFFECTS OF ANTIBIOTICS AND GVHD? AND THERE IS A NICE INSIGHT HERE IN THAT IF YOU GO BACK IN TIME AND LOOK AT THE PATIENT RECORDS, YOU DON’T NECESSARILY NEED STOOL SAMPLES. YOU CAN JUST LOOK AT THEIR ANTIBIOTIC EXPOSURES BASED ON ELECTRONIC CHARTS AND TRY TO CONNECT THOSE WITH THE OUTCOMES. SO THAT IS WHAT WE TRIED TO DO. WE LOOKED AT 850-ODD PATIENTS AT SLOAN-KETTERING THAT UNDERWENT ALLOTRANSPLANT OVER A 23-YEAR PERIOD. SO HERE IS THE INCIDENTS OF GVHD MORTALITY IN THIS POPULATION. ABOUT 15%, WHICH IS PRETTY TYPICAL. HERE I’M SHOWING YOU THE MOST COMMONLY ADMINISTERED ANTIBIOTICS AND I STRATIFIED THE PATIENTS BASED ON EXPOSURE WHETHER THE CLINICIAN DECIDED TO GIVE THAT PATIENT THAT ANTIBIOTICS OR NOT. THE ONLY ANTIBIOTICS ON THIS CHART THAT HAD A SIGNIFICANT P-VALUE WERE [ INAUDIBLE ] BOTH OF THESE HAD A SIGNIFICANT ASSOCIATION WITH GVHD MORTALITY AND INCIDENTALLY BOTH ARE USED TO TREAT NEWT PINNIC FEVER WHICH CURSE COMMONLY IN THESE PATIENTS. SO HERE ARE THE DINS DENSE CURVES. — INCIDENCE SERVICES. AND FOR BOTH, THE PATIENTS THAT RECEIVE ANTIBIOTIC ARE IN RED AND THEY ARE THE ONES THAT DID POORLY. SO THIS IS INTERESTING. IT TURNS OUT THERE WAS ANOTHER ANTIBIOTIC, ANOTHER COUPLE THAT WE USED TO TREAT PATIENTS WITH NEWT PENIC FEVER. AND THESE ARE GIVEN AS SECOND LINE TO PATIENTS WHO HAVE THE HISTORY OF A SEVERE PENICILLIN ALLERGY. IF THEY HAVE A HISTORY OF A RASH, THEY TEND TO GET SEFY PEOPLE, IF THEY HAVE HIVES OR SOMETHING LIKE THAT, THEY TEND TO GET AZTREONAM. SO THE INFECTIOUS DISEASE FOLKS IN THE ROOM WILL NOTICE THAT THESE ARE MORE NARROW SPECTRUM ANTIBIOTICS. THEY TEND TO SPARE THE ANAEROBES PARTICULARLY OF GRAND POSITIVES IN GENERAL. SO IT WAS A NATURAL EXPERIMENT THAT OCCURRED. AND WE LOOKED AT THE INCIDENCE OF GVHD MORTALITY RELATIVE TO EXPOSURE TO THESE ANTIBIOTICS AND THERE WAS NO ASSOCIATION. SO WE THOUGHT THAT WAS INTERESTING. I MENTIONED EARLIER, I HAVE SEEN LEFT SLOAN-KETTERING AND NOW AT MD ANDERSON. WE DID A SIMILAR STUDY THERE. AND LOOKED AT ALMOST 300 PATIENTS. LOOKED AT THEIR ANTIBIOTIC EXPOSURES AND FOUND THAT SIMILAR RESULTS WERE SHOWN. MEROPENEM HAD INCREASED GVHD WHILE CEFEPIM. PATIENTS DID NOT. WE USED A MOUSE MODEL AND ADD MINISTER THE SAME ANTIBIOTICS AND IT RECAPITULATED THE FINDINGS. THE EFFECTS WERE LOCALIZED AND WHEN WE LOOKED AT THE MICROBIOME, WE FOUND THERE WAS A BLOOM OF ACKER MANSIA. IT’S MUSE IN-LOVING SO WE LOOKED AT THE MUCUS LOVER USING THIS METH AND WE FOUND THAT THESE TREATED MICE HAD LOST THEIR MUCUS LAYER. AND THERE IS A BACTERIA THAT TRANSLOCATED INTO THE LAMINA PROPRIA. THIS LED TO IMPAIRED BARRIER FUNCTION AND SO THEN WE ASKED WHAT IF WE CAN TRY TO GET RID OF ALL THE BACTERIA? SO WE ADDED ORAL AMPICILLIN TO THE DRINKING WATER AND WE FOUND THAT INDEED, ON THE BOTTOM RIGHT HERE THAT THOSE MICE DESPITE TREATMENT WERE SPARED FROM THE THINNING OF THE MUCUS LAYER. AND THIS LED TO OR QUANTIFIED HERE AND LED TO REDUCED GVHD SEVERITY SCORES. SO, THIS IS SOARED OF OUR MODEL, OUR FRAMEWORK. WE THINK IF YOU CAN AVOID ANTIBIOTICS AND YOU NEED A BONE MARROW TRANSPLANTED, YOU’RE PROBABLY IN GOOD SHAPE. IF YOU RECEIVE HIGH DISRUPTION AREN’T BIOTICS THEN THIS LEADS TO A HIGH GVHD RISK STATE. AND IN TERMS OF WHAT CAN YOU DO, ONE ONES WOULD BE TO PUSH PEOPLE ALL THE WAY TO THE OTHER END OF THE SPECTRUM WHERE THEY ARE GUT DECONTAMINATED AND ALTERNATIVELY TRY TO PUSH THEM BACK TO THED SORT OF ORIGINAL HEALTHY STATE OF THE MICROBIOME. SO I WANT TO ACKNOWLEDGE MY FORMER MENTOR AND OUR CLOSE COLLABORATORS: [ READING ] THANK YOU. [ APPLAUSE ]>>DR. MARUVADA: QUESTIONS FOR THE SPEAKERS?>>PLEASE IDENTIFY YOURSELF BEFORE YOU ASK A QUESTION.>>AUDIENCE MEMBER: I’M [ INAUDIBLE ] MY QUESTION IS FOR DR. MARIA GLORIDA DOMINGUEZ-BELLO SO C SECTIONS WERE COMMON A FEW DECADES AGO. SO ANY EPIDEMIOLOGICAL DATA THAT ASSOCIATES C-SECTIONS WITH HEALTH OR DISEASE OUTCOMES AND ALONG THOSE LINES, COULD YOU THEN TAKE YOUR COHORT AND FOLLOW THEM, THE RESTORED COHORT AND FOLLOW THEM OVER TIME FOR THOSE DISEASE AND HEALTH OUTCOMES?>>DR. BELLO: THAT IS A VERY GOOD QUESTION. I THINK THERE IS A COMPELLING EPIDEMIOLOGICAL ASSOCIATION IN BIG COHORTS SHOWING THAT C-SECTION INCREASES RISK OF ASTHMA, SILLIAC DISEASE AND OBESITY. THE DIRECT CAUSATION AND THE MECHANISM HASN’T BEEN SHOWN. OUR COHORT IS TOO SMALL. WE ARE FOLLOWING THOSE CASES BUT ONLY HAVE 84. IT’S VERY SMALL. AND SO TO DO OR TO ASSESS EFFECT ON HEALTH, WE NEED ABOUT 1000 CHILDREN. WE DON’T HAVE THE MONEY TO DO THAT.>>AUDIENCE MEMBER: JANET JANSEN FROM THE PACIFIC NORTHWEST NATIONAL LABORATORY. MY QUESTION IS ALSO FOR YOU, MARIA. I WAS VERY INTRIGUED BY YOUR IDEA FOR A HUMAN MICROBIOME SEATBELT. AND I WAS WONDERING FOR THE SAMPLES THAT ARE EXTREMELY VALUABLE FROM THE INDIANS THAT YOU HAVE, IS THERE ANY ATTEMPT TO CULTIVATE ISOLATES FROM THOSE SAMPLES?>>DR. BELLO: THAT IS A VERY IMPORTANT QUESTION. WE HAVE THE SPECIMENS IN MY LAB. WE HAVE THOSE IN VENEZUELA. SO YOU CAN IMAGINE HOW RISKY THEY ARE THAT THE MOMENT. SO THAT IS PART OF WHY REALLY LED ME TO THINK THAT WE SHOULD SAVE THAT FOR THE FUTURE. WE HAVE DONE SOME CONSULTEDIVATION FROM FECAL. WE HAVE ORAL SPECIMENS AND SKIN. THOSE COLLECTIONS ARE SUBJECT TO SOME RESTRICTIONS LIKE WE CANNOT PATENT ANYTHING ON THEM. EVERYTHING HAS TO BE CULTURE. BUT I WOULD LIKE TO HAVE COLLABORATORS TO IMPROVE THE SUCCESS IN CULTURING AND ALSO TO COMPARISONS OF EVOLUTION OF THESE MICROBES AND THOSE PEOPLE WHO WERE ISOLATED FOR 24,000 YEARS. AND THE REST OF THE ASIANS OR WESTERN POPULATIONS. THAT IS SOMETHING TO BE DONE. VERY LITTLE HAS BEEN DONE. BASICALLY BECAUSE MY LIMITATIONS>>AUDIENCE MEMBER: THANKS. THESE WERE GREAT TALKS. AND I HAVE TWO QUESTIONS BUT I THINK THEY ARE TWO SHORT ANSWERS THAT COULD BE GOTTEN. FIRST, THE QUESTION IS TO PETER. AND YOU KNOW, I LIKE THE IDEA OF ENGINEERING MICROBES TO DO THIS METABOLISM TO GET THE ACTIVE PRODUCT. BUT, THE MORE PRACTICAL SOLUTION MIGHT BE JUST ADMINISTERING THE ACTIVE INGREDIENT. AND I THINK THAT YOU CAN SOLVE A LOT OF DELIVERY ISSUES AS WELL AS COLONIZATION ISSUES WITH THE SUPERBUG. I WAS WONDERING WHAT YOUR THOUGHTS ON THAT WERE.>>DR. TURNBAUGH: THANK YOU FOR THE QUESTION. THAT’S A GREAT POINT. AND I GUESS WHAT I DIDN’T REALLY GET INTO VERY MUCH FOR PHYTOESTROGENS IS THAT IN BREAST CANCER, AS FAR AS I’M AWARE, MOST OF THE EPIDEMIOLOGICAL DATA SUPPORTS PREVENTATIVE EFFECT OF THE PHYTOESTROGEN. SO THAT IS SOMETHING THAT IS LONG-TERM PRODUCTION OF PHYTOESTROGEN PREVENTS THE DEVELOPMENT OF CANCER. THERE IS SAY LOT LESS DATA ON TREATMENT OF CANCER WITH PHYTOESTROGENS EVEN IN ANIMAL MODELS, TYPICALLY THE EXPERIMENTS ARE DONE WHERE THE PHYTOESTROGEN IS GIVEN PRIOR TO OR AT THE SAME TIME OF INITIATION OF CANCER. SO IT’S NOT SUPER CLEAR WHETHER OR NOT THAT WILL ULTIMATELY BE EFFECTIVE. I THINK THERE IS ALSO A POTENTIAL ADVANTAGE IN BEING ABLE TO DELIVER THE COMPOUND AT THE SAME LOCATION WHERE IT IS NATURALLY PRODUCED. NO ONE HAS REALLY DONE AS FAR AS I’M AWARE, CAREFUL STUDIES OF WHAT HAPPENS IF PHYTOESTROGEN IS PRODUCED IN THE SMALL INTESTINE VERSUS LARGE INTESTINE AND WHETHER OR NOT THAT WOULD HAVE A DIFFERENCE IN OUTCOME.>>AUDIENCE MEMBER: THANK YOU. SO MY SECOND QUESTION IS TO DR. JEN. I LIKE THE IDEA OF THIS ACRO MANSIA AND THEN EROSION OF THE BARRIER, BUT IS IT POSSIBLE THAT MORE NARROW SPECTRUM ANTIBIOTICS ALSO PRESERVE MICROBIAL GROUPS THAT MIGHT BE IMMUNOTOIZING?>>DR. JENQ: SO I AGREE WITH THAT COMPLETELY. WE DID LOOK IN THAT STUDY TO SEE IF THERE WERE INCREASED REGULATORY T-CELLS IN THE SETTING OF THE NARROW SPECTRUM ANTI-BY ON THETIC AND TRIED MEASURE BUTYRATE LEVELS FROM THE STOOL AND THERE WAS NO DIFFERENCE AND THAT’S WHY WE HAD TO GO HUNTING FOR AN ALTERNATIVE MECHANISM AND WE STUMBLED UPON THIS ACRO MANSIA MUSE IN FINDING>>AUDIENCE MEMBER: HI, MY QUESTION IS FOR MARIA. THOSE WERE ALL GREAT TALKS. I WANTED TO ASK ABOUT THE INOCULATION OF THE BABIES. SO, THE DATA ON C-SECTIONS DONE IF THE MOTHER WAS IN LABOR OR HAD RUPTURE OF MEMBRANES, SHOWS THE OUTCOMES ARE BETTER FOR THOSE INFANTS WITH REGARDS TO ALLERGIES AND DEVELOPMENT OF DISEASES IN THE FUTURE. IS THERE AN ALTERNATE WAY TO INOCULATE THESE BABIES PERHAPS BY PREMATURE RUPTURE? AND ALSO ARE WE DISCOUNTING THE EFFECT OF LABOR? PERHAPS THERE IS SOME HORMONES THAT EFFECT THE BABY IN UTERO. BECAUSE EVEN LABOR WITHOUT RUPTURE IN BABIES DELIVERED BY C-SECTION HAVE BETTER OUTCOMES. SO COULD THAT ALTER HOW THEY ACQUIRE THE MICROBIOME?>>DR. BELLO: THOSE ARE VERY GOOD QUESTIONS. AND I THINK THERE SHOULD BE A LOT MORE EFFORT PUT INTO ANSWERING THEM. WE ABSOLUTELY DON’T KNOW. THERE HAS BEEN VERY LITTLE EFFORT PUT INTO OPTIMIZING LABOR, OPTIMIZING THE NATURAL WAY OF GIVING BIRTH; AND STUDY WHY THAT IS IMPORTANT. I DON’T HAVE ANSWERS TO YOUR QUESTIONS. VERY GOOD QUESTIONS.>>AUDIENCE MEMBER: HI, BRIAN HERE. DR. TURNBAUGH, YOUR TALK WAS FANTASTIC. I THINK YOU INSPIRED A GAP IDENTIFICATION FOR ME. WE HAVE MILLIONS OF THESE COMPOUNDS AND SO, I’M WONDERING HOW WE MIGHT BE ABLE TO TAKE YOUR WORK AND SPEED IT UP A LITTLE BIT AND DO MORE HIGH-THROUGHPUT DISCOVERY IN A SIMILAR MANNER MINUS HEARDS OF UNDERGRADUATES. HOW CAN WE POTENTIALLY PUT THESE ON SMALL CHIPS OR STARTS TO DO SOME TYPE OF MET AT GENOMIC ANALYSIS IS TO GET DOWN TO GETTING SCORES OF THESE THINGS IDENTIFIED AND KNOWING THAT YOUR GUT BACTERIA IS DIFFERENT THAN MINE AND START TO GO TOWARDS MORE POPULATION-LEVELS SO WE CAN BETTER FORMULATE DIETS AND NUTRITION AND DRUGS. THANK YOU.>>DR. TURNBAUGH: THAT’S A GREAT QUESTION. I THINK THE SOLUTION IS OUR LAB NEEDS APPROXIMATELY 500 RO1s. [ LAUGHS ] WE JUST PUT ONE PERSON ON EVERY COMPOUND. I THINK THERE IS A HUGE NEED FOR SPEEDING UP THE PROCESS. I THINK ONE THING THAT YOU MENTIONED IS EVEN IN THE REDUCTIONIST APPROACHES, WHAT HAS PROVEN TRUE FOR HUMAN METABOLISM IS THERE INCREDIBLY LIMITED SET OF ENZYMES THAT PERFORMANCE A VAST DIVERSITY OF REACTIONS AND SO, EVERY NEW ENZYME IS THAT WAS DISCOVERED IN THE HUMAN BODY THAT METABOLIZES A DRUG, TAUGHT US ABOUT MANY DIFFERENT DRUGS, DIETARY COMPOUNDS AND ENDOGINOUS COMPOUNDS. AND WHAT WE DON’T KNOW IS WHETHER OR NOT THAT WILL ALSO BE THE CASE FOR MICROBIAL XENOBIOTIC METABOLISM. SO WILL THE SUBSTRATES GO FOR EACH ENZYME BE RESTRICTED TO THE COMPOUND WE ARE ORIGINALLY STUDYING OR TEACH US ABOUT A BROADER ARRAY OF COMPOUNDS THAT ARE METABOLIZED BY BACTERIA? I CAN TELL YOU FOR THE ONE ENZYME THAT WE HAVE STUDIED IN THE — THAT I DIDN’T HAVE TIME TO GET INTO, THE CARDIAC GLYCOSIDE — [ INAUDIBLE ] IT HAS SHOWN THAT INTERESTINGLY THAT ENZYME CAN METABOLIZE MANY, SO THIS IS SAY BROADER FAMILY OF TOXIC COMPOUNDS THAT ARE IN DRUGS AS WELL AS PLANTS. BUT IT DOES NOT SEEM TO METABOLIZE MANY OTHER RELATED GLYCOSIDES.>>AUDIENCE MEMBER: I’M MARK ROADS FROM HOUSTON, TEXAS. AND FOR MORE THAN 30 YEARS I HAVE STUDIED INFANT GI WELL TRACTS INCLUDING RECENT OBSERVATIONS THAT WE FOUND THAT BABIES OF COLIC HAVE A DIFFERENT MICROBIAL POPULATION COMPARED WITH BABIES THAT DON’T CRY MORE THAN THREE HOURS A DAY. AND ELEVATED CALL PROTECT IN. SO, WE THINK THIS IS VERY IMPORTANT EARLY IN LIFE AND I ENJOYED THE PRESENTATIONS TODAY THAT RELATE TO INFANTS. BUT MY REAL QUESTION IS FOR THE ENTIRE PANEL. IF ANYBODY KNOWS ANYTHING ABOUT THE MICROBIOME OF CENTENARIANS. PEOPLE THAT LIVE TO BE 100. DO THEY HAVE A DIFFERENT PROFILE? I DON’T KNOW HOW MANY CENTENARIAN DOCTORS THERE ARED.>>DR. BELLO: I WOULD COMMENT THAT WHAT WOULD BE INTERESTING — THE PROBLEM IS THE CENTENARIANS ARE OLD. RIGHT? [ LAUGHS ] AND THAT IS A PROBLEM. BECAUSE IT IS TOO LATE. THE IDEA WOULD BE TO HAVE THE CENTENARIANS EARLIER MICROBIOME TO PREDICT.>>AUDIENCE MEMBER: I HAD A QUESTION. SO IF MY MEMORY SERVES — BECAUSE I HAVEN’T BEEN FOLLOWING AS MUCH BUT SOME OF THE HDAC INHIBITORS IN THE PAST IN THE CLINICAL TRIALS HAVE NOT DONE REALLY WELL. SO DO YOU KNOWLEDGES THAT GLUTAMATE MAY HAVE MUCH MORE IMPORTANT — DO YOU THINK — THAN THE MODEL YOU HAVE?>>YES, I THINK BUTYRATE HAS A LOT OF FUNCTIONS AND THAT’S ONE OF THE CHALLENGES ASSOCIATED WITH IT. AND THERE SUSPECT EVEN DIFFERENT PEOPLE HAVE DIFFERENT OPINIONS ON THE IMPORTANCE OF THE MECHANISM OF ACTION AND SO, I’M ALWAYS PRETTY CAREFUL TO — ALTHOUGH I’M MORE FOCUSED ON THE HDAC INHIBITION MECHANISM AND THE FIRST TO ADMIT THAT IT ALSO FUNCTIONS AS A LIGAND FOR G PROTEIN COUPLED RECEPTORS AND VARIOUS GROUPS HAVE SLONE THAT THAT IS AN IMPORTANT MECHANISM, INCLUDING FOR CANCER. AND THEN A NUMBER OF OTHER GROUPS HAVE SHOWN THAT BUTYRATE CAN ACTUALLY IMPROVE BARRIER FUNCTION AND IT CAN ALSO IF GIVEN TO EITHER NAIVE T-CELLS OR EVEN DENDRITIC CELLS, IT CAN DIRECT THEM INTO A T-REG CELL. SO THAT IS ALSO GOING TO BE IMPORTANT FOR CANCER AND OTHER DISEASE STATES. BUTYRATES HAVE BEEN IMPLICATED IN A LOT OF THINGS, NOT JUST COLORECTAL CANCER. AND SO, THOSE IMMUNE FUNCTIONS ARE GOING TO BE REALLY IMPORTANT AND ESPECIALLY CURIOUS ABOUT THE T-REG CELL FUNCTION BECAUSE ON THE ONE HAND, MIGHT BE TUMOR SUPPRESSIVE IF IT IS DAMPENED DECREASING OVER ALL SISS STEMMATIC INFLAMMATION BUT ON THE OTHER HAND, IF BUTYRATE IS INCREASING T REG CELLS IN THE TUMOR MICRO-ENVIRONMENT, IT COULD BE IMMUNE SUPPRESSIVE AND GIVE RISE TO A MORE AGGRESSIVE TUMOR PHENOTYPE. SO THERE ALMS HAVE BEEN SOME REPORTS BOTH BUTYRATE HAVING OPPOSITE EFFECTS AND THAT COULD BE ONE WAY IT IS DOING IT. SO THAT IS ONE OF THE CHALLENGES I THINK THAT WE ARE STILL KIND OF SCRATCHING THE SURFACE. WE KNOW A LOT OF MICROBIAL METABOLITES AND FOCUSING ON BUTYRATE AND A FEW OTHERS THAT HAVE BEEN STUDIED A LOT, A LOT ARE PRETTY PLEAO TROPEIC AND ACT BY MULTIPLE MECHANISMS.>>I HAVE A QUESTION FOR YOU ALSO. CAN I ASK A QUESTION. SO IN YOUR SYNTHETIC CRISP, DO YOU THINK THAT SYSTEM CAN BE USEFUL TO STUDY THE FUNCTION OF BACTERIA THAT ATTACH TOTS EPITHELIUM?>>I THINK SO. THEY DO MAKE MUCUS ALSO. SO AN IMPORTANT QUESTION IN A DEVICE LIKE THIS, AN ORGANOID LIKE THIS IS TO HAVE A SUFFICIENTLY THICK MUCUS LAYER. WE DO HAVE MUCUS — DOING MORE CAREFUL MEASUREMENTS RIGHT NOW TO SEE IF THE THICKNESS OF THE MUCUS REALLY IS — BECAUSE IN-VIVO YOU’RE LOOKING AT 100 OR 150 MICRON THICKNESS OF MUCUS LAYER. SO I DO THINK IT IS GOING TO BE AMENABLE FOR LOOKING AT MICROBIOTA ASSOCIATED WITH MUCUS LAYER AND SOME THAT CAN EVEN TRANSLOCATE INSIDE. IT’S NOT THE MOST HIGH-THROUGHPUT DEVICE AS YOU MIGHT EXPECT. WE DO HAVE A WAY OF CONVERTING THIS TO 2-D CULTURES. YOU LOSE THE POLARIZED ORGANIZATION BUT FOR SOME SCREENS IT COULD BE USEFUL AND PEOPLE IN THE AUDIENCE HAS DONE REALLY NICE SCREENS WITH MICROBIAL METABOLITES ON ORGANOID TECHNOLOGY AND HE MADE SOME BIG CONTRIBUTIONS ON BUTYRATE AND HE IS IDENTIFYING OTHER COMPOUNDS TOO. SO I DO LIKE THE IDEA OF ORGANOIDS AS A WAY TO SCREEN MICROBIAL METABOLITES FOR FUNCTION IN A MEDIUM THROUGH PUT MATTER.>>DR. MARUVADA: THANK YOU AND LET’S GIVE A WONDERFUL APPLAUSE. [ APPLAUSE ] SO ON BREAK UNTIL 10:55. I’M PROGRAM DIRECTR FROM THE NCI. THE MODERATOR FOR THIS SESSION. IT’S FOCUS ON THE MICROBIOME FOR TREATMENT. SO PURPOSE OF THIS SESSION IS TO HIGHLIGHT CONCRETE EXAMPLES OF MICROBIOME-BASED TREATMENT FOR SPECIFIC DISEASES AND THAT THEIR OUTCOMES, NEW AND NOVEL MICROBIOME-BASED INTERVENTIONS. WE HAVE THREE OUTSTANDING SCIENTISTS HERE. YOU WILL HEAR THEIR INNOVATIVE INTERVENTION AND PRODUCTIVE STRATEGIES. SO OUR FIRST SPEAKER IS ERIC PAMER FROM MEMORIAL SLOAN-KETTERING. TOPIC IS MIKE CROW BIOTA-MEDIATED DEFENSE AGAINST ANTIBIOTIC-RESISTANT INFECTIONS.>>THANK YOU. I WANT TO THANK LETTA AND RYAN FOR THE INVITATION TO SPEAK AMONG THESE REALLY SPECTACULAR SPEAKERS AND PRESENTATIONS. SO I’M GOING TO TALK ABOUT SOME OF THE WORK THAT HAS ALREADY BEEN PARTIALLY COVERED IN PATIENTS UNDERGOING BONE MARROW TRANSPLANTATION. THIS IS A LONGITUDINAL ANALYSIS OF COMPOSITION IN FIVE PATIENTS UNDERGOING BONE MARROW TRANSPLANTATION. WHAT SURPRISED US AT THE TIME WE DID THIS STUDY WERE THE DRAMATIC CHANGES THAT WE SAW FROM ONE SAMPLING TO ANOTHER. HERE WE’RE GOING WITH WEEKLY SAMPLING. SOME PATIENTS, C&D, SEEM TO MAINTAIN THEIR MICROBIOTA QUITE WELL, WE WERE ABLE TO MAKES CORRELATIONS BETWEEN CHANGES IN THE MICROBIOTA AND CLINICAL OUTCOMES AS WELL AS CLINICAL INTERVENTIONS AND THEIR IMPACT ON THE MICROBIOTA. NOW, IN MORE RECENT YEARS WHAT WE HAVE BEEN DOING IS INCREASING COLLECTIONS FROM THESE PATIENTS SO WE ARE NOW QUITE ROUTINELY COLLECTING DAILY FECAL SAMPLES FROM OUR PATIENTS. THE OTHER THING I SLIPPED THIS SLIDE SLIDE TO MAKE A POINT THAT WITH SOMETHING THAT HAD BOTHERED US A BIT DURING OUR PREVIOUS STUDIES WHERE WE JUST SHOWED THE PROPORTIONS OF BACTERIA AND EVERYTHING WAS ON A 100% Y AXIS. TO QUANTIFYING BACTERIAL DENSITY IN THE FECAL SAMPLES BY QUANTITATIVE 16S AND THEN OVERLYING ON THOSE BARS, THE COMPOSITION. AND I THINK WHAT THIS SHOWS IS THAT WHEN PATIENTS COME IN, THEY HAVE A LOT OF COMPLEXITY BUT ALSO HAVE HIGH BACTERIAL DENSITY. THEN ONCE WE STARTED WITH ANTIBIOTICS WHICH WAS JUST TALKED ABOUT, HAS A VERY DRAMATIC EFFECT NOT JUST ON THE COMPOSITION OF THE MIKE ROBES BUT A 6-LOG DECREASE IN THE DENSITY OF BACTERIA IN THE FECAL SAMPLES THAT WE ARE COLLECTING. AND THAT HAS TO BE TAKEEN INTO CONSIDERATION. NOW I WANT TO REVIEW VERY, VERY QUICKLY A STUDY THAT WE PUBLISHED ALSO A FEW YEARS AGO WHERE WE HAD COLLECTED FECAL SAMPLES FROM A COHORT OF 94 PATIENTS UNDERGOING TRANSPLANTATION AT ABOUT THE TIME WHEN THEIR IMMUNE SYSTEM WAS STARTING TO REDEVELOP. THIS WAS A TIME OF ENGRAFTMENT. WE REASONED THIS MIGHT BE A VERY IMPORTANT TIME GIVEN THE IMPORTANCE OF MICROBES IN THE INTESTINE AND IMMUNE DIFFERENTIATION THAT THE COMPOSITION OF THE MICROBIOTA SO WE RANKED PATIENTS FROM TOP-TO-BOTTOM ACCORDING TO THEIR MICROBIOTA DIVERSITY. AND YOU CAN SEE LOTS OF DIFFERENT COLORS HERE. I’LL POINT OUT THE PINK, WHICH IS BLAUTIA. WHICH ROB MENTIONED IN HIS TALK. YOU CAN SEE THAT AS GO DOWN THIS LIST HERE THAT IT DISAPPEARS AND BY THE TIME YOU GET DOWN TO INDIVIDUALS WITH VERY LOW DIVERSITY, YOU ARE ALSO LOSING THE ANAEROBIC COMPARTMENT. AND AT THE TIME WE HAD COLLECTED THESE, WE HAD SEQUENCED THEM. HAD ALREADY THREE YEARS OF FOLLOW-UP, CLINICAL FOLLOW-UP. SO WE COULD ASK WHAT IMPACT MICROBIOTA DIVERSITY AT THIS ONE SINGLE TIME POINT HAD ON OUTCOMES. AND THESE ARE THE TIME LINES THAT ARE SHOWN HERE, OPEN CIRCLES INDICATE THE PATIENT IS ALIVE AND THE BLACK DOTS GIVE THE CAUSE OF DEATH. WHEN YOU PLOT THIS JUST FOR EITHER GRAPH VERSUS HOST OR INFECTION-RELATED HOARTALITY, WHAT WE FOUND IS THE — MORTALITY — HIGH DIVERSITY INDIVIDUALS HAD A MORTALITY OF 8%. WELL, INDIVIDUALS WHO HAVE LOW DIVERSITY HAD MORTALITY OF 52% ATTRIBUTABLE EITHER TO GDH OR TO INFECTION. AND THAT THIS DIFFERENCE IN MORTALITY ACTUALLY ACCRUED OVER THE COURSE OF TWO YEARS FOLLOWING THIS SINGLE TIME POINT MEASUREMENT HERE. AND THAT SUGGESTED THAT THE COMPOSITION OF THE MICROBIOTA MAY BE HAVING A LONG-TERM IMPACT, COMPOSITION AT THE TIME OF ENGRAFTMENT. AND SO, THAT LED US, A COUPLE OF YEARS AGO, TO PROPOSE TO PERFORM A RANDOMIZED TRIAL OF WHAT WE CALL AUTOLOGOUS FECAL TRANSPLANTATION. AND WHAT WE DO IS WE COLLECT FECAL SAMPLES FROM PATIENTS. WE CHARACTERIZE THEM. WE FREEZE THEM AND THEN WE WAIT FOR THE PATIENT TO GO THROUGH BONE MARROW TRANSPLANTATION. WE WAIT FOR THEM TO ENGRAFT AND THEN ABOUT A MONTH LATER, WE THANK YOU THE SAMPLE AND — THAT YOU THE SAMPLE AND RANDOMIZE THE PATIENTS TO GET THE OWN MICROBIOTA BACK OR UNDERGO ROUTINE MANAGEMENT AND NOT GET IT BACK. WE RANDOMIZED 51, 26 HAVE GONE TO THE TREATMENT ARM AND 25 TO THE CONTROL ARM. AND WE HAVE BEEN ABLE TO ON 25 PATIENTS NOW TO LOOK AT THE EFFECTIVENESS AT A MICROBIOLOGICAL LEVEL OF FMT. WE HAVE COLLECTED FECAL SAMPLES, BEFORE, AFTER, FMT AND BECAUSE AS ROB POINTED OUT, WE HAVE SEQUENCED NOW LOTS OF DIFFERENT MICROBIOTAES FROM OUR BONE MARROW TRANSPLANT PATIENTS. WE CAN PLOT THEM ON THESE PLOTS AND PUT ANY PARTICULAR SAMPLE WITHIN A REGION OF EITHER DIVERSITY, STREPTOCOCCUS DOMINATION, ENTER CAUCUS DOMINATION OR LACTOOR STAFF DOMINATION. AND SO, THIS ALLOWS US NOW TO LOOK AT EACH OF THE PATIENTS EITHER IN THE CONTROL ARM OR IN THE TREATMENT ARM TO SEE WHERE THEY STARTED AND WHERE THEY ENDED UP FOLLOWING RANDOMIZATION AND WHAT WE FIND IS THAT THE TREATED PATIENTS BY-AND-LARGE END UP BACK WITHIN THE DIVERSITY REGION AND THEY ALSO HAVE VERY HIGH PERCENTAGES OF REACQUISITION OF THEIR STARTING — OF THE MICROBIOTA THEY CAME INTO THE HOSPITAL WITH. THIS IS PERHAPS A BIT MORE SIMPLER WAY OF LOOKING AT THINGS. THIS IS LOOKING AT REPRESENTATION OF ALL THESE DIFFERENT BACTERIAL TAXA, EACH HORIZONTAL SIDELINE A PATIENT. AND WE CAN SEE THAT PRE-TRANSPLANT, THEY HAVE REPRESENTATION OF LOTS. POST-TRANSPLANT, THEY LOST MANY OF THESE SPECIES AND FOLLOWING FMT, MANY OF THESE ARE REGAINED N OUR CONTROL PATIENTS WE SEE MANY OF THE LOSSES THAT HAVE OCCURRED PERSIST FOLLOWING TRANSPLANTATION. NOW, WE HAVE — WE ARE AT THE MIDPOINT OF THIS TRIAL AND WE DO HAVE FOLLOW-UP NOW ON MANY OF THESE PATIENTS. THIS IS OUR MOST RECENT DATA WHERE WE ARE SHOWING THE 26 PATIENTS WHO HAVE UNDERGONE FMT AND THESE ARE OUR CONTROL PATIENTS. HERE WE ARE DOCUMENTING BLOODSTREAM INFECTIONS WHICH ALL OF THESE BLOODSTREAM INFECTIONS HERE OCCURRED IN ONE PATIENT WHO ULTIMATELY ENDED UP DYING OF GRAFT-VERSUS-HOST DISEASE. WE HAVE ONE DEATH IN THE TREATMENT GROUP DUE TO DISEASE PROGRESSION WHILE WE HAVE THREE DEATHS THAT OCCURRED DUE TO INFECTION AT RELATIVELY EARLY TIME POINTS IN OUR CONTROL POPULATION. SO THIS TRIAL IS CONTINUING TO ACCRUE. WE HAVE ALSO LOOKED AT THINGS LIKE VIRAL REACTIVATION AND WE SEE IN BOTH GROUPS QUITE A BIT OF VIRAL REACTIVATION ALTHOUGH THE SEVERITY AT LEAST IN THIS POINT IN THE TRIAL, SEEMS TO BE SOMEWHAT GREATER IN THE CONTROL POPULATION. AND I’M GOING JUMP AROUND A LITTLE BIT NOW BECAUSE I WANT TO COVER SEVERAL AREAS WHERE WE HAVE TRIED TO IDENTIFY BACTERIAL SPECIES THAT CONFER RESISTANCE AGAINST THE MAJOR PATHOGENS WE ENCOUNTERED IN OUR HOSPITAL. SO THIS IS A PAPER THAT WAS PUBLISHED A COUPLE OF YEARS AGO NOW WHERE THE STRATEGY THAT WE USED WAS TO TREAT MICE WITH DIFFERENT ANTIBIOTICS AND THEN TO SEE HOW SUSCEPTIBLE THEY WERE AND HOW LONG WERE THEY SUSCEPTIBLE TO C-DIFF INFECTION. AND WHAT THIS STRATEGY ALLOWED US TO DO WAS TO SEQUENCE THE MICROBIOTA OF MICE IN THIS CASE THAT WERE EITHER SUSCEPTIBLE OR RESISTANT TO INFECTION. AND TO BEGIN TO CORRELATE THE PRESENCE OR ABSENCE OF SPECIFIC BACTERIAL SPECIES COMMENSAL SPECIES, WITH SUSCEPTIBILITY TO INFECTION. AND WE ENDED UP WITH USING A SPEAR MAN RANK CORRELATION. A NUMBER OF DIFFERENT SPECIES THAT WERE HIGHLY-CORRELATED WITH RESISTANCE TO C-DIFF INFECTION, PARTICULARLY IN MICE AND SHOWN IN RED HERE, WHERE THE DIVERSITY WAS VERY LOW BUT THE RESISTANCE WAS VERY HIGH. AND SO THAT POINTED OUT AN ORGANISM IN PARTICULAR THAT JUMPED OUT, AND IT WAS HIGHLY ASSOCIATED WITH RESISTANCE. WHAT CHARLIE BUFFY AND M.D., PH.D. STUDENT IN THE LAB WAS ABLE TO ADMINISTER THIS TO NICE AND IT REDUCED SUSCEPTIBILITY, INCREASED SURVIVAL AND IN PARTICULAR, WHEN WE PAIRED IT WITH OTHER ORGANISMS WE COULD GET 100% SURVIVAL, MARKED REDUCTION IN C-DIFF GROWTH AS WELL AS TOXIN PRODUCTION AND SUGGESTING AT LEAST THAT SOME OF THESE OTHER ORGANISMS WERE FACILITATING THE ABILITY OF THIS WHICH WE KNOW MODIFIES BIOASS IDS THAT MAKES THEM MORE INHIBITORY. HERE WE KNOW THAT IF WE TREAT MICE WITH AMPICILLIN WE CAN MAKE THEM VERY SUSCEPTIBLE TO INTESTINAL DOMINATION. IF WE DILUTE NORMAL MICROBIOTA, WE THOUGHT THAT WE MIGHT REACH A DILUTION WHERE SOME MICE WOULD BE PROTECTED AND SOME WOULD BE RESISTENT AND IN FACT, WHEN WE DILUTED TO 10 TO THE MINUS 6, AND ADMINISTERED IT TO MICE, WE SAW SOMEWHERE FULLY RESISTANT AND SOMEWHERE FULLY SUSCEPTIBLE AND SOMEWHERE IN THE MIDDLE. SEQUENCING THE COMPOSITION, WE AGAIN CAME UP WITH A LIST OF ORGANISMS THAT SYLVIA WORKED WITH. SHE THEN SPENT A COUPLE OF YEARS TRYING TO GROW SOME OF THESE BUGS AND FINALLY ENDED UP GETTING A CONSORTIUM OF SEVEN BACTERIA THAT WE COULD ADMINISTER TO MICE AND DEMONSTRATE HIGH LEVEL OF RESISTANCE TO VRE COLONIZATION. SO THAT WAS EXCITING. ULTIMATELY, SHE WAS ABLE TO SHOW THAT BLAUTIA AND THESE OTHERS WERE THE FOUR BUGS THAT WHEN ADMINISTERED TOGETHER DEALT WITH THIS HIGH-LEVEL RESISTANCE. NOW, WE WANTED TO GET AT MECHANISM BY WHICH THESE ORGANISMS ARE CONFERRING RESISTANCE AND WHAT WE FOUND WAS THAT COCULTUREING BLAUTIA BUT NOT THE OTHERS, STRONGLY INHIBITED GROWTH IN CO-CULTURE. THIS INHIBITION WAS MEDIATED BY THE MEDIUM THAT IT HAD BEEN GROWN IN. WE KNEW IT WAS SOMETHING IT WAS RELEASING. NOW, IT TURNED OUT THAT IT DIDN’T JUST INHIBIT VRE. IT ALSO INHIBITS OTHERS MOST EFFECTIVELY. SO, THEN WE WONDERED IS THIS SOMETHING THAT IS TRUE OF ALL BLAUTIA SPECIES AND AND WE WERE LUCKY TO HAVE FROM A COLLECTION OF ANOTHER BLAUTI. THAT WE TESTED AND SURPRISINGLY IT DIDN’T INHIBIT VRE GROWTH AT ALL. AND THAT WAS A BIT OF A MYSTERY SO WE WENT TO OUR SEQUENCING FACILITY AND WE SEQUENCED BOTH STRAINS AND THEN DID A GENOMIC COMPARISON. AND WHAT WE FOUND USING THESE SOFTWARE PLATFORMS TO LOOK FOR BACTEROSINS, THAT OUR STRAIN, THE SLOAN-KETTERING PRODUCTIVE STRAIN, HAD FOUR LOCI THAT ENCODED FOR BACTEROSINS AND THERE WAS ONE IN PARTICULAR THAT WAS A COMPLETE OPERON FOR SOMETHING THAT REFERRED TO AS AULANTY BIOTIC. AND THESE ARE FASCINATING MOLECULES THAT ARE PRODUCED BY A NUMBER OF GRAND POSITIVE ORGANISMS. THE BEST KNOWN IS CALLED NICE IN. AND YOU CAN SEE ALL THESE STRANGE BONDS THAT ARE FORMED BY THE BACTERIUM. THE BLAUTIA PRODUCTIVE SEQUENCES IS DIFFERENT BUT SIMILAR IN STRUCTURE TO THE NISIN MOLECULE AND WHAT WE SUSPECT IS MEDIATING INHIBITION OF VRE. SO, VERY SIMILAR LINES, WE HAVE NOW ALSO RECENTLY STARTED TO LOOK AT RESISTANCE TO AN IN TEARICALLY REQUIRED PATHOGEN MONOCY KNOWLEDGE TO NIECE. WE WERE SURPRISED, PEOPLE SAY THAT MICE ARE INTRINSICALLY RESISTANT TO INFECTION WITH WISTERIA BUT TURNS OUT IF YOU TREAT THEM WITH STREPTOMYCIN, YOU CAN GET MICE HIGHLY INFECTED WITH DISSEMINATED WISTERIAL INFECTION — LISTERIA INFECTION. AND IT CORRELATES WITH A LOSS OF VARIETY OF ANAEROBIC ORGANISM AND WE WERE ABLE TO ASSEMBLE FOUR STRAINS THAT WERE MOST INHIBITORY THAT PROVIDED VERY HIGH-LEVEL RESISTANCE IN-VIVO AGAINST LISTERIA INFECTION. SO THESE ARE NOW THREE CIRCUMSTANCES WHERE ASSEMBLY OF ANAEROBIC ORGANISMS CAN PROVIDE THIS HIGH-LEVEL OF RESISTANCE. SO, I WANTED TO JUST POINT OUT MY CRITICAL GAP. I THINK THAT A KEY GAP IS INCOMPLETE REPRESENTATION CHARACTERIZATION AND OPEN AND UNFETTERED AVAILAILITY OF HUMAN MY COUNTRY BIOTA DERIVED COMMENSAL BACTERIAL SPECIES. I THINK THAT — MICROBIOTA DERIVED — AND I THINK THIS COULD BE A TREMENDOUS RESOURCE, A BIOBANK OR BIOREPOSITORY THAT WE COULD GO TO SO THAT PETER TURNBAUGH DOESN’T HAVE TO WORRY ABOUT GROWING 20 OR 30 SPECIES OF BLA. TIA TO TAKE THE NEXT STEP BUT JUST THO ORDER THEM. I THINK THEY SHOULD BE GENOME SEQUENCED AND WE SHOULD KNOW THEIR METABOLIC PRODUCTS AND DEPENDENCY AND BIOSYNTHESIS AND POTENTIALLY BE TESTED IN GERM-FREE MICE MODELS. IN MY CASE, TO DETERMINE COLONIZATION RESISTANCE AND FINALLY, I JUST NEED TO THANK — I CONSIDER THESE THE FOUNDING FATHERS OF OUR MICROBIOTA PROJECT: [ READING ] THANK YOU. [ APPLAUSE ] SNOOP DR. XI: SO OUR SECOND SPEAKER IS TIMOTHY LU FROM MASSACHUSETTS INSTITUTE OF TECHNOLOGY. HIS TOPIC IS ENGINEERING BIOLOGICAL COMPUTERS FOR HUMAN HEALTH APPLICATIONS.>>DR. LU: THANK YOU FOR THE INVITATION. OUR LAB IS INTERESTED IN TRYING TO DEVELOP TOOLS TO ALLOW US TO MORE PRECISELY SENSE AND RESPOND AND MANIPULATE WHAT IS GOING ON IN THE MICROBIOME. WE REALIZED THAT IN ORDER TO BE ABLE TO DO PRECISION CHANGES, WE NEED NEW TECHNIQUES TO BE ABLE TO DELETE SPECIFIC MEMBERS OF THE COMPLEX MICROBIAL COMMUNITY IN A TARGETED WAY RATHER THAN USING BROAD SPECTRUM ANTIBIOTICS WHICH HAVE MANY COMPLICATING FACTORS. AS WELL AS CAN WE INTRODUCE SPECIFIC MICROBES INTO THE GUT THAT ALLOW US TO DETECT PERHAPS IN REALTIME, WHAT IS GOING ON INSIDE OF A COMPLEX MICROBIAL COMMUNITY LIKE IN THE GUT AND BE ABLE TO RESPOND BY TRYING TO TREAT DISEASE. THAT IS WHAT I’M GOING TO TELL BUT TODAY. SEVERAL TECHNOLOGIES WE HAVE BEEN WORKING ON TO ENABLE SUCH RESEARCH GOING FORWARD. SO I WANT TO START OFF FIRST ON THE SUBTRACTIVE SIDE. HOW DO WE BUILD MORE NARROW SPECTRUM ANTIMICROBIAL STRATEGIES THAT ALLOW US TO PERTURB MEMBERS OF THE COMMUNITY. SO WE HAVE BEEN INTERESTED IN THIS PROBLEM. CAN WE MOVE AWAY FROM THE USE OF VERY BROAD SPECTRUM ANTIMICROBIALS AND GET TO THE POINT WHERE WE CAN DEVELOP TARGETED ANTIMICROBIALS YOU CAN READILY REPROGRAM TO GO AFTER WHATEVER ORGANISM YOU WANT? ONE OF THE CHALLENGES WHICH I WENT TALK IN MUCH DETAIL ABOUT IS, IF YOU HAVE NARROW SUSPECT RUM ANTIMICROBIALS FOR THEM TO BE PRACTICALLY USEABLE IN THE CLINIC, WE ALSO NEED RAPID DIAGNOSTICS TO ALLOW US IN THERE WHICH ANTIMICROBIALS TO BE USED IN CLINIC. THERE ARE A LOT OF FOLKS TRYING TO DEVELOP MORE RAPID DIAGNOSTIC TOOLS THESE DAYS FOR MICROBIAL INFECTIONS. SO I’LL FOCUS ON HOW TO TARGET ANTIMICROBIAL AGENTS. WE HAVE BEEN EXPLORING A FEW WAYS. ONE USING ENGINEERED ANTIMICROBIAL PEPTIDES. TODAY I WANT TO TELL YOU ABOUT HOW WE INCORPORATE THE CRISPR NUCLEASE TECHNOLOGY. SO THE IDEA IS, CAN WE DEVELOP ANTIMICROBIALS THAT DON’T TARGET BACTERIA BASED ON CONSERVED MECHANISMS BUT RATHER ALLOW US TO BUILD ANTIMICROBIAL AGENTS THAT TARGET BACTERIA AT THE LEVEL OF DNA. USING THE CRISPR SYSTEM WE MAY BE ABLE TO REPROGRAM AGAINST. SO I THINK EVERYONE IN THE AUDIENCE KNOWS ABOUT THIS SYSTEM BUT BRIEFLY MENTION BASICALLY TRYING TO TURN THE CAS9 NUCLEASE INTO A SEQUENCE SPECIFIC CLEAVAGE SYSTEM WHERE YOU CAN REDIRECT THAT TASTY AGAINST A TARGETED GENOME. AND IN BACTERIA IF YOU ADD A SPECIFIC TARGET GENE, COULD YOU BASICALLY FORCE THAT BACTERIA TO DIE WHEN YOU MUTATE THAT SEQUENCE? ONE OF THE STRATEGIES HOW TO GET THIS THING DELIVERED? ONE STRATEGY WE DEVELOPED WAS TO ENCODE THE CAS9 SYSTEM ON A PHAGE MID WHICH THEN PACKAGE AND PRODUCE IN THE LAB AND THEN THROW ON TO OUR BACTERIA OF ITEREST. SO THE IDEA HERE WAS THAT THE BACTERIA WOULD DELIVER CAS9 WHICH WE CAN REPROGRAM TO GO AFTER THE TARGET. FOR EXAMPLE, WE DESIGNED THE CAS9 SYSTEM TO GO AFTER GENOMIC TARGET IN THIS CASE A POINT MUTATION IN GYRUS AGING THAT CONFERS RESISTANCE. WE HAVE TO ENGINEERED PHAGES HERE. AND SO WHEN WE PUT THESE TWO AGAINST THE WILDTYPE POPULATION WHICH ARE BOTH SUSCEPTIBLE TO PHAGE INFECTION BUT YOU DON’T GET ANY TOXICITY AGAINST THESE, IT’S BECAUSE THEY DON’TS CONTAIN A FAR GET FOR THE CAS9 BUT IF YOU PUT THIS ON TO THE ANTIBIOTIC RESISTANT VERSION OF THE E.COLI, YOU CAN GET A 4-ORDER MAGNITUDE DROP IN THE VIABILITY OF CELLS WITH THE SPECIFIC CAS9 SYSTEM INDICATING THAT POTENTIALLY NOW WE CAN USE THIS METHOD TO USE SEQUENCE-SPECIFIC NUCLEASES TO DESTROY PARTICULAR BACTERIA WHILE SPARING THE REST. THIS PAPER WE SHOWED ULTIMATELY DEPENDING ON HOW YOU CONFIG THE ANTIMICROBIAL, YOU GENERATE DIFFERENT EFFECTS. SO TARGET GENOMIC LOCATIONS AND TARGET THINGS ON PLASMIDS WHICH MANY OF THESE — IF THEY HAVE ADDICTION SYSTEMS OR TOXIC EFFECT SYSTEM, CAUSE OUR CELLS TO DIE. IN OTHER CASES, YOU CAN CURE THE CELLS OF THOSE PARTICULAR PLASMIDS WITHOUT EFFECTING THE CELL VIABILITY. ULTIMATELY WHERE WE ARE GOING WITH THIS IS TO TRY TO DENTAL COMPLEX COMMUNITIES. STER AN EXAMPLE WHERE WE MADE A COMMUNITY COMPOSED OF BLUE, PURPLE AND YELLOW BACTERIA AND ENGINEERED A CRISPR SYSTEM TARGETED THE YELLOW BACTERIA AND IN THIS CASE, ANOTHER SYSTEM THAT ONLY TARGETED BLUE BACTERIA AND THE IDEA IS EVEN THOUGH ALL THREE CAN BE PRODUCTIVELY EFFECTED BY THE PHAGE MID, ONLY ONE GETS KILLED BASED ON THE SEQUENCE SPECIFIC NUCLEUS. ONE OF THE KEY CHALLENGES HERE IS REALLY TO TRY TO DEAL WITH THE DELIVERY ISSUE. HOW TO GET THESE SYSTEMS DELIVERED EFFICIENTLY? AND IN THE LAB, JUST BECAUSE OF TIME, WE HAVE BEEN DEVELOPING LIBRARIES OF PHAGES NOW THAT GIVE MORE EFFICIENT DELIVERY OF WIDER SPECTRUM OF BACTERIA. ALTERNATIVELY WE ARE EXPLORING COG GATED PLASMID STRATEGIES. IF YOU COULD PIGGYBACK UPON A MECHANISM HAVE A GENE DRIVE FOR BACTERIAL SYSTEMS, THIS COULD BE ANOTHER WAY FOR US TO THINK ABOUT EDITING BACTERIAL COMMUNITIES. I TALKED ABOUT THE SUBTRACTIVE TECHNIQUES AND I WANT TO SPEND THE REST THE OF THE TIME TELLING BUT ENGINEERING BACTERIA THAT COULD BE DELIVERED INTO THE GUT FOR A VARIETY OF DIFFERENT APPLICATIONS. SO THE ULTIMATE IDEA HERE IS VERY SIMPLE. CAN WE GENETICALLY MODIFY BACTERIA AND DELIVER THESE INTO THE GUT THROUGH AN ORAL FASHION? AND WE HAVE BEEN EXPLORING TWO DIFFERENCE APPLICATIONS. FIRST CAN WE ENGINEER SENSORS OF DIAGNOSTIC BACTERIA THAT DETECT BIOMARKERS OF DISEASE AND THEN REPORT THAT OUT TO THE REAL WORLD? AND THE SECONDLY, CAN WE TAKE THE BACTERIA AND ENGINEER THEM TO PROVIDE TREATMENT LOCALLY IN THE GUT? STOW CAN WE DO SENSE AND RESPOND TYPE OF BEHAVIORS? TO DO THIS WE SPENT A LOT OF TIME DOING GENETIC ENGINEERING OF STRAINS SO WE SPENT A LOT OF TIME AS ENGINEERS GETTING EFFICIENT AT MODIFYING THESE BACTERIA. SO I SHOW YOU SOME OF THE PROJECTS ONGOING IN THE LAB. ONE WE HAVE BEEN DOING WITH THE LAB AT MIT IS TO CO-HOUSE ENGINEERED BACTERIA THAT DETECT BIOMARKERS OF DISEASE ON TO A PILL THAT TRANSMITTAL THAT INFORMATION WIRELESSLY FROM THE INSIDE OF THE BODY TO THE OUTSIDE. SO THE IDEA SHEAR COULD YOU SWALLOW A PILL? WHAT IF YOU HAD A FRONT END SENTENCER, THE CASE BACTERIA BUT OTHER CASES CELL-FREE SYSTEMS THAT ALLOWS YOU TO SENSE WHAT IS GOING ON INSIDE THE GUT, TRANSMIT THAT TO THE UNITED STATES WORLD. SO THIS PARTICULAR CASE WE SPENT TIME OPTIMIZING MICROELECTRONICS AND ALSO ENGINEER THE BACTERIA TO SENSE SPECIFIC BIOMARKERS TO DETECT A SIGNAL. IN THIS CASE IT’S BACTERIAL LUCIFEROUS. YOU CAN SWALLOW THIS PILL AND THE FIRST SUBSTANCATION IS TO SHOW WE CAN SHOW SOMETHING LIKE BLEEDING INSIDE THE GUT. SO WE ENGINEERED A BACTERIA THAT SENTENCED HEATING AND PRODUCES LUCIFERASE AS A RESPONSE. SO HERE YOU CAN SEE IN THE PRESENCE OF BLOOD AS WELL AS THE SENSOR IN ABOUT 15 OR 30 MINUTES IN THIS IN-VITRO CASE, THE CIRCUIT TURNS ON AND IF WE MAKE A DELETION IN ONE OF THE COMPONENTS IN THE CELLS, BASICALLY THE SYSTEM STAYS OFF. WE HAVE BEEN WORKING NOW WITH ANOTHER LAB TO THEFT NOW TO PIG MODEL BLEEDING WHERE WE TAKE AND I GUESS BASICALLY GIVE THEM BLOOD OR NOT AND THEN TEST WHETHER THE CHIP IS ABLE TO THEN DETECT BLEEDING IN THE GUT. AND HERE IS SOME OF THE PRELIMINARY DATA WE GENERATED. HOT OFF THE PRESS JUSTICE WHERE WE JUST GENERATED SOME OF THESE PILLS AND PUT THEM IN THE AND I GUESS SHOWED THAT WITH THE SENSORS WE COULD DETECT APPROXIMATELY 45 MINUTES THE PRESENCE OF BLEEDING IN THE GASTROSYSTEM VERSUS THE NEGATIVE CONTROLS. WE ARE CONTINUING TO OPT MICE THIS BUT I THINK THERE IS PROMISE HERE AND ONCE WE HAVE THIS SYSTEM UP AND RUNNING IT SHOULD BE RELATIVE STRAIGHTFORWARD FOR US TO SENSOR THE COMPONENT TO DETECT OTHER METABOLITES OF INTEREST. THIS PILL COULD BE TALKING TO YOUR BLUETOOTH CONNECTION ON YOUR PHONE. SO, A LOT OF THE WORK THAT WE HAVE DONE SO FAR HAS BEEN IN ECOLEY. ONE OF THE THINGS WE WANT TO DO MOVING FORWARD IS TO TRY TO GENETICALLY DOMEST KATE THE COOL ORGANISMS WE HEARD ABOUT OVER THE LAST FEW DAYS S THE CHALLENGE WHEN DOING THAT FIRST YOU HAVE TO BE ABLE TO GROW THE ORGANISM AND I THINK A LOT OF FOLKS ARE TRYING TO DO THAT. AND MAKING THEM GENETICALLY TRACTABLE TO THE POINT WHERE WE CAN DO GENETICS AND THEN STUDY FUNCTION IS A CHALLENGE. SO A FEW YEARS AGO TOGETHER WITH ANOTHER WE DECIDED TO SEE IF WE CAN PORT A LOT OF TOOLS WE ARE USED TO USING IN E.COLI GENETICS INTO AN ORGANISM. SO WE NOW IMPORT A LOT OF TOOLS SPY VARIETY OF STRAINS AS I’LL SHOW YOU AND NOW HAVE THE ABILITY TO INTRODUCE GENETIC CIRCUITS AND BUILD SENSORS AND THEY’RE PEWS NIX THIS CONTEXT. SO BASICALLY — THEY’RE PEWSICS. THIS IS BORING FROM GENETIC ENGINEERING PERSPECTIVE BUT IMPORTANT TO BUILD LARGE LIBRARIES OF GENE REGULATORY PARTS THAT WE TAKE FOR GRANTED WHEN WE ARE WORKING WITH OTHER ORGANISMS. SO WE BUILD LIBRARIES THAT WILL ALLOW US TO REGULATE GENE EXPRESSION OVER FIVE ORDERS OF MAGNITUDE. WE BUILT FOUR DIFFERENT INDUCIBLE SYSTEMS TURNED ON BY METABOLITES AND YOU CAN DO FUNCTIONAL GENETIC STUDIES ON WHAT GENES LEAD TO WHAT FUNCTION. SO HERE ARE SOME EXAMPLES. WE HAVE AN INDUCIBLE SYSTEM AND OTHER SYSTEMS – AUDIO ALLOWING US TO CONTROL GENE EXPRESSION IN ORTHOGONAL WAYS. WE CROSS ALL 4 INDUCERS WITH THE PROMOTORS, WE GET PRETTY ORING TOINOUS REDUCTIONS. ORING TOINOUS. WE INCORPORATED MEMORY CIRCUITS INTO THESE CELLS SO IMAGINE EATING A BACK RIGHTIES AND HAVING IT SENSE IN YOUR GUT AND THEN WHEN IT COMES OUT THE OTHER END, SEQUENCE THEM OR A TEST TO SEE WHAT HAPPENED TO IT GOINGS THROUGH YOUR BODY. SO ONE OF THE WAYS TO DO THAT IS USE A CLASS OF PROTEINS. THEY BASICALLY FLIP A PIECE OF DNA UPSIDE DOWN. SO IF WE ADD RAM NOSE TO CELLS IT INDUCES AND RECOGNIZES THE SITES THAT CORRESPOND AND FLIP IT UPSIDE DOWN AND BY SEQUENCINGS AND LOOKING AT THE ORIENTATION OF DNA YOU HAVE A 01 NIT OUR COMPUTER. SO BY ADDING MORE RAM, WE CAN SWITCH ON MEMORY CIRCUIT AND GET NEAR 100% WRITING OF THAT PARTICULAR MEMORY UNIT AND THE CIRCUIT TOWNS IN ABOUT TWO HOURS OR SO. WE HAVE MOVED ON TO SHOW CIRCUITS CAN WORK WHEN YOU COLONIZE MICE AND FEED THEM DIFFERENT INDUCERS. WE HAVE TAKEN MICE SMEAR COLONIZED AND COLLECTED SCHOOL LOOKED AT WHETHER IT IS GLOWING OR NOT. SO IS IN THIS PARTICULAR EXAMPLE WE FED THE MICE THIS FROM DAY TWO AND DAY 4. WE SHOW THAT YOU CAN SWITCH ON ABOUT TWO ORDERS OF MAGNITUDE OF LUCIFERASE AND THEN IT GOES AWAY. AND WE HAVE ALSO DONE THE OPPOSITE. SO USING CRISPR I, WE CAN SHUT A REPORTER AND AGAIN FROM DAY 2 TO DAY 4, THEY DROP THE EXPRESSION OF LUCIFERASE AND IT RECOVERS ONCE YOU REMOVE THAT FROM THEIR FOOD SOURCE. SO ESSENTIALLY WHAT WE HAVE BEEN DOING IS BUILDING UP TOOLS IN THE LAB AND WE ARE CONTINUING TO PUSH FORWARD TO PROVIDE THESE AS A RESOURCE TO THE COMMUNITY SO THAT YOU CAN INTRODUCE SENSORS INTO A MICROBIAL SPACE AND GENETICALLY MODIFY MORE AND MORE ORGANISMS TO DO FUNCTIONAL GENETICS ON THEM AND ULTIMATELY OUR INTEREST IS TO PUSH TECHNOLOGIES INTO THE CLINIC. I’LL TELL BUT THAT WORK. SO ABOUT A FEW YEARS AGO, WE EXPLAINED SOME OF THE TECHNOLOGIES INTO A COMPANY THAT IS NOW TRYING TO USE THESE CIRCUITS AS A WAY OF TREATING DISEASE. SO, THE IDEA IS TO TAKE THE CIRCUITS WE DIVIDES AND INTRODUCE THEM INTO A PRO BIOTIC STREAM THAT CAN BE CONSUMED ORALLY TO TRY TO TREAT METABOLIC DISEASES. THE APPROACH WE HAVE TAKEN IS TO TRY TO DEVELOP THESE ENGINEERED PROBIOTICS TO TREAT RARE DISORDERS INCLUDING INBORN ERRORS OF METABOLISM. TWO OF THE ONES WE ARE FOCUSED ON IS THE DISORDER WHERE THE PROBLEM IS TOXIC BUILDUP OF AMMONIA IN THE BLOODSTREAM AND ANOTHER DISEASE WHERE PATIENTS DON’T HAVE THE ABILITY TO METABOLIZE 15 ALANIN. WE ARE DEVELOPING PRE-CLINICAL CANDIDATES TO GO AFTER SOME OTHER DISEASE TYPES. SO, HERE IS JUST AN OVERVIEW OF WHY WE THINK THIS IS AN INTERESTING APPROACH. WE WANT TO BE ABLE TO GIVE PATIENTS AN ORAL DOSE OF ENGINEERED PRO BIOTIC AND HAVE THAT LOWER SYSTEMIC AMMONIA LEVELS. SO INSTEAD OF HAVING TO INJECT YOURSELF, WHAT IF YOU COULD DO THIS THROUGH A NON-INVASIVE ORAL ROUTE? THIS COULD POTENTIALLY HAVE BENEFITS IN POPULATIONS WHERE PATIENTS HAVE ACQUIRED LIVER DISEASE AND CAN’T PROCESS AMMONIA PROPERLY. SO THE BASIC APPROACH IS STRAIGHTFORWARD. WE TAKEN ENGINEERED PROBIOTICS AND WE GENETICALLY MODIFY THAT ORGANISM HERE AND IN PARTICLAR WASM UP THIS PATHWAY FOR CONSUMING AMMONIA AND MAKING ARGININE. THERE IS A 10-MEMBER PATHWAY YOU HAVE TO MODIFY TO GET VERY EFFICIENT CONVERSION AND THE IDEA IS IF YOU FEED THIS ORALLY CAN YOU CONVERT THE LOAD IN THE GUT AND HAVE THAT FLUSH OUT OVER TIME? WE ALSO PUT THIS CIRCUIT UNDER ANEROBICALLY INDUCIBLE SWITCH AND THIS WAS DONE FOR TWO REASONS, ONE TO MAKE THUR THIS IS ONLY ON IN HIGH LEVELS AND TWO MORE MANUFACTURING REASONS. THESE BACTERIA GENETICALLY MODIFIED CAN BE EFFICIENT IN DOING SOMETHING THAT DOESN’T HELP THEM AT ALL IN TERMS OF SURVIVING. WE NEED A SWITCH TO KEEP THEM OFF DURING THE MANUFACTURING PHASE TO MAKE A LOT OF IT AND THEN SWITCH IT ON BEFORE WE GIVE TO THE PATIENT. HERE ARE EXAMPLES OF THE STRAIN. SO IF YOU LOOK AT THIS IN-VITRO AND THE ABILITY TO PRODUCE ARGININE IT IS LOW. BUT THESE GENETIC ENGINEERED ARE EFFICIENT AT IT AND THEN IN A MOD WELYOU GIVE MICE HIGH-PROTEIN DIET AND LOOK AT THEIR AMMONIA LEVELS, YOU CAN SEE NORMALLY IF THEY ARE ON WATER NORMAL CHOW YOU HAVE A RELATIVELY NORMAL BLOOD AMMONIA LEVEL AND ON HIGH PROTEIN CHEW IT ELEVATES. WHEN WE TREAT THESE MICE AND FEED THEM THE ENGINEERED PRO BIOTIC, IT DROPS DOWN TO SYSTEMIC LEVELS. SO AS I MENTIONED, THIS IS NOW IN THE PHASE I STUDY. WE ARE HOPEFUL IT WILL GET READ OUTS OF THIS AND SEE HOW THIS STRAIN PERFORMANCE. WE HAVE OTHER WORK GOING ON IN SEVERAL OTHER AREAS INCLUDING PKU. I THINK THIS IS AN EXCITING AWAY OF SOME GENETICALLY ENGINEERED PROBIOTICS IN THE CLINIC. I WANT TO ADDRESS SOME OF THE CRITICAL KNOWLEDGE GAPS WE ARE TRYING TO ADDRESS WITH OUR TECHNOLOGIES. WE WANT TO MOVE FORWARD AND TRY TO UNDERSTAND THE FUNCTIONAL INTERACTIONS BETWEEN MICROBES AND THE HOST. IN ORDER TO BE ABLE TO DO THAT, WE NEED BETTER SENSORS AND BETTER TOOLS TO BE ABLE TO SEE WHAT IS GOING ON IN MORE RETIME IN SPACIAL LOCATIONS AND DIFFERENT BACTERIA. WE ARE TRYING TO DEVELOP KEY RESOURCES AND TOOLS FOR THAT. I LIKE TO ECHO THE PREVIOUS SPEAKER’S TALK AROUND WE NEED BETTER COLLECTIONS OF THESE ORGANISMS THAT ALLOW A WHOLE COMMUNITY TO WORK ON THE SAME SET OF ORGANISMS PREFERABLY WELL CHARACTERIZED ONES WE CAN BUILDUP GOOD LIBRARIES AND CHARACTERIZE THEM SO THEY ARE ALSO AVAILABLE FOR THE COMMUNITY TOO USE. SO WITH THAT, I’D LIKE ON TO SUMMARIZE WITH THIS SLIDE. WE ARE TRYING TO DEVELOP TOOLS AND SOLVE THIS PARTICULAR SET OF PROBLEMS AND THANK THE PEOPLE WHO DID THE WORK: [ READING ] THANK YOU VERY MUCH. [ APPLAUSE ]>>DR. XI: THANK YOU. THAT WAS VERY INTERESTING. SO WE HAVE THE LAST SPEAKER OF THIS SESSION, DR. EUGENE CHANG FROM UNIVERSITY OF CHICAGO. HIS TOPIC IS CONNECTING THE GUT AND MICROBIOME AND THE CANCER THROUGH CIRCADIAN RHYTHMS.>>DR. CHANG: THANK YOU. SO, I WANT TO THANK LETTA AND THE ORGANIZING COMMITTEE IF FOR INCLUDING ME IN THIS STELLAR BUT I ALSO WANT TO THANK THE AUDIENCE FOR STICKING IT OUT TO THE END. AND SO, ONE OF THE THINGS ABOUT BEING VERY LAST IN THE LAST DAY OF A PROGRAM, IS THAT IT’S SORT OF AN UNDESIRABLE POSITION TO BE IN BUT I’M AN OPTIMIST. WHEN THEY TALKED TO AUDIENCES AFTER MEETINGS, THEY ASKED WHAT DO YOU REMEMBER? AND THEY REMEMBER WHAT WAS SET IN THE BEGINNING AND WHAT WAS SAID AT THE END. SO I’M HOPING THAT LIKE YOU GUYS ARE LIKE THE TRUMP CORE SUPPORTERS. NO MATTER WHAT I SAY, YOU’LL REMEMBER WHAT I SAY. [ LAUGHS ] SO I’M GOING TALK ABOUT A TOPIC THAT IS A LITTLE BIT OFF BEAT FOR WHAT I DO. BUT IT DOES CONNECT A FEW THINGS. AND IT IS GERMANE TO THE THEME OF THIS SESSION. AND THAT IS CONNECTING THE GUT MICROBIOME AND CANCER THROUGH CIRCADIAN RHYTHMS. AND THERE IS SOME LOGIC TO THIS. AND I JUST AM GOING TO GO THROUGH THIS. FIRST INTRODUCTORY SLIDE WHICH IS THAT THERE ARE THREE PARTS TO THIS STORY, CANCER, METABOLISM, AND THE INTESTINAL MICROBIOME. AND I THINK THERE IS A LARGE AMOUNT OF LITERATURE THAT CONNECTS CANCER TO METABOLISM AND MICROBIOME TO METABOLISM AND INTESTINAL MICROBES TO CANCER. AND OFTEN THESE ARE DIRECTIONAL, BIDIRECTIONAL PATHWAYS. BUT WHAT I’M GOING TO DO TODAY IS PROVIDE AN EXAMPLE OF A PATHWAY THAT STARTS WITH THE INTESTINAL MICROBIOME AND THROUGH THIS VARIATION THAT WE AND OTHER GROUPS HAVE OBSERVED, ALTERING HOST METABOLISM BY EFFECTING CIRCADIAN RHYTHMS WHICH DO HAVE RELEVANCE TO CANCER BIOLOGY. HOW DO WE BEGIN? WE BEGAN WITH A VERY SIMPLE OBSERVATION AND WE HAD NOTICED THAT GERM-FREE MICE ARE RESISTANT TO WESTERN TYPE OF HIGH-FAT DIET. THAT IS SHOWN ON THE LEFT. IF YOU PUT SPF MICE ON A HIGH-FAT DIET, THEY GAIN WEIGHT IN COMPARISON TO THEIR COUNTERPARTS ON LOW-FAT DIET, SHOWN IN THE BLUE. BUT IF YOU GAVE THE EXACT SAME DIET TO THESE MICE THAT ARE GERM-FREE, THEY ACTUALLY DON’T GAIN ANY WEIGHT. THEY ARE RESIST TONIGHT THESE HIGH-FAT DIETS. AND THIS WOULD SUGGEST THAT SOMEHOW GUT MICROBES ARE VERY IMPORTANT IN THE METABOLISM AND WHAT WE DO WITH THE CALORIES THAT WE EAT. NOW, ANOTHER INTERESTING OBSERVATION IS SHOWN IN THE LEFT PANEL AND THAT IS, IF YOU LOOK AT THE GERM-FREE MOUSE ON A REGULAR CHOW, THIS HOUSE HAS TO EAT MORE PER DAY IN ORDER TO MAINTAIN THE SAME AMOUNT OF WEIGHT. AND YOU CAN SEE THAT IT’S MUCH MORE THAN THE OTHER THREE GROUPS. AND SO WHAT THIS SUGGESTS IS THAT SOMEHOW WITHOUT HAVING GUT MICROBES, THE MEMETABOLISM OF THE HOST HAS BEEN ALTERED. SO WE WANTED TO DRILL DOWN ON THIS A LITTLE BIT BETTER AND WE DID A VERY SIMPLE STUDY AND THIS WAS TO LOOK AT THE LIVER TRANSCRIPTOME AND COMPARE IT BETWEEN THE GERM-FREE MOUSE AND THE CONVENTIONALIZED MOUSE. AND WHY THE LIVER — THE LIVER IS YOUR MAJOR METABOLIC ORGAN. SO, WHAT WE DID WAS, WE DID A TRANSCRIPTOMIC ANALYSIS AND IT TURNS OUT THAT THERE ARE THOUSANDS OF GENES THAT ARE DIFFERENTIALLY EXPRESSED BETWEEN THESE TWO GROUPS. AND IF YOU DO THE PATHWAY ANALYSIS, WHAT WAS REALLY EYE-OPENING AT LEAST FOR ME, WAS THAT TWO-THIRDS OF THESE GENES ARE RELATED TO METABOLISM. ONLY 1/3 WAS RELATED TO IMMUNE MECHANISMS. AND FOR ME, IT REALLY BEGAN TO UNDERSCORE THE POTENTIAL RELATIONSHIP BETWEEN GUT MICROBES AND OUR METABOLISM. NOW IF YOU DRILL DOWN ON THAT DATA AND YOU LOOK AT THE PATHWAY ANALYSIS, WHAT COMES AT THE VERY TOP WHERE MANY OF THE MEMBERS ARE INCLUDED IN THESE NETWORKS, ARE CIRCADIAN CLOCK GENES EVOLVED IN REGULATING CIRCADIAN RHYTHM. NOW AT FIRST, I DIDN’T KNOW ANYTHING ABOUT CIRCADIAN RHYTHM AND WASN’T SURE WHAT THIS MINUTED BUT AFTER READING ABOUT IT, IT MADE A LOT OF SENSE. SO, CIRCADIAN RHYTHMS ARE BASICALLY CONTROLLED BY A SERIES OF SO-CALLED CLOCK GENES. THESE GENES FOR EXAMPLE INCLUDE INDUCERS LIKE CLOCK AND OTHERS WHICH ACTIVATE THROUGH TRANSCRIPTION A NUMBER OF GENE PATHWAYS THAT ULTIMATELY ARE SHUT OFF BY REPRESSORS LIKE CRJPUR, WHICH DO IT THROUGH A TRANSLATIONAL REGULATION. SO THE BOTTOM LINE IS HAVE YOU OSCILLATORY BEHAVIOR THROUGH THE COURSE OF THE DAY WHICH IS BASICALLY LIKE AN ON AND OFF SWITCH. AND WHAT IF DOES IS THIS KIND OF CORE LOOP REGULATES A SERIES OF GENETICS PATHWAYS THAT ULTIMATELY WILL CONTROL PERIPHERAL CIRCADIAN CLOCKS IN A WAY THAT WE BASICALLY TELL OUR BODY WHEN TO BURN ENERGY AND WHEN TO STORE IT. AND MOST OF THIS IS DRIVEN BY LIGHT AND DARK SIGNALS. THAT IS WHEN YOU WAKE UP IN THE MORNING, YOUR CIRCADIAN SWITCH GOES ON AND SAYS, OKAY, YOU HAVE TO BURN ENERGY BECAUSE YOU’RE GOING TO USE IT AND WHEN YOU GO TO BED AT NIGHT, YOU START TO STORE IT. SO IT’S A VERY IMPORTANT THAT YOU HAVE THIS KIND OF REGULATORY SYSTEM AND IT IS VERY INHERENT TO ALMOST ALL LIFE FORMS. NOW IT TURNS OUT THAT SIR DADEIAN RHYTHMS ARE MORE THAN JUST REGULATING METABOLISM — CIRCADIAN. THEY REGULATE BEHAVIOR, WEIGHT WAKING AND SLEEPING. BUT RELEVANT TO THE DISCUSSION TODAY IS THAT IT TURNS OUT THAT CIRCADIAN CLOCKS ARE VERY IMPORTANT FOR CANCER BIOLOGY. AND THIS IS SHOWN HERE. THIS IS AN EXCELLENT REVIEW BY THE COURSEY GROUP. AND I SEEM TO HAVE LOST MY POINTER. HERE IT IS. SO, THIS IS JUST A VERY BROAD GENERALIZATION OF HOW CIRCADIAN CLOCKS ARE RELEVANT TO CANCER. IT’S KNOWN FOR EXAMPLE THAT EPIGENETIC REGULATION IS VERY IMPORTANT FOR CIRCADIAN REGULATION OF TRANSCRIPTOME EVENTS AND THIS OCCURS THROUGH ACETYLATION AND METHYLATION OF HISTONES, DNA METHYLATION, MICRORNA AND ALSO RECRUITMENT OF OTHER TRANSCRIPTION FACTORS. BUT ANOTHER POINT THAT CIRCADIAN RHYTHMS ARE IMPORTANT IS THAT SOME OF THESE CIRCADIAN CLOCK CHAINS, FOR EXAMPLE, PE R AND CRY, INTERACT WITH A NUMBER OF KEY PROTEINS THAT ARE INVOLVED IN CELL CYCLE REGULATION. ED AND OTHER TARGETS INCLUDE THINGS LIKE TUMOR SUPPRESSOR GENES AND OTHER REGULATORS OF CELL CYCLE. SO NOT SURPRISINGLY, IF YOU DISRUPT CIRCADIAN FUNCTION, AS SHOWN HERE, AND THIS CAN OCCUR THROUGH MANY DIFFERENT WAYS, FOR EXAMPLE IT COULD BE THROUGH SLEEP DISORDERS, SHIFT WORKERS WHO BY THE WAY EP DEEM LOGICALLY HAVE BEEN FOUND TO BE AT INCREASED RISK FOR CANCERS, TO EXPERIMENTAL SYSTEMS WHERE YOU CAN PINPOINT SPECIFIC DISRUPTIONS OF THE CIRCADIAN CLOCK. AND THERE YOU CAN SEE THAT YOU WILL EFFECT BOTH TUMORIGENESIS AS WELL AS PROGRESSION OF TUMORS. SO THERE IS A LINK BETWEEN CIRCADIAN RHYTHMS AND CANCERS AND IT OCCURS AT MULTIPLE LEVELS. NOW HOW IS THIS ALL RELEVANT TO THE GUT MICROBIOME? SO I’M GOING TO GO BACK TO THIS GERM-FREE MODEL AND IN THIS INSTANCE, WHAT WE LOOKED AT IS, WE KNEW THAT THERE WAS SOME KIND OF METABOLIC ABNORMALITY OF THESE MICE, MAYBE A METABOLIC ADVANTAGE SINCE THEY CAN EAT ALL THEY WANT AND THEY NEVER GET FAT. BUT ON THE OTHER HAND WHAT WE DID WAS ASKED A VERY SIMPLE QUESTION, THAT’S THEIR CIRCADIAN RHYTHM UNDER BOTH HIGH-FAT AND LOW-FAT FEEDING CONDITIONS? AND WE LOOKED IN THE BRAIN SO THE MASTER REGULATORS CIRCADIAN RHYTHM IS SOMETHING IN A PLACE CALLED THE SUPER NUCLEUS WHICH IS LOCATED IN THE MENIAL BASAL HYPOTHALAMUS. PERIPHERY AND LOOKED AT THE LIVER SPECIFICALLY, WHICH IS YOUR MAJOR METABOLIC OREGON. AND WHAT YOU CAN SEE IS THAT HIGH-FAT DIETS DO ALTER CIRCADIAN BEHAVIOR, IN THIS CASE SHOWN FOR ONE INDUCER, AND SHOWN IN THE BLUE IS THE COMPARISON OF WHAT THIS RYTH MISTY IS FOR BHO-N A LOW-FAT FED ANIMAL. SO THIS CHANGE IS NOT SURPRISING. IT’S BEEN REPORTED BY MANY GROUPS. IN THE LIVER, THE CHANGES WERE NOT AS DRAMATIC BETWEEN HIGH-FAT AND LOW-FAT DIET SUGGESTING THAT THIS REGULATION DOES HAVE DIFFERENTIAL EFFECTS DEPENDING ON WHERE THE CIRCADIAN CLOCK GENES ARE LOCATED. BUT THE MOST STRIKING THING I THINK IS SHOWN ON THE RIGHT PANELS. AND THIS IS DATA FROM THE GERM-FREE MOUSE. WHAT CAN YOU SEE HERE IS IT DOESN’T MATTER WHETHER IT IS HIGH-FAT OR LOW-FAT DIET. SOMETHING HAS HAPPENED TO THE AMPLITUDE AS WELL AS THE RHYTHM OF FOR EXAMPLE THIS BMAL1. SO THIS IS SEEN IN OTHER CIRCADIAN CLOCK GENES AS WELL. AND I THINK THAT YOU CAN SEE THAT THIS EFFECT OCCURS BOTH IN THE CENTRAL AS WELL AS AS IN THE PERIPHERAL REGIONS. NOW, THIS WAS REALLY PROFOUND AT LEAST TO ME, BECAUSE IT WAS ALWAYS THOUGHT THAT LIGHT AND DARK STIMULI WERE THE MAJOR DRIVERS OF CIRCADIAN RHYTHM BUT WHAT THIS STUDY SHOWED WAS IN ABSENCE OF A GUT MICROBIOTA, THOSE LIGHT AND DARK SIGNALS ARE NOT GETTING THROUGH. THESE MICE WERE UNDER THE SAME LIGHT AND DARK CONDITIONS AS THEIR SPF COUNTERPARTS. SO THIS REALLY UNDERSCORED THE IMPORTANCE OF GUT MICROBES IN REGULATING OUR CIRCADIAN RHYTHMS IT WASN’T JUST NECESSARY BUT IT WAS ABSOLUTELY ESSENTIAL FOR NORMAL CIRCADIAN FUNCTION. SO WHAT HAPPENS ON THE MICROBICIDE? CIRCADIAN BIOLOGY IS ALL ABOUT TIME. SO WHAT HAPPENS TO THE MICROBIOME OVER THE COURSE OF 24 HOURS? AND THIS IS SHOWN HERE IN A A PLOT. ON A LOW FAT, FAIRLY DIVERSE DIET, THERE ARE CHANGES THROUGHOUT THE DAY. SO IS ZERO IS WHEN THE LIGHTS ARE TURNED ON AND 12 SELL WHEN THE LIGHTS ARE TURNED OFF. AND YOU CAN SEE THAT THERE IS A FLUCTUATION OF THESE POPULATIONS OVER THE COURSE OF THE DAY. THAT BEHAVIOR IS LOST WHEN THESE ANIMALS ARE PLACED ON HIGH-FAT DIET. NOT ONLY ARE THE OSCILLATIONS LOST, BUT THERE IS A SHIFT IN THE MEMBERSHIP OF THESE TWO POPULATIONS. SO, WHAT IS THE CONSEQUENCE OF THIS? THE CONSEQUENCE MIGHT BE THAT SOME OF THESE METABOLITES THAT MICROBES MAKE, PARTICULARLY THE ONES THAT WERE OSCILLATING THROUGH THE COURSE OF THE DAY, WHICH TEND TO BE MOSTLY FERMENTIVE ORGANISMS, MIGHT HAVE SOME EFFECTS ON OUR OWN BIOLOGY. SO JUST TO ASK THE QUESTION, WHAT IS HAPPENING TO SOME OF THESE METABOLITES? I SHOWED TWO OF THEM HERE, ONE IS BUTYRATE AND THE OTHER IS HYDROGEN SULFIDE. SO YOU CAN SEE THAT BUTYRATE HAS NICE OSCILLATIONS OVER 24 HOURS ON A LOW FAT DIETED BUT ON A LOW-FAT DIET, A MILK FAT-TYPE OF DIET, THE LEVELS AND OSCILLATIONS OF BUTYRATE ARE FAIRLY ATTENUATED. NOW IF YOU LOOK AT HYDROGEN SULFIDE, YOU SEE THE OPPOSITE. SO ON A LOW-FAT DIET, THE OSCILLATIONS ARE MODEST BUT THEY SEEM TO BE ACCENTUATED IN THE HIGH-FAT DIET AND THE AMPLITUDE SEEMS TO BE HIGHER. SO, WHAT IS THE IMPACT OF THESE METABOLITES? AGAIN WE ARE LOOKING AT ACETATE, BUTYRATE AND HYDROGEN SULFIDE WITH THE SURROGATE SODIUM HYDROGEN SULFIDE. AND ON THE LEFT SIDE OF THE PANEL WE ARE LOOKING AT PER 2 AND THE RIGHT SIDE WE ARE LOOKING AT BMAL1. IF YOU LOOK AT THE MIDDLE LINE HERE, YOU CAN SEE THAT BUTYRATE, GIVEN TO THESE HEPPAINOIDS, THESE ARE HEPATIC CELLS DERIVED FROM STEM CELLS THAT WE DERIVED, AND THEY GROW AS ORGANOIDS AND WHEN YOU EXPOSE THEM TO BUTYRATE, YOU CAN SEE THERE IS SAY VERY PROFOUND SHIFT IN THEIR PHASE. IT’S A PHASIC SHIFT, WHICH IS SEEN WITH BOTH PER 2 AND BMAL1. IT’S SPECIFIC BECAUSE YOU DON’TS SEE IT WITH PER 2 WITH ACETATE OR WITH HYDROGEN SULFIDE. WHEN SHE ADDS THE BUTYRATE HERE, THERE IS ALMOST 108 DEGREE PHASE SHIFT WHICH YOU CAN SEE QUANTITATIVE HERE. SO THIS IS VERY PROFOUND IN TERMS OF CLONAL BIOLOGY. TO SUMMARIZE THE FINDINGS UP TO THIS POINT, ON A LOW-FAT DIET WHAT WE SEE IS A NICE OSCILLATION OF MICROBIAL POPULATIONS AND METABOLITES THAT PROVIDE IMPORTANT CUES FOR NORMAL CIRCADIAN FUNCTION AND THAT LEADS TO STATES OF LEANNESS. IN HIGH-FAT DIETS, THESE MICROBIAL OSCILLATIONS ARE LOST LEADING TOW AB RANT MICROBIAL SIGNALS AND EFFECTING CENTRAL AS WELL AS PERIPHERAL CIRCADIAN FUNCTION TO LEAD TO STATES OF OBESITY. IN THE GERM-FREE MOUSE, WE LOSE THIS TRANSDUCER AND IN ESSENCE, NO MICROBIAL SIGNALS AND THAT CAUSES DISRUPTION BY IN THIS CASE, TO DEFAULT PATHWAY OF LEANNESS. SO, I END JUST WITH ONE SLIDE WHICH SUGGESTS THAT MAYBE WE CAN LEVERAGE THIS KNOWLEDG TO A THERAPEUTIC BENEFIT. SO THIS IS A STUDY WHERE WE DID ADMINISTRATION OF BUTYRATE BY AND INTERPERITONEAL APPROACH IN MICE THAT WERE ON A HIGH FAT DIET. WHAT CAN YOU SEE IS THAT WE HAVE CIRCADIAN DESTRUCTION WITH HIGH-FAT DIET BUT WHEN WE GIVE BUTYRATE AT A PARTICULAR TIME OF THE DAY, WE CAN CORRECT IT AND THAT IS ASSOCIATED WITH IMPROVEMENT IN THE ACCUMULATION OF FAT AND GONADAL FAT PADS. SO I’M GOING TO END WITH WHAT I THINK ARE THE CURRENT GAPS AND CHALLENGES AND ALSO OPPORTUNITIES. SO THE GAPS ARE IN AN ADEQUATE UNDERSTANDING OF MECHANISMS CONNECTING THE MICROBIOME, METABOLISM AND CANCER, THE CHALLENGE IS DEVELOPING BETTER TOOLS FOR IDENTIFYING MICROBIAL AND METABOLIC OSCILLATORS. AND THEN I ALSO THINK THAT ANOTHER GAP IS THAT HUMANS ARE VERY DIFFICULT TO STUDY PARTICULARLY WITH CIRCADIAN BIOLOGY. THIS IS I THINK GARY WILL YOU BROUGHT THIS UP YESTERDAY. THIS IS AN OBSTACLE WHEN YOU’RE TRYING TO DO TIME SEQUENCE COLLECTIONS ON A HIGH RESOLUTION SCALE. HOW DO YOU DO THAT? THE OPPORTUNITIES ARE DEVELOPING MICROBIOME-BASED PREDICTIVE MARKERS AND INTERVENTIONS FOR THE PREVENTION AND TREATMENT OF CANCER THROUGH THIS KIND OF CIRCADIAN LINK. AND THEN GOING BEYOND DESCRIPTION IN HUMAN STUDIES SO THAT WE CAN DEVELOP EFFECTIVE AND SUSTAINABLE THERAPEUTICS. AND I JUST WANT TO ACKNOWLEDGE ALL THESE PEOPLE. IT’S A TEAM. IT INVOLVES MULTIPLE INSTITUTIONS FROM MANY DISCIPLINES. BUT I PARTICULARLY WANTED TO POINT OUT VANESSA WHO HAS BEEN THE HEAVY LISTENER THESE STUDIES. THANK YOU VERY MUCH. [ APPLAUSE ]>>DR. XI: THANK YOU. VERY PROVOCATIVE. SO NOW WE OPEN FOR QUESTION. AND PLEASE IDENTIFY YOURSELF.>>AUDIENCE MEMBER: I HAD A COUPLE OF QUESTIONS. ONE FOR ERIC. SO, THIS IS VERY EXCITING, THE BLAUTIA STORY. THE QUESTION IS, HAVE YOU DONE EXPERIMENTS BEYOND — DOT IN-VIVO — A MAJOR FACTOR FOR MEDIATION OF RESISTANCE, THE PEPTIDE OR YOU DON’T KNOW YET?>>WE SUSPECT IT IS. WE KNOW THE TWO STRAINS, ONE IS HIGHLY EFFECTIVE AND THE OTHER WHICH LACKS THE ANTIBIOTIC IS NOT. IT’S INEFFECTIVE BUT AS YOU WELL KNOW, ONE OF THE BIG CHALLENGES RIGHT NOW IS TO PERFORM GENETICS OR GENETIC MANIPULATIONS OF THESE STRAINS AND SO WE ARE WORKING VERY HARD TO KNOCKOUT THE LOCUS IN THE SLOAN-KETTERING BLAUTIA AND THE WE ARE STARTING TO HAVE SUCCESS WITH THAT AND I THINK THAT WILL ANSWER THAT IMPORTANT QUESTION.>>AUDIENCE MEMBER: THE SECOND QUESTION IS FOR DR. LU. SO, THE ENGINEERING OF THESE STRAINS IS BEAUTIFUL. THE SENSORS, POTENTIALLY AND THE OTHER CONCERN I HAVE WITH THIS WITH THE KNOWN FACT THAT THERE IS RESISTANCE NOT JUST PATHOGENS BUT ALSO AGAINST ALSO THE COMMENSAL BACTERIA. WE SEE THAT IN THE EXPERIMENTS IN MICE AND ALSO IN HUMANS. SO, DID YOU RELY A A MAJOR POTENTIAL PROBLEM HERE, ENGINEER A BEAUTIFUL SENSOR BUT THEN DO THEY PROVIDE CONVERSATION FOR YEARS OR MONTHS? HOW DO YOU ADDRESS THAT BECAUSE THIS IS POTENTIAL BIG PROBLEM.>>DR. LU: SO IT’S A GREAT POINT. I THINK RIGHT NOW WE HAVE THE STUFF THAT WE ARE PUSHING THE CLINIC ARE STRAIN THAT IS ARE PURPOSELY MODIFIED SO THEY DON’T COLONIZE FOR FDA OR SAFETY REASONS. AND SO THESE WOULD BE THINGS YOU HAVE TO TAKE ON A BASIS WITH THE CURRENT DIVISIONS. I THINK WE ARE VERY EXCITED ABOUT THE POTENTIAL FOR MOVING INTO COMMENSAL ORGANISMS POTENTIALLY PERSIST FOR MUCH LONGER PERIOD OF TIME SUCH AS THE ONES PEOPLE ARE INVESTIGATING IN A LOT OF STUDIES. I THINK IT’S MORE OF A REGULATORY QUESTION OF WHAT IS THE PATH BEING ABLE TO USE THE ORGANISMS IN PEOPLE IF THEY ARE GENETICALLY MODIFIED.>>AUDIENCE MEMBER: MY QUESTION IS FOR EUGENE. WE’LL SPREAD THEM AROUND. I LOVE THE CIRCADIAN PART. HAVE YOU TRIED LOOKING AT SEASONAL EFFECTS OR THINGS LIKE THAT OR MAYBE IN HUMANS IT WOULD BE INTERESTING TO LOOK AT WEEKENDS VERSUS WEEKDAYS TO SEE WHAT KIND OF OTHER PATTERNS MIGHT APPEAR IN PEOPLE’S MICROBIAL FLUCTUATIONS?>>DR. CHANG: SO WE HAVEN’T DONE THOSE STUDIES, MIKE. BUT THEY HAVE BEEN DONE SPIRITALLY. PEOPLE HAVE DONE THINGS LIKE FREE-RUNNING, WHICH IS KEEPING THESE MICE IN CONDITIONS OF TOTAL DARKNESS OR TOTAL LIGHT OR THEY WILL DO TIME SHIFT-TYPE OF EXPERIMENTS. AND I THINK THAT THEY UNDERSCORE THE IMPORTANCE OF NORMAL CIRCADIAN RHYTHM AND HOW DISRUPTIONS OF IT CAN BE VERY DELL TEARUOUS TO THINGS LIKE CANCER GROWTH AND DEVELOPMENT AS WELL AS METABOLISM.>>AUDIENCE MEMBER: SO ROB, COLLEGE OF MEDICINE. THIS QUESTION IS FOR DR. LU. SO WHEN WE DO PROBIOTICS IN MICE, I WOULD ARGUE THAT WE ELIMINATE SOME OF THE BIOGEOGRAPHY BECAUSE WE SLAM THEM WITH SUCH A HIGH DOSE OF BACTERIA AND ESSENTIALLY THE SAME DOSE WE GIVE TO HUMANS AND OF COURSE THERE IS SUCH A HUGE AREA DIFFERENCE. SO DO YOU HAVE ANY SENSE OF WHAT KIND OF DOSE YOU’RE GOING TO NEED TO GIVE PEOPLE TO BE EFFECTIVE AND MAKE SURE YOU ACTUALLY ENCOUNTER THE METABOLITES?>>DR. LU: THAT IS PARTLY WHAT THE DOSE FINDING WE NEED TO DO AND THE CURRENT TRIAL. I THINK IT IS IN PART BASICALLY THE MORE POTENT WE CAN MAKE THESE STRAINS SO WE REDUCE THE PRIMER FOR NUMBERS. WE ARE AT A A LITTLE BIT OF INHERENT DISADVANTAGE THAT THE E.COLI MISSILE DOESN’T COLONIZE AT HIGH LEVELS SO IT DOESN’T STAY AROUND AT HIGH LEVELS AND THAT POSES A CHALLENGE. I THINK THE DOSES THAT WE PUT INTO NON-HUMAN PRIMATES HAVE BEEN UP TO 10 OR 11 AND HAVE BEEN ABLE TO LOOK AT STUDIES AND SEE AN EFFECTED IN THAT SYSTEM BUT WE HAVE TO SEE IF THAT REPLICATES IN PEOPLE.>>AUDIENCE MEMBER: [ INAUDIBLE ] DID YOU GET A CHANCE TO HAVE A GLIMPSE OF THE LINK BETWEEN THE IMMUNE SYSTEM AND THE GUT MICROBIOTA DRIVEN BY THIS CIRCADIAN RHYTHM?>>THE LINK BETWEEN THE IMMUNE SYSTEM AND THE GUT MICROBIOTA DRIVEN BY THE CIRCADIAN RHYTHM.>>DR. CHANG: SO ACTUALLY THAT IS A GREAT QUESTION. SO, WORK THAT LAURA HOOPER HAS DONE AND ALSO VANESSALY OWN. MANY SYSTEMS, INNATE IMMUNITY IN PARTICULAR IS VERY CIRCADIAN UNDER STRONG CIRCADIAN REGULATION. AND BOTH LAURA AND VANESSA HAVE DATA THAT SUGGESTS THAT THAT IS ALSO IMPORTANT IN MAINTAINING THIS VARIATION IN THE MICROBIOME SO THAT WHEN THINGS BEGIN TO BLOOM, YOU NEED TO SORT OF BRING THEM BACK DOWN. AND SO, THERE IS THIS SORT OF SEE SAW REGULATION WHERE THE BLOOM OF CERTAIN ORGANISMS INDUCE INNATE IMMUNITY AND THAT BRINGS THE POPULATION DOWN. SO I DO BELIEVE THAT IMMUNITY IS IMPORTANT IN THIS KIND OF COORDINATION BETWEEN HOST AND MICROBE.>>AUDIENCE MEMBER: NANCY, MEDICAL SUBJECT HEADINGS OF THE NATIONAL LIBRARY OF MEDICINE. THERE HAS BEEN A GREAT CONFERENCE AND I FIND IT IN VERY SUPPORTING OF THE COMMUNITY IN THE CHALLENGE QUESTION AND THE GAPS QUESTIONS. WE HAVE BEEN PUTTING IN MICROBIOME ORGANISMS INTO THE MEDICAL VOCABULARY RECENTLY AND I WOULD LIKE TO ENCOURAGE PEOPLE TO, IF YOU HAVE ANY CONCEPTS THAT YOU THINK ARE IMPORTANT TO BE SEARCHABLE, IN THE LITERATURE , TO PLEASE LET US KNOW THAT AT MEDICAL — IF YOU GO TO THE NATIONAL LIBRARY SITE YOU WILL BE ABLE TO GET TO THE MEDICAL SUBJECT HEADING SITE AND THERE IS A LINK WHERE YOU CAN MAKE REQUESTS FOR CONCEPTS TO BE SEARCHABLE. AND ALSO I JUST, THE WAY THAT THIS HAS BEEN SUCH A SUPPORTIVE COMMUNITY, I JUST WANTED TO SAY THAT WE ARE A COMMUNITY OF SCIENTISTS GOING THROUGH LIFE TOGETHER AND WE ARE SUPPORTING EACH OTHER AND WE HOLD EACH OTHER VERY DEARLY AND WE ALSO MUST HOLD THE REST OF HUMANKIND DEARLY. SO I JUST WANTED TO APPLAUD DR. OWEN WHITE YESTERDAY OR WEDNESDAY, FOR ANNOUNCEING THE REMOVAL OF THE CONFEDERATE STATUES, THESE ARE STATUES OF HEROES OF PEOPLE WHO BELIEVE THAT IT’S OKAY TO ABUSE OTHERS AND TAKE AWAY THE RIGHTS OF OTHERS. AND SO I THINK WE NEED TO SUPPORT WHEN PEOPLE STAND UP TO SAY WHAT IS NOT RIGHT JUST LIKE WE SUPPORT EACH OTHER IN OUR CAREERS AND OUR LIVES. [ APPLAUSE ]>>DR. XI: I THINK WE ARE AT THE END OF THE SESSIONS. LET’S GIVE A BIG APPLAUSE FOR ALL THE SPEAKERS. [ APPLAUSE ] NOW WE GO TO LUNCH AND A POSTER SESSION.>>>WELCOME. WE ARE WRAPPING UP THIS WORKSHOP WITH AN EXPERIMENT WHICH IS TO — WE ARE ALL SCIENTISTS HERE. TO GET AGENCIES TOGETHER — SO LET ME TELL YOU WHO THESE PEOPLE ARE. ALL OF US SERVED ON THE MICROBIOME INTERAGENCIES WORKING GROUP, THE FEDERAL COMMITTEE UNDER THE OFTP’S NATIONAL MICROBIOME INITIATIVES. THERE ARE 16 AGENCIES BUT I ASKED THOSE REPRESENTATIVES TO COME JOIN THIS JOINT AGENCY YAM I ASK SOME PARTICULAR OFFICES AT NIH TO JOIN THIS PANEL AS WELL BECAUSE THEY DON’T NECESSARILY ALWAYS GET A VOICE IN THESE DISCUSSIONS. ONE OFFICE IS THE OFFICE OF AGE RESEARCH. RAISE YOUR HAND. SO YOU KNOW WHO THE NIH PEOPLE ARE. AM I NOT TALKING LOUD ENOUGH? I ALWAYS THINK I’M REALLY LOUD. THE OFFICE OF RESEARCH ON WOMEN’S HEALTH, AND THE NATIONAL INSTITUTE FOR MINORITY HEALTH DISPARITIES. SO THOSE ARE THE THREE NIH OFFICES BUT THE REST ARE OTHER FEDERAL AGENCIES. AND REMEMBER THE THEME OF THIS WORKSHOP IS NOT ONLY TO ASSESS WHERE WE STAND IN THE HUMAN MICROBIOME RESEARCH FIELD BUT TO ALSO REALLY MORE IMPORTANTLY IDENTIFY OBSTACLES, CRITICAL GAPS, NEEDS AND CHALLENGES, THAT WE NEED TO ADDRESS IN ORDER TO ADVANCE THIS FIELD OVER THE NEXT 10 YEARS. YOU HEARD OVER THREE DAYS LOTS AND LOTS OF IDEAS. SO I THOUGHT IT WOULD BE VALUABLE TO ALSO HEAR FROM THE AGENCIES THAT ARE EITHER CURRENTLY MOUNTING HUMAN MICROBIOME RESEARCH ACTIVITIES AND FUNDING THESE ACTIVITIES OR UNDERTAKING INTERNAL STUDIES ON THE HUMAN MICROBIOME. THEY HAVE A SERIES OF SLIDES. THEY ARE GOING TO BE VERY QUICK SLIDES SO YOU’RE NOT GOING TO HEAR A BIG LONG DISCUSSION ABOUT THE AGENCY AND CLIFF IS SMILING BECAUSE I WAS REALLY HARD NOSED ABOUT JUST A COUPLE OF SLIDES. ZERO IN ON YOUR MAIN THEME. BECAUSE IT’S JUST TO GIVE YOU A QUICK SNAPSHOT OF WHAT THE AGENCY’S INTEREST IS IN THAT AREA. AND THEN, WE ARE GOING TO HAVE A DISCUSSION BETWEEN US ABOUT WHAT EACH PERSON MIGHT HAVE CALLED OUT AS AN OBSTACLE. BUT, THE REASON I ASKED THEM TO SIT IN ALPHABET CALL ORDER AND ASK THE AUDIENCE TO MOVE FORWARD IS, I DIDN’T WANT THIS STAGE, THIS PANEL, TABLE, TO ACT AS AN OBSTACLE TO DIALOGUE BETWEEN THE PANELISTS AND THE AUDIENCE. SO, I’M HOPING TO ALSO INVITE CONVERSATION AND DEBATE AND DIALOGUE FROM THE AUDIENCE WITH THE PANELISTS. YOU HAVE BEEN TALKING ABOUT THE OBSTACLES FOR THREE DAYS. THEY’LL MENTION SOME. LET’S SEE IF WE ACTUALLY COME TO SOME CONSENSUS AROUND THE PRIORITY OBSTACLES OR MAYBE JUST IT ENDS UP BEING A HUGE LAUNDRY LIST. WE DON’T KNOW YET. I’M ALSO GOING TO CLOSE, FOREWARN YOU THAT I MENTIONED
TO& EVERYBODY ELSE, I’M GOING TO CLOSE WITH AT LEAST ONE QUESTION I HAVE BEEN ASKED TO ASK, AND THAT IS, IF AN AGENCY OR AGENCIES WERE TO MOUNT A VERY LARGE RESEARCH COHORT STUDY, DIDN’T HAVE ENOUGH MONEY TO SAMPLE THE ENTIRE MICROBIOME, WHAT WOULD BE THE MICROBIOME SAMPLE THAT SHOULD BE BIOBANKED FOR FUTURE ANALYSIS? I’VE GOT A LOT OF DIFFERENT ANSWERS FROM PEOPLE I ASKED AROUND THE AUDIENCE AND I WANT TO GET AN ANSWER FROM THIS GROUP. SO, LET’S THEN GET STARTED. IT’S ALPHABET CALL ORDER AND I HAVE BEEN ASKED BY LOIS FROM THE NATIONAL INSTITUTE FOR NURSING RESEARCH AND SHE IS TAKING NOTES FOR THE WHOLE PANEL. SO SHE IS ASKING YOU WHEN YOU START TO TALK ABOUT YOUR AGENCY, JUST REMIND THEM WHICH AGENCY OR OFFICE YOU’RE FROM WHEN YOU’RE TALKING JUST SAY THE VA THINKS THIS OR FDA THINKS THIS. THAT WOULD HELP LOIS KEEP TRACK. GO AHEAD. WALTER, IT’S NOT HAPPENING.>>GOOD AFTERNOON. I’MRA JEFE FROM OFFICE OF RESEARCH ON WOMEN’S HEALTH AND TODAY I’M GOING TO SHOW YOU WHY SEX IS IMPORTANT FOR EXPANDING KNOWLEDGE AND IMPROVING HEALTH OF MEN AND WOMEN. SO THE OFFICE WAS ESTABLISHED IN 1990 BY THE CONGRESS AND IN 1991, THE THE OFFICE HAS WOMEN’S HEALTH INITIATIVE AND IN 93, NIH MANDATED TO INCLUDE WOMEN AND MINORITY GROUP IN CLINICAL RESEARCH. TODAY, OUR OFFICE OF RESEARCH AND WOMEN’S HEALTH IS THE FOCAL POINT FOR RESEARCH ON SEX AND GENDER INFLUENCES WHICH BENEFIT EVERY HUMAN BEING INCLUDING GIRLS, WOMEN, BOYS, MEN. SO THE MISSION OF THE OFFICE IS TO EXAMINE SEX AND GENDER INFLUENCES ON HEALTH AND DISEASES STRENGTHEN RESEARCH RELATED TO DISEASES, DISORDERS AND CONDITIONS THAT EFFECT WOMEN. I’M NOT GOING THROUGH THE THIRD ONE WHICH IS PROMOTING WOMEN IN BIOMEDICAL. SO WHAT IS THE RATIONAL FOR THE NEW POLICY? OVER THE YEARS THERE WAS OVER RELIANCE ON MALE ANIMALS AND CELLS, ANNOTATION SEX EFFECTS, LACK OF TRANSFERENCEY AND INCONSISTENT FINDINGS IN PUBLICATION WHICH LED TO INCOMPLETE KNOWLEDGE BASE, RISK OF ERRONEOUS CONCLUSIONS AND IR REPRODUCIBLE RESULTS, TOXICITY SURPRISES AND EROSION OF PUBLIC TRUST AND NOT A GOOD RETURN ON INVESTMENT. TO GIVE YOU AN EXAMPLE, THIS IS AGGREGATE DATA AND IT LOOKS LIKE THERE IS NO TREATMENT EFFECT COMPARED TO THE CONTROL GROUP. IF YOU DISSEGREGATE THE DATA [ INAUDIBLE ] WHEN TREATED WITH MALE ANIMALS, BY ONSET, THIS INFECTION IN MALE MICE COMPARED TO THE ANIMALS WHEREAS IN THE FEMALE THIS HAS A SIGNIFICANT INCREASING CHANGE COMPARED TO THE CONTROLS. SO, [ INAUDIBLE ] BECAUSE OF THIS REASON, 8-10 DRAWN BY FDA DURING 1997 AND 2010 HAD MORE ADVERSE EFFECTS FOR WOMEN THAN MEN. SO WE ALL AGREE THAT SCIENCE IS NOT SCIENCE IF IT IS REPRODUCIBLE. SO BECAUSE OF THIS REASON, NIH CLARIFIED THIS POLICY AND EXPECTS THAT SEX IS A BIOLOGICAL VARIABLE TO RESEARCH DESIGN ANALYSIS AND REPORTING IN ANIMALS AND HUMAN STUDIES. THIS IS JUST TO SHOW YOU THAT SEX DIFFERENCES IN IMMUNITY RESULTS IN DISEASE BY US AND ON THE LEFT-HAND SIDE THE DISEASES ARE MORE PRONE TO FEMALES WHEREAS ON THE RIGHT-HAND SIDE ON THE MALE SIDE. SINCE THIS IS A MICROBIOME MEETING IT WILL NOT BE GOOD IF I DON’T TALK ABOUT SABB IN MICROBIOME. THIS IS A RECENT PUBLICATION WHERE THE AUTHORS SHOWN THAT POST RESPONSES TO PATHOGEN BACTERIA AND BENEFICIAL MICROBES, EXHIBIT HOST SPECIFICITY. THEY USE MICROBACTERIA AS PATHOGENIC BACTERIA AND TREATED MICE, MALES AND FEMALES, AND THEY ANALYZED THE IMMUNE PROFILE. AND YOU CAN SEE VERY DIFFERENT IMMUNE PROFILE IN MALES AND FEMALES. SO THIS IS A METAGENOMIC ANALYSIS WHICH SHOWS DIFFERENCES IN COLON BETWEEN MALES AND FEMALES. BECAUSE OF THE TIME, I’M NOT GOING INTO THE DETAILS BUT YOU CAN SEE IT’S A VERY DIFFERENT MICROBIOME ANALYSIS OF MALES AND FEMALES. AND THANK YOU VERY MUCH. [ APPLAUSE ]>>I’LL STARTED BEFORE MY SLIDES ARE UP THERE. SO, I’M COMING AT THIS FROM A SLIGHTLY DIFFERENT STANDPOINT. SO WE ARE A REGULATORY AGENCY FROM THE FDA. BUT WE ALSO HAVE A SIGNIFICANT RESEARCH PROGRAM AT THE FDA. SO, WHAT I WANT TO GO THROUGH RIGHT NOW IS THE RESEARCH THAT IS BEING DONE IN TERMS OF MICROBIOME AT FDA THROUGHOUT OUR VARIOUS CENTERS AND I’M AT THE CENTER BIOLOGICS WHICH I’LL TALK ABOUT LATER. SO I BROKE THIS UP INTO TWO OFFICES, FOODS AND VETERINARY MEDICINE AND THEN AFTER THAT, WE’LL TALK ABOUT MEDICAL PRODUCTS AND TOBACCO. BUT I ALSO WANT TO POINT OUT THIS LOGO THAT WILL POP UP ALL OVER THE PLACE, THIS IS THE NATIONAL CENTER FOR TOX LONG CALL RESEARCH. THIS IS THE CENTER AT FD. THAT IS RESEARCH ONLY. THEY DON’T HAVE TO DO THE REGULATORY WORK THE REST OF US DO. THEY ARE THERE TO SUPPORT RESEARCH AND REGULATORY-BASED QUESTIONS AND WE ALL, EVERY CENTER, THEY WILL POP UP EVERYWHERE. SO TO GO THROUGH THE FOODS AND VETERINARY MEDICINE SIDE. THE CENTER IS FOCUSING ON PROJECTS LOOKING AT ANTIMICROBIAL PRESSURE ON MICROBIOME IN FARM ANIMALS AND IN ECOSYSTEMS. AND RESISTANCE GENES AND THE POTENTIAL OF THE MICROBIOME TO SERVE AS A RESERVOIR FOR ANTIBIOTIC RESISTANCE GENES IN WHAT IS FARM TO FORK CONTINUUM. AND THEN THE CENTER FOR FOOD SAFETY AND NUTRITION, I HAVE LISTED DOWN HERE, THEY ARE REALLY DOING A LOT OF RESEARCH INTO THE MICROBIOME AND I LISTED A FEW THINGS HERE AND I’M GENERALIZING. THERE ARE A LOT OF PROJECTS INVOLVED BUT THE ROLE OF DIET AND NUTRITION IN THE MICROBIOME, SPECIFICALLY ALSO LOOKING AT THE MICROBIOME OF FOODS, WHAT ORGANISMS ARE PRESENT IN THE FOODS. THESE ARE THINGS WE ARE GOING TO BE INVESTING, GOES ALONG WITH DIET. AND THEN PATHOGEN DETECTION IN FOODS IN THE CONTEXT OF THAT MICROBIOME. THE OFFICE OF MEDICAL PRODUCTS AND TOBACCO, I’M GOING TO TALK ABOUT THREE DIFFERENT CENTERS. THE FIRST IS THE CENTER FOR DRUG EVALUATION AND RESEARCH. AND THE PROJECTS THAT I HAVE LISTED UP HERE ARE LOOKING AT THE EFFECTS OF DRUGS, IN THIS CASE, ANTIMICROBIALS OR TNF AGONISTS ON THE MICROBIOME. AND SO, WE HAVE A FEW RESEARCH PROJECTS GOING ON IN THE CENTER FOR DRUGS AND ALSO IN COLLABORATION WITH NCTR AS I SAID BEFORE. THE CENTER FOR TOBACCO PRODUCTS HAS RESEARCH ONGOING LOOKING AT SMOKELESS TOBACCO AND THE ORAL MICROBIOME. THERE ARE A FEW PROJECTS BASED ON THESE AND A PUBLICATION IS LISTED HERE FROM SOME IN-VITRO WORK THAT WAS DONE AND AGAIN, IN COLLABORATION WITH NCTR. FINALLY, THE CENTER FOR BIOLOGICS IS A CENTER THAT I’M IN AND SOME OF THIS IS MY DATA BUT IF YOU THINK ABOUT IT IN TERMS OF PRODUCTS, WE ARE FOCUSED ON FECAL TRANSPLANTS, LIVE BIOTHERAPEUTIC PRODUCTS WHICH SOME CALL PROBIOTICS AND PHAGE THERAPY. THESE ARE THE THINGS THAT WE ARE REGULATING IN TERMS OF MICROBIOME-BASED PROJECTS. WE HAVE PROJECTS LOOKING AT FMT. THIS IS DATA ON C.DIFF AND PROJECTS ON LBPs LOOKING FOR MECHANISMS OR WAYS TO MEASURE PUREITY AND POTENCY IN THESE PRODUCTS THAT ARE FULL OF BACTERIA INTENTIONALLY. HOPEFULLY YOU SAW SOME OF THE POSTERS THAT WE HAD OUT TODAY AND AGAIN, THESE ARE ALSO IN COLLABORATION WITH NCTR. AND THE LAST THING I WANTED TO MENTION IS HIVE IS BASED IN CBER IT’S OUR BIO INFORMATICS CORE AND THEY HAVE DONE A REALLY GOOD JOB OF STARTING TO INCORPORATE THE COMMONLY-USED MICROBIOMES ANALYSIS TOOLS INTO THEIR SYSTEM ON THE RESEARCH SIDE AND SEPARATES IS FOR ANALYZING REGULATORY DATA. THEY ARE MICROBIOME SPECIFIC. AND I WANTED TO ACKNOWLEDGE THE PEOPLE WHO CONTRIBUTED DATA SLIDES AND OTHER INFORMATION FOR THIS. AND I’D SAY JUST TO GO BACK, I DON’T HAVE THE GAPS POTENTIAL GAPS LISTED UP HERE BUT NOT SO MUCH FROM THE RESEARCH SIDE MAYBE THINKING ABOUT THIS IN TERMS OF THE REGULATORY SIDE, I THINK SOME OF THE GAPS WOULD BE MOVING BEYOND ASSOCIATION AND STARTING TO GET INTO MECHANISM. I THINK A LOT OF PEOPLE SAID THAT TODAY. BUT ALSO ASSAY VALIDATION. WE GOT A LOT OF STEPS IN THE PROCESS OF LOOKING AT A MICROBIOME AND TO REALLY MAKE SURE THOSE ARE BEING CONSISTENT ACROSS-THE-BOARD IN ORDER TO HAVE REGULATORY QUALITY DATA.>>MINE IS GOING TO BE REALLY SHORT AND I DON’T HAVE ANY DATA TO SHOW BUT I’M IN THE OFFICE OF AIDS RESEARCH AND THIS IS AN OFFICE THAT IS IN THE OFFICE OF THE DIRECTOR FOR NIH. WE ARE RESPONSIBLE FOR THE SCIENTIFIC BUDGETARY LEGISLATIVE AND POLICY ELEMENTS OF THE — SURE. SO WE ARE RESPONSIBLE FOR THE SCIENTIFIC BUDGETARY LEGISLATIVE AND POLICY ELEMENTS FOR THE NIH AIDS RESEARCH PORTFOLIO HERE AT NIH. WE’VE HAD A LONG-STABBING INTEREST IN THE MICROBIOME, PROBABLY CLOSE WHEN THE HMP WAS BEING DEVELOPED, SO AROUND 2007. NCI HAD A WORKSHOP, WHICH FOCUSED ON HIV CANCER AND MICROBIOME. AND THEN IN 2009, WE ADDED MICROBIOME AS A SPECIFIC AREA WITHIN OUR TRANS-NIH STRATEGIC PLAN FOR HIV RESEARCH. AND WE HOPE THAT THIS WOULD ENCOURAGE NOT ONLY THE INSTITUTES TO FUND MORE RESEARCH IN THIS AREA BUT ALSO AS A CALL TO INVESTIGATORS IN THE HIV FIELD TO SUBMIT APPLICATIONS IN THIS AREA. AND WE REALLY DIDN’T SEE SORT OF OUR INVESTMENT IN THE AREA INCREASE UNTIL PROBABLY ABOUT 2012. THAT’S WHEN WE CAN SEE SOME APPRECIABLE RESEARCH SUPPORT BEING SPECIFIC FOR THE MICROBIOME. AND AS YOU CAN SEE, WITHIN A 5-YEAR PERIOD, THE INVESTMENT HAS JUST ABOUT TRIPLED AND I SUSPECT THAT IN 2017, IT PROBABLY WILL BE SUBSTANTIALLY MORE. SO, IN THE OFFICE OF AIDS RESEARCH, AS I MENTION THE, WE HAVE THESE SPECIFIC AREAS OR PRIORITY AREAS THAT FOCUS ON THE SCIENTIFIC PRIORITIES FOR HIV/AIDS RESEARCH. AND WITHIN THOSE PRIORITY AREAS, ONE BEING REDUCING INCIDENTS, THERAPEUTICS, CO-MORBIDITIES AND COFINNECTIONS AND BASIC RESEARCH AS WELL AS RESEARCH FOR THE CURE, YOU CAN SEE HOW THE INVESTMENT HAS BEEN BROKEN OUT. YOU CAN LOOK AT 2017 — OR 2016. MOST OF THE RESEARCH IS BEING DONE LOOKING AT BASIC ASPECTS OF THE MICROBIOME AND HIV AS WELL AS AREAS TO REDUCE INCIDENTS OF HIV IN AT RISK POPULATIONS. SOME OF THE RESEARCH, ESPECIALLY IN REDUCING INCIDENTS, I THINK WAS PRESENTED HERE, AND THERE WERE QUITE A FEW POSTERS LOOKING AT THE VAGINAL MICROBIOME AND HOW IT IMPACTS HIV ACQUISITION AS WELL AS TREATMENT. AND THESE ARE SOME OF OUR HIGH PRIORITY AREAS FOR HIV MICROBIOME RESEARCH HERE AT NIH. SITTING HERE THROUGH THE THREE DAYS OF THE WORKSHOP, I CAN PROBABLY ADD ABOUT 10 OR 20 MORE THINGS HERE, BUT THESE ARE THINGS THAT WE HAVE BEEN WORKING ON AS WELL AS THOSE THAT WE WOULD LIKE TO FURTHER INVEST IN. IT’S A LONG LIST. I DON’T KNOW IF I SHOULD READ IT. THE IMPACT OF THE MICROBIOME ON HIV RISK, ACQUISITION DISEASE PROGRESSION. THE ROLE OF THE MICROBIOME IN HIV TREATMENT EFFECTIVENESS, INCLUDING PREVENTION AND INTERVENTIONS SUCH AS PREP. PRE-EXPOSURE PROPHYLAXIS. THE MICROBIOME AS A BIOMARKER FOR ASSESSMENT OF HIV DISEASE AND OVERALL HEALTH OF AN INDIVIDUAL. AND THERE WERE QUITE A FEW STUDIES THAT WERE PRESENTED HERE. I THINK THAT WILL GIVE US SOME CLUESES TO HOW TO DO THAT. HOW TO INFLUENCE AND PERTURB THE MICROBIOME TO IMPROVE HIV TREATMENT, AND PLEA VENTION AND PATHOGENESIS. AND SOMETHING I DIDN’T HEAR MUCH ABOUT WAS GEOGRAPHIC DIVERSITY AND HOW IT INFLUENCES THE ESTABLISHMENT AND COMPOSITION OF THE MICROBIOME AND FOR HIV SPECIFICALLY, HOW THAT IMPACTS HIV TRANSMISSION ESTABLISHMENT OF INFECTION AND OUTCOMES OF DISEASE. AND LAST BUT NOT LEAST, THE IMPACT OF THE MATERNAL MICROBIOME AND DYSBIOSIS ON THE HEALTH OF THE HIV-INFECTED AND EXPOSED UNINFECTED INFANTS AND CHILDREN. WHILE THIS ISN’T AN EXHAUSTIVE LIST, I THINK THESE ARE AREAS WHERE WE WOULD LIKE TO SEE A LOT MORE RESEARCH ON THE MICROBIOME FIELD AND HIV RESEARCH. AND I THINK THAT IS IT.>>HI, I’M LANED CHRISY FROM THE OFFICE OF NAVAL RESEARCH HERE REPRESENTING THE DEPARTMENT OF DEFENSE SPECIFICALLY OUR RECENT NEWLY-ESTABLISHED TRISERVICE MICROBIOME CONSORTIUM. CONSORTIUM IS COMPOSED OF BOTH RESEARCH SPONSORS WITHIN DOD OF MICROBIOME RESEARCH AS WELL AS PERFORMERS OF THE VARIOUS DOD LABS IN THIS SPACE. SO KEY PURPOSES OF OUR ORGANIZATION ARE TO ENHANCE COLLABORATION, COOPERATION, COMMUNICATION OF MICROBIOME RESEARCH AMONG DOD ORGANIZATIONS, SERVE AS A FORUM FOR SHARING OF MICROBIOME-RELATED RESOURCES, ET CETERA. MONITOR GLOBAL ADVANCES IN THIS AREA AND PROVIDE THAT INFORMATION TO OUR LEADERSHIP, AND THEN TO ENGAGE OUR OPERATIONAL END USERS TO IDENTIFY SPECIFIC AREAS OF RESEARCH THAT MIGHT BENEFIT THEM. SO, IN MANY WAYS THERE IS PARALLELS TO THE ORGANIZATION THAT NIH HAS ESTABLISHED ALTHOUGH I’D SAY WE ARE MORE COMPACT. SO, UNLIKE THE NIH, DOD’S INTEREST IN MICROBIOME ARE COMPLEMENTARY TO THE NIH BUT DEFINITELY DISTINCT AND PROBABLY DISTINCT FOR MANY OF THE OTHER AGENCIES ON THE PANEL. WE ARE NOT REALLY FOCUSED ON DISEASE. WE ARE FOCUSED ON ENHANCING READINESS AND RESILIENCE OF OUR WAR FIGHTERS. SO, WE DO ACROSS THE DOD, HAVE INVESTMENT OR RESEARCH GOING ON IN MANY DIFFERENT MICROBIOME AREAS INCLUDING THE ONES I LISTED HERE. SO FOR THE GUT MICROBIOME AND GUT BRAIN AXIS, THE KINDS OF THINGS WE THINK ABOUT ARE THE KINDS OF STRESSORS OUR PEOPLE ARE EXPOSED TO. SOME OF THE ENVIRONMENTS THEY WORK IN ARE REALLY RATHER UNIQUE AND WE NEED A BETTER UNDERSTANDING OF HOW THESE STRESSORS EFFECTED THE ABILITY OF THOSE PEOPLE TO FUNCTION EFFECTIVELY FOR LONG PERIOD OF TIME. SO FOR EXAMPLE, SINCE I WORK FOR THE NAVY I’LL SHARE THE SUBMARINER CASE. WE HAVE PEOPLE IN A VERY ARTIFICIAL ENVIRONMENT WITH NO SUNLIGHT WITH SLIGHTLY ELEVATED CO2. THEY ARE SHARING BUNKS. HAVE AN ALTERED CIRCADIAN RHYTHM CYCLE. YOU DO HAVE MEN AND WOMEN ON THE SUBMARINES WHICH IS ANOTHER FACTOR THAT WE MIGHT NEED TO CONSIDER. THEY EAT THE SAME FOOD. THEY RUN OUT OF FRESH FOOD VERY QUICKLY AND SO, WE ARE ASKING HOW DOES THE MICROBIOME CHANGE AND ARE THERE SIGNATURES THERE THAT COULD HELP US UNDERSTAND PERHAPS SOME, HOW TO MAKE THESE PEOPLE MORE RESILIENT TO LIVING IN THAT KIND OF VERY ARTIFICIAL ENVIRONMENT. IT’S NOT UNLIKE NASA AND WHAT THEY GO THROUGH, ALTHOUGH WE DON’T HAVE A REPRESENTATIVE HERE TODAY. SO, ALSO WITH THE GUT MICROBIOME, WE HAVE INTEREST IN THE ARMY AND THE AIR FORCE AND UNDERSTANDING BIOTRANSFORMATION OF TOXIC INDUSTRIAL CHEMICALS THAT PEOPLE MIGHT BE EXPOSED TO. ON THE SKIN, WE THINK ABOUT SKIN INFECTIONS. SO SOME OF THE BOOTCAMP TRAINING THAT PERSONNEL ARE EXPOSED TO CRAWLING AROUND IN THE DIRT A LOT AND OFTEN DEVELOP SKIN INFECTIONS. ARE THERE WAYS TO PREDICT THAT OR PREVENT THAT? WE ARE UNDERSTANDING MICROBIOME CAN INFORM THOSE PROCESSES. WOUNDER HEELING IS ANOTHER ONE. AND THEN IN THE LUNG ALSO UNDERSTANDING EXPOSURE TO TOXIC INDUSTRIAL CHEMICALS IN WAYS THE LUNG MICROBIOME MIGHT BE ABLE TO UNDERSTAND THAT BETTER AND INSULATE OUR PEOPLE FROM THOSE EFFECTS. THAT’S IT.>>GOOD AFTERNOON. I’M HERE TO REPRESENT DEPARTMENT OF VETERAN’S AFFAIRS OFFICE OF RESEARCH AND DEVELOPMENT. OUR MAIN GOAL IS TO DO RESEARCH IN THE AREA WHICH ARE OF INTEREST TO VETERANS. WE HAVE A LARGE NUMBER OF VETERAN POPULATION IN OUR HOSPITALS. SO WE ARE MORE VETERAN-CENTRIC. I HAVE PROVIDED SOME OF THE DETAILS IN SLIDES TO WHICH I THINK WE ARE NOT SHOWING HERE BUT IN THE DECK I’M FOCUSING HERE ONLY THOSE AREAS WHICH ARE MORE FOCUSED IN THE MICROBIOME SPECIFICALLY THE ORD SUPPORTS MICROBIOME RESEARCH RELATED TO IMPROVING THE HEALTH AND CARE OF OUR NATION’S VETERANS. IT SUPPORTS MICROBIOME RESEARCH AND SPANS SPECTRUM OF DISEASES AND MEDICAL CONDITIONS, INCLUDING INVESTIGATING THE ROLE OF MICROBIOMES IN DISEASE AND CIRRHOSIS. CHARACTERIZING COMPONENTS OF THE NASAL MICROBE BIOME THAT COULD PREVENT TRANSMISSION OF MAX LINN RESISTANT — MORESSA IN VA HOSPITALS AND DETERMINING THE ROLE OF THE MICROBIOME IN PREVENTING OR REDUCING INFECTION AT THE IMPLANT SITES OF VETERANS RECEIVING PROSTHETIC LOWER-LIMB IMPLANTS. THE MAJORITY OF THE SUPPORTED RESEARCH IS INVESTIGATOR INITIATED AND BASED AT VA MEDICAL CENTERS ACROSS THE COUNTRY. THE BREATH AND SCOPE OF MICROBIOME RESEARCH HAS INCREASED STEADILY OVER THE LAST DECADE AS MORE ADVANCED TOOLS IN NEXT GENERATION SEQUENCING AND BIOME INFORMATICS HAVE BECOME MORE WIDELY AVAILABLE TO THE VA RESEARCHERS AND ACADEMIC AFFILIATES. THE MAGNITUDE OF MICROBIOME RESEARCH WITHIN THE VA IS ANTICIPATED TO CONTINUE TO INCREASE IN THE COMING YEARS AS MORE VA INVESTIGATORS GAIN EXPERTISE IN MOLECULAR AND GENOMIC SIGNS, METRICS AND BIO INFORMATICS DATA AND ANALYSIS TECHNIQUES THROUGH THEIR ONGOING TRAINING AND RESEARCH ACTIVITIES. CORRECTLY WE ARE TRYING TO EXPLORE WHETHER CHANGES IN MICROBIOMES PLAY IN THE HIGH PRIORITY AREA OF SUCH AS PTSD, TBI, ADDICTION AND SUICIDALITY OR RESPONSES TO THERAPY, ESPECIALLY IN GUT FOR VETERANS RELATED AREAS SUCH AS ONE OF THE DISEASES LIKE IRRITABLE BOWEL-SYNDROME. THANK YOU. [ APPLAUSE ]>>HI, EVERYONE. I’M SCOTT JACKSON FROMANIST. ANIST IS THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY. I’M GOING TO TALK TO YOU ABOUT WORK THAT WE ARE STARTING OVER THE LAST FEW YEARS RELATED TO MICROBIOME. SO, JUST AN EXAMPLE OF HOWANIST PLAYED A ROLE IN THIS FIELD PREVIOUSLY. A COUPLE OF YEARS AGO WE RELEASED A HUMAN GENOME REFERENCE MATERIAL. IT’S THE MOST WELL CHARACTERIZED GENOME IN EXISTENCE IT’S BEEN SEQUENCED TO THOUSANDS OF COVERAGE BY ALL DIFFERENT SEQUENCING PLATFORMS AND USED BY INDUSTRY TO SEAS THE ACCURACY OF DNA, HUMAN GENETIC TESTING. SO, JUST FOR AN EXAMPLE HOW IT PLAYED A ROLE IN THE GENOMIC SPACE RECENTLY. WE IN THE DEPARTMENT OF COMMERCE SO INDUSTRY IS OUR STAKEHOLDER. BUT WE TYPICALLY INTERACT WITH THE BIOTECHNOLOGY INDUSTRY THAT IS REGULATED BY THE FDA SO WE HAVE A CLOSE WORKING RELATIONSHIP WITH FDA AND OUR INDUSTRY STAKEHOLDERS AND TYPICALLY WHEN WE COLLABORATE IT’S TO DEVELOP INDUSTRY STANDARDS AND HUMAN GENOMIC DNA REFERENCE MATERIAL. SO WE HAVE CLOSE TIES WITH FDA AS WELL AS INDUSTRY STAKEHOLDER. WE ARE NOT A REGULATORY AGENCY. SO WHAT ARE OUR ONGOING MICROBIAL EFFORTS? AS I SAID, OUR PROGRAM IS RELATIVELY NEW. IT STARTED AROUND 2014, 2015. SO WE ARE IN THE PROCESS OF DEVELOPING MICROBIAL REFERENCE MATERIALS BOTH GENOMIC DNA, WHOLE CELL, MIXTURES, AS YOU MIGHT IMAGINE THAT ARE NEEDED FOR THE MICROBIOME COMMUNITY. WE ARE HOSTING INTER-LAB STUDIES OR CHALLENGES AS WE CALL THEM. WE ACTUALLY JUST FINISHED ONE UP AND BEGAN LOOKING AT SOME PRELIMINARY DATA FROM IT AND FOUND INTERESTING FINDINGS FROM A QUICK AND DIRTY INTERLAB STUDDEDY WE HOSTED OVER A PERIOD OF 6 MONTHS. WE HOST ANNUAL WORKSHOPS. WE ALTERNATE YEARS BETWEEN THE FOCUS ON STANDARDS FOR MICROBIOME MEASUREMENTS AND STANDARDS FOR PATHOGEN DETECTION. ACTUALLY THIS WEEK, MONDAY AND TUESDAY, WE HAD OUR SEMI-ANNUAL STANDARDS FOR PATHOGEN DETECTION WORKSHOP IN GAITHERSBURG. IT WAS GREAT WORKSHOP, I THOUGHT. WE HAD WORLD LEADERS COME OUT. I WANT TO POINT OUT THAT STANDARDS FOR PATHOGEN DETECTION, THESE ARE THE CLINICIANS, INFECTIOUS DISEASE CLINICIANS LOOKING FOR PATHOGENS. THAT COMMUNITY IS BEGINNING TO USE MET GENOMIC METHODS. SO I JOKINGLY TELL OUR AUDIENCE, WE HAVE THE SAME DISCUSSION EVERY YEAR WHETHER WE ARE TALKING ABOUT MICROBIOME OR PATHOGEN DETECTION. THE IT’S THE SAME NEEDS. IT’S THE SAME MEASUREMENTS AND THE SAME UNDERLYING PROBLEMS. SO NEXT YEAR, 2018 WILL BE OUR STANDARDS FOR MICROBIOME MEASUREMENTS WORKSHOP, KEEP AN EYE OUT FOR AN ANNOUNCEMENT. WE HOST CONSORTIA. I ENCOURAGE YOU ALL TO VISIT THE WEBSITE WHICH I DIDN’T PUT ON HERE. BUT IT’S RATHER EASY TO REMEMBER. MICROBIAL STANDARDS.ORG. SO IT IS ONE-STOP-SHOP FOR EVERYTHING MICROBIAL STANDARDS INCLUDING THE HOME OF OUR NEW CONSORTIA WHICH IS THE INTERNATIONAL MICROBIOME STANDARDS ALLIANCE. WE HAVE MONTHLY WEBEXS. I DID PUT THE WEBSITE ON THERE T IS OPEN FOR EVERYONE. IT’S AN OPEN GATHERING DISCUSSION FORUM IF WE ARE TALKING ABOUT ANYTHING MICROBIOME STANDARDS RELATED WHETHER IT IS SAMPLE COLLECTIONS, STORAGE, METHODS, DNA EXTRACTION TECHNIQUES, ET CETERA. WE HAVE INTERNAL LABORATORY RESEARCH PROGRAMS FOCUSED ON DEVELOPING NEW MEASUREMENTS. I’LL TALK ABOUT THAT LATER WHEN WE TALK ABOUT GAPS AND AS LITA POINTED OUT, WE ON INTERAGENCY WORKING GROUPS AND THE MICROBIOME COALITION. SO IS WITH THAT, I WILL STOP. [ APPLAUSE ]>>SO MY NAME IS CLIFF AND I’M REPRESENTING THE CDC, CENTERS FOR DISEASE CONTROL AND PREVENTION. I’M IN THE DIVISION OF HEALTH CARE QUALITY AND PROMOTION. WE WERE CALLED THE HOSPITAL INFECTIONS PROGRAM, IT’S OUR FOCUS, INCLUDING MANGE MICROBIOME MEDIATED DISEASES AND I’M HERE TO TALK ABOUT RESISTANCE IN THE MICROBIOME IT’S WHERE WE THINK PUBLIC HEALTH AND MICROBIOME ARE MEETING RIGHT NOW IN THE CURRENT TIME. AND WE TALK ABOUT THIS IN TERMS OF A FORREST THAT A HEALTHY FORREST KEEPS MOST OF THE MULTIDRUG RESISTANT ORGANISMS OUT OR OFF THE SKIN OR OUT OF THE GUT. THAT MICROBIOME DISRUPTION USUALLY FROM ANTIBIOTICS IS LIKE A FORREST FIRE THROUGH THE FORREST, THE ECOLOGY, PROVIDING ECOLOGICAL NICHE WHERE THESE ORGANISMS SEEM ARE NIGHTMARE BACTERIA IN TERMS OF RESISTANCE. DEADLY DIARRHEA KILLS 15,000 TO 25,000 PEOPLE A YEAR IN THE UNITED STATES CLOSE HALF A MILLION INFECTIONS. THESE ORGANISMS TAKE ADVANTAGE OF THE DISRUPTIVE MICROBIOME AND TAKE AND PROLIFERATE AND THEY SPREAD TO OTHER PATIENTS. SO OUR WORK IS AROUND DEVELOPING MICROBIOME SOLUTIONS TO THE ANTIBIOTIC RESISTANCE PROBLEM. TRYING TO PREDICT THE IMPACT OF DIFFERENT ANTIBIOTICS ON THE MICROBIOME, TAILORING ANTIBIOTIC USE, ONE OF THE MAJOR EFFORTS TO PREVENT ANTIBIOTIC RESISTANCE IS TO BETTER USE THESE, WE CALL IT ANTIBIOTIC STEWARDSHIP AND IT’S LIKELY THAT MICROBIOME DIAGNOSTICS WILL PLAY A ROLE FROM THAT IN THE FUTURE. DEVELOP AND TEST MICROBIOME DIAGNOSTICS AND PROTOCOLS AND DEVELOPMENT OF SOME OF THOSE TESTS. AND THEN ALSO WHERE WE CAN, WORKING WITH OTHER AGENCIES, FDA, NIH, NIST, AND OTHERS AT THIS TABLE TO DEVELOP AND SUPPORT THE DEVELOPMENT OF THERAPEUTICS THAT COULD RESTORE AND PROTECT THE MICROBIOME. WE HAVE CURRENTLY THREE COLLABORATIVES DISCOVERING NEW WAYS TO PROTECT PATIENTS. WE HAVE FOUR PREVENTION EPICENTER PROJECTS THAT ARE CENTERS OF EXCELLENCE, 11 ACROSS THE UNITED STATES AND SEVERAL OF THEM DOING MICROBIOME PROJECTS AND WE FUNDED OVER 15 STUDIES AN CONTRACTS IN 2016. IT WILL BE LESS THAN THAT IN 2017. THESE ARE MOSTLY AROUND LOOKING AT PREDICTING MICROBIOME PREDICTORS OF BECOMING COLONIZED OR ONCE BECOMING COLONIZED DOMINATED OR INFECTED. THIS IS POOR GEORGE. HE IS OFTEN A PATIENT WHO BECOMES COLONIZED OR INFECTED WITH A MULTI-DRUG RESISTANT ORGANISM AND WE USED HIM IN PREVIOUS PUBLIC COMMUNICATIONS ABOUT THIS PROBLEM AND IN THIS CASE FROM THE FAR LEFT, HE HAS A NORMAL MICROBIOME AND GETS AN ANTI-BY ON THETIC AND IT DISRUPTED AND THEN A MULTIDRUG RESISTANT ORGANISM OR GENETIC RESISTANCE ELEMENTS COMES INTO HIM AND DEVELOPS COLONIZATION FOLLOWED BY DOMINANCE AND TRANSMISSION AND INFECTION. AND SO, WE ARE ENVISIONING THE DEVELOPMENT OF MICROBIOME INDEXES. A LOT OF THINGS WE TALKED ABOUT HERE, WE HEARD ABOUT DOMINANE. WE HEARD ABOUT KEYSTONE SPECIES. PROTECTIVE SPECIES. ALL THESE THINGS WE TRY TO CATEGORIZE AND CATALOG AND DEVELOP INTO EITHER DIAGNOSTIC BUT ALSO TO USE AS YARDSTICKS FOR NEW DRUG DEVELOPMENTENTS BIOTICS AND THEN ALSO THE MICROBIOME PROTECTANTS AND RESTOREATIVES. IS. [ APPLAUSE ]>>MY NAME IS JACK AND I’M FROM THE USDA AGRICULTURAL RESEARCH SERVICE. I’M IN THE DIVISION OF CROP PRODUCTION AND PROTECTION. WE HAVE TWO AGENCIES WHICH ARE THE PRY MARE RESEARCH AGENCIES FOR THE US IS DA. AGRICULTURAL RESEARCH SERVICE OR ARS IS THE INTERNAL INTRAMURAL RESEARCH AGENCY AND NATIONAL INSTITUTE OF FOOD AND AGRICULTURE OR NIFA IS THE EXTRAMURAL GRANT AWARDING AGENCY. BEFORE I GET INTO MUCH ABOUT AGRICULTURE AND RELATING THAT TO THE HUMAN MICROBIOME. HOW MANY OF YOU AFTER THIS MEETING IS DONE ARE GOING TO TAKE OFF AND GO CHASE THE SOLAR ECLIPSE? ANYONE HERE? JUST A FEW HANDS. A FEW YEARS AGO, YOU WOULD HAVE OR COULDN’T DESCRIBE THE MICROBIOME AS THE DARK MATTER OF THE UNIVERSE OF LIFE. BUT IT’S CLEAR FROM THIS SYMPOSIUM THAT THAT IS RAPIDLY CHANGING. AND YOU GUYS ARE THE HUBBLE TELESCOPE FOR THE MICROBIOME. OKAY? SO, KEEP UP THE GOOD WORK AND ALSO THINK ABOUT AGRICULTURE. ALL RIGHT? LET’S TAKE A FEW STEPS OUT OF THE LABORATORY NOW AND INTO THE FIELD AND TALK ABOUT WHAT THE POTENTIALLY HIGH IMPACT MICROBIOME RESEARCH TARGETS ARE AT THE USDA. AND THEY COVER BOTH HUMAN AND NUTRITION AND HEALTH AND ALSO VETERINARY AND AGRICULTURAL PRODUCTION. ONE OF THOSE HIGH IMPACT TARGETS IS TO PROLONG THE EFFECTIVENESS OF ANTIBIOTICS FOR TREATING PEOPLE AS WELL AS ANIMALS AND ALSO CROPS. HOW MANY OF YOU SAID, CROPS? ANYBODY? JIM DOES. THANK YOU, JIM. HOW MANY OF YOU HEARD ABOUT CITRUS SCREENING? JUST FIVE YEARS AGO IN FLORIDA, SO THIS IS A DISEASE OF CITRUS. IT’S BEEN DEVASTATING IN FLORIDA. OVER THE LAST FIVE YEARS FLORIDA STATE HAS GONE FROM PRODUCING 270 MILLION CRATES OF CITRUS FRUIT JUICE JUST 70 MILLION CURRENTLY. SO THE INDUSTRY IS JUST HANGING ON BYINGS FINGERNAILS. THE DISEASE IS CAUSED BY A BACTERIUM CALLED [ INAUDIBLE ] AND RIGHT NOW, IT’S NOT UNDER CONTROL. AND WE GROWERS AND RESEARCH SCIENTISTS ARE TRYING A NUMBER OF STRATEGIES TO CONTROL THE DISEASE AND OF COURSE ONE OF THOSE IS TO USE ANTIBIOTICS. ANTIBIOTICS ARE A TOOL WE USE NOT ONLY ON THE ANIMAL HEALTH SIDE AND HUMAN HEALTH SIDE BUT ALSO ON THE COP SIDE. WE ARE STILL IN THE MIDDLE OF THIS WAR AND DON’T KNOW HOW IT WILL END UP BUT ANTIBIOTIC RESISTANCE AND ALSO A CONCERN ON THE AGRICULTURAL SIDE. I’LL GIVE YOU ANOTHER EXAMPLE OF POTENTIALLY HIGH IMPACT TARGETS. HOW MANY OF YOU HAD A SANDWICH TODAY FOR LUNCH? MADE OF WHEAT. NO WE’RE GOING TO TALK ABOUT SOME OF THE GOOD GUYS IN THE FIELD AND WE’LL TALK ABOUT SOIL HEALTH AND OF COURSE THERE ARE GOOD MICROORGANISMS IN THE SOIL WHICH ARE VERY BENEFICIAL. IF YOU GO TO THE WASHINGTON STATE AND TAKE NAIVE LAND AND TRY TO PLANT WHEAT SEED WHICH IS WASHINGTON STATE IS A BIG COMPLETE PRODUCING STATE. CHANCES ARE YOUR FIELD WILL COME DOWN WITH SOMETHING WHICH IS CALLED TAKE-ALL DISEASE. TAKE-ALL DISEASE. BASICALLY IT WIPES OUT THAT FIELD. VERY HIGH PROBABILITY. AND IF YOU GET A SEVERE ENOUGH CASE, IF YOU COME BACK THE NEXT YEAR AND PLANT YOUR WHEAT, IT MAY DO BETTER AND OVER SEVERAL YEARS, IF YOU KEEP PLANTING WHEAT, IT WILL DO BETTER AND BETTER UNTIL NOW YOU HAVE A WHEAT-GROWING FIELD. SO THERE IS A SPECIES OF — I DIDN’T TELL YOU WHAT WAS CAUSING THE DISEASE BUT I’LL TELL YOU BECAUSE I CAN’T PRONOUNCE THE LATIN NAME. I’M TERRIBLE WITH LATIN NAMES BUT THERE ARE OTHER SPECIES WHO PRODUCE ANTIMICROBIAL COMPOUNDS WHICH ARE ACTIVE AGAINST THE DISEASE-CAUSING ORGANISM. SO THEY ARE GOOD PLAYERS IN THE MICROBIOME AS WELL AND WE ARE JUST AS INTERESTED IN THOSE IN AGRICULTURE AS WE ARE IN HUMAN AND ANIMAL HEALTH. ANYWAY, I’M GOING TO BE RUNNING OUT OF TIME HERE. SO, WHAT ARE THE KEY GAPS? WE HAVE STAKEHOLDER LISTENING SESSIONS, NOT ONLY HERE IN THE URBAN CENTERS BUT ALSO IN THE AGRICULTURAL-PRODUCING REGIONS AND ONE THING THAT WE HEAR ALL THE TIME IS WORKFORCE. SO, NOT ENOUGH COMPUTATIONAL BIOLOGISTS, SCIENTISTS WHO CAN SPEAK THE LANGUAGE OF GENOMICS AND GENETICS BUT ALSO AG ROW NOMMICS AND PRODUCTION AND PLANT BIOLOGY AND PLANT PATHOLOGY AND ANIMAL PATHOLOGY AND ANIMAL HEALTH AS WELL AS HUMAN NUTRITION AND HUMAN SAFETY. SO I’LL STOP THERE. THAT’S MY CONTRIBUTION FOR KEY GAPS. [ APPLAUSE ]>>GOOD AFTERNOON, EVERYBODY. MY NAME IS JIM OLSON LIFE SCIENCES AT THE NATIONAL SCIENCE FOUNDATION AND JACK’S AGENCY AND MY AGENCY DO A LOT OF WORK TOGETHER. WE ALSO WORK WITH OUR FRIENDS AT THE NIH BUT I’M A MOLECULAR NEUROSCIENTIST TRAINED AT THE NIH ORIGINALLY BUT I HAVE BECOME FASCINATED WITH PLANT BIOLOGY AND IT’S BECAUSE FOOD PRODUCTION IS SO INCREDIBLY IMPORTANT. OUR SURVIVAL DEPENDS ON FOOD PRODUCTION. SO, JACK I’D LIKE TO ECHO SCIENTIFICALLY WHERE YOU’RE COMING FROM. I THINK IT’S INCREDIBLY IMPORTANT.>>THANK YOU.>>LOOK, THE DRIVERS OF MICROBIOME STRATEGY COME OUT OF THE WHITE HOUSE LIFE SCIENCES SUB-COMMITTEE ON NATURAL SCIENCE AND TECHNOLOGY COUNCIL WHICH I CO-CHAIR. AND THEY CHART EVERYBODY THE FAST TRACK ACTION COMMITTEE ON MAPPING THE MICROBIOME. THE REPORT OF THAT GROUP FOUND LESS ACTIVITY THAN EXPECTED IN AGRICULTURAL MICROBIOME RESEARCH PARTICULARLY IN FOOD-BASED STUDIES, VIRAL MICROBIOME RESEARCH AND APPLIED MICROBIOME RESEARCH AND TOOL DEVELOPMENT COMPARED TO BASIC MICROBIOME RESEARCH. SO, SOME ACTIVITIES THAT ARE ONGOING AT OUR AGENCY WHICH HAS A BUDGET OF ABOUT 8 BILLION DOLLARS A YEAR. MICROBIOME RESEARCH IN LIFE SCIENCES HAS FLOWERISHED BY LETTING THE RESEARCH COMMITTEE DRIVE THE IMPORTANT QUESTIONS. THIS HAS RESULTED IN A SUBSTANTIAL INVESTMENT IN MICROBIOME RESEARCH THAT IS PART AND PARCEL TO CORE RESEARCH ACROSS ALL THE BIOLOGICAL SCIENCES DIRECTORATE WHICH I HAD. THIS ATHROWS FOCUS ON A FEW PROGRAMS WHERE WE BELIEVE INVESTMENT COULD HAVE THE GREATEST POTENTIAL TO IMPACT BROAD RESEARCH COMMUNITIES AND PRACTICAL WAYS. THE MICROBIOME PORTFOLIO AT NSF HAS IMPORTANT AND DIRECT AND INDIRECT IMPACTS ON HUMAN HEALTH AND ON THE FURTHERERANCE OF MICROBIOME RESEARCH. THESE ARE A FEW EXAMPLES OF THE ACTIVITIES. THE PLANT BIOTIC INTERACTIONS PROGRAM SUPPORTS RESEARCH ON THE PROCESSES THAT MEDIATE BENEFICIAL AND ANTAGONISTIC INTERACTIONS BETWEEN PLANTS AND THEIR VIRAL BACTERIAL, FUNGAL, PLANT AND SIMIANS. SO WHAT WE HAVE HERE IS SAY COMPLEX ADAPTIVE SYSTEM GOING ON THAT IS ABSOLUTELY CRITICAL FOR FOOD PRODUCTION. THE PROGRAM SUPPORTS PROJECTS FOCUSED ON CURRENT AND EMERGING MODEL AND NON MODEL SYSTEMS IN AGRICULTURALLY RELEVANT PLANTS. NOW THE ARA CAPS NETWORK COMPRISES EIGHT EUROPEAN COUNTRIES AND THE US AND 11 OBSERVER COUNTRIES, 10 FUNDING ORGANIZATIONS. ED AND COORDINATED BY THE U.K. BBSRC, ONE OF THE RESEARCH WELL COUNCILS, OUR COUNTERPARTS IN THE U.K. ERA CAPS AIMS AT ENLARGING EUROPEAN COOPERATION IN THE AREA OF PLANT SCIENCES WHICH SHOULD SIGNIFICANTLY HELP PLANT SCIENCES TO BOTH ADDRESS CURRENT AND FUTURE CHALLENGES AND FOOD AND NON FOOD CROP PRODUCTION. THINK HEALTHY SAFE, SUFFICIENT FOOD AND PLANT-BASED PRODUCTS, CHEMICALS AND ENERGY. ONE THING THAT I LEARNED COMING TO NSF IS THAT YOUR CELL IS ABOUT 20% EFFICIENT. THE HAPPIEST PLANT AND THE HAPPIEST CROP FIELD IN AMERICA IS 2% EFFICIENT MAYBE. SO YOU COULD GET DEPRESSED ABOUT THAT BUT THERE IS SAY LOT OF POSITIVE UP SIDE IS THERE ALSO. AND THAT IS ONE WAY OF THINKING ABOUT WHERE WE COULD GO IN TERMS OF IMPROVING FOOD PRODUCTION. THE EDGE PROGRAM ENCOURAGES DEVELOPMENT OF TOOLS THAT CAN IMPACT BROAD COMMUNITIES OF INVESTIGATORS, PROJECTS OF INTERESTED COULD INCLUDE BUT ARE NOT LIMITED TO FUNDAMENTAL PRINCIPLES BY STUDYING DIFFERENT ECOSYSTEMS AND THE DEVELOPMENT F COMPUTATION AND MODELING TOOLS FOR STUDYING MICROBIOMES. I’M GOING TO JUMP AHEAD HERE AND TALK ABOUT OUR EEID PROGRAM WHICH WE DO IN PARTNERSHIP WITH THE NIH. THAT’S THE ECOLOGY AND EVOLUTION OF INFECTIOUS DISEASES. SO, I THINK ZIKA AND — SO ONE FOCUS OF THE PROGRAM IS TO GIVE INSIGHTS INTO THE DISEASE SYSTEM THAT IS REQUIRE INTEGRATION ACROSS SEVERAL SCALES INCLUDING MOLECULAR, INDIVIDUAL POPULATION, SOCIETAL AND ECOSYSTEMS. AND I’M REALLY EXCITED ABOUT HOW THAT IS GOING TO INTERSECT WITH OUR NATIONAL EEK LONG CALL OBSERVATORY NETWORK JUST NOW FINISHING COMPLETION ON. 500 MILLION DOLLAR APPROXIMATELY CONSTRUCTION PROJECT WHICH HAS ECOLOGICAL CENTERS GOING FROM ALASKA TO PUERTO RICO AND STORES ARCHIVE SOIL SAMPLES THAT AND BIO– BICATCH, WHICH ON A SYSTEMATIC BASIS CAN REALLY CONTRIBUTE HERE. SO, HERE SAY CURRENT AND RELEVANT EXAMPLE. I WANT YOU TO THINK ABOUT THIS ONE AS SORT OF THINK THE HUMAN MICROBIOME PROJECT AND THE EARTH MICROBIOME PROJECT. SO THE TOOLS HERE IN THIS PROJECT BY FRANK STEWART AS THE PI AT GEORGIA TECH WILL PROVIDE IMPROVED METHODS TOO REMEMBERED ORGANIZE EXPRESSION DATA INTO METABOLIC PATHWAYS WHICH INFORM PREDICTIONS ON HOW BIOCHEMICAL PROCESSES TRANSFORM MATTER AND ENERGY. THE DEVELOPMENT SOFTWARE TOOLS WILL BE MADE AVAILABLE AS OPEN-SOURCE PACKAGES AND DEPLOYED ON CLOUD COMPUTING ENVIRONMENTS. THANK YOU VERY MUCH. [ APPLAUSE ]>>SO I’M MIKE SAYER FROM THE NATIONAL INSTITUTE ON MINORITY HEALTH AND HEALTH DISPARITIES. NIMHD IS THE NEWEST GRANT MAKING INSTITUTE AT THE NIH ELEVATED FROM A CENTER TO AN INSTITUTE IN 2010 WITH THE PATIENT PROTECTION AND AFFORDABLE CARE ACT. UNDER OUR NEW DIRECTOR, DR. PEREZ, WE ORGANIZED EXTRAMURAL MINORITY HEALTH AND HEALTH DISPARITIES RESEARCH EFFORTS AROUND THREE BROAD PRIORITY AREAS AND THEY ARE LISTED HERE. INTEGRATED BIOLOGICAL AND BEHAVIORAL SCIENCES IS MY AREA. I’M THE CHIEF OF THAT BRANCH. WE HAVE CLINICAL AND HEALTH RESEARCHERS AND COMMUNITY HEALTH AND POPULATION SCIENCES. I WANT TO SAY THAT WHEN I WAS A GRADUATE STUDENT IN 1980S, MY WORK WAS ON THE BACTERIA PHAGE THAT INFECTED BACILLUS. SO I’M REALLY GLAD TO SEE PHAGE BACK IN VOGUE HERE AS A POTENTIAL THERAPEUTIC AGENT. THAT’S VERY EXCITING. EACH OF THESE AREAS FOCUSES ON A RANGE OF HEALTH DEPARTMENT NANTS AND PROCESS THAT IS CONTRIBUTE TO POOR HEALTH OUT ANDS AND HEALTH DISPARITIES IN DISADVANTAGED POPULATIONS AND SOME EXAMPLES ARE LISTED HERE, INCLUDING HUMAN MICROBIOME. WITH RESPECT TO MICROBIOME RESEARCH, WE ARE A DISEASE AGNOSTIC INSTITUTE SO INTERESTED IN MICROBIOTA AT ALL BODY SITES SO IT WILL MAKE IT HARD TO ANSWER YOUR QUESTION AT THE END. BUT WE ARE ESPECIALLY INTERESTED IN RESEARCH ON HUMAN HOST MICROBIOTA INTERACTION THAT IS MAY CONTRIBUTE HEALTH AND DISEASE IN DISADVANTAGED POPULATIONS. AND HOW THOSE INTERACTIONS ARE INFLUENCED BY BEHAVIORAL, SOCIAL AND ENVIRONMENTAL FACTORS. SO, IN THE INTEREST OF TIME I’M GOING TO JUST BRIEFLY SUMMARIZE TWO NEW EXAMPLES JUST TWO FROM OUR GROWING MICROBIOME RESEARCH PORTFOLIO. THIS PROJECT LED BY ROBERT KAPLAN, ROB KNIGHT AND ROBERT BURKE, EXAMINES THE ROLE OF THE GUT MICROBIOME IN PREDIABETES AND DIABETES IN LATINOS. IT LEVERAGES NHLBIs HISPANIC COMMUNITY HEALTH SURVEY STUDY OF LATINOS, LONGITUDINAL COHORT STUDY, AND THIS ANCILLARY STUD LE TEST THE HYPOTHESIS AT SPECIFIC GUT MICROBIOME PATTERNS ARE SIGNIFICANTLY ASSOCIATED WITH PREDIABETES AND DIABETES IN THIS POPULATION. THE PROJECT WILL COLLECT AND DETERMINE GENETIC COMPOSITION OF FECAL MICROBIOME FROM OVER 2000 COHORT MEMBERS. AND I THINK THIS IS THE FIRST MAJOR EPIDEMIOLOGIC PROJECT FOCUSING ON HISPANIC LATINO POPULATIONS AND THEIR MICROBIOME. THE NEXT PROJECT, SECOND PROJECT LED BY STEPHANIE AT UNC CHAPEL HILL IN COLLABORATION WITH VIRGINIA COMMONWEALTH UNIVERSITY LEVERAGES DATESSA FROM A DIVERSE COHORT OF WOMEN ENROLED IN THE NICHD’S PREGNANCY INFECTION AND NUTRITION STUDY AND THE HMP PHASE II MULTIOMIC MICROBIOME STUDY PREGNANCY INITIATIVE OR MOMS PI STUDY. TO INVESTIGATE MECHANISMS BY WHICH UNFAVORABLE VAGINAL MICROBIOME PROFILES CONTRIBUTE TO DISPARITIES IN PRETERM BIRTH AMONG AFRICAN-AMERICANS. THEY WILL BE LOOKING AT THE INFLUENCE OF MATERNAL POLYMORPHISMS IN INNATE IMMUNITY GENES, EXPRESSED IN THE VAGINAL MUCOSA AND ASSOCIATION BETWEEN MATERNAL PSYCHOSOCIALITY STRESS AND DEPRESSION AND MY CROW BY EAT AND PRETERM BIRTH RISK. INFLUENCE OF BEHAVIORAL RISK FACTORS ON THE VAGINAL MICROBIOTA AS POOR DIET AND SMOKING AND OTHER BEHAVIORS AND METAGENOMIC ANALYSIS IN A SUB SET OF PRETERM BIRTH CASES WITH ETIOLOGY, PARTICULARLY BACTERIAL VAGUENESSES. SO, I KNOW WE ARE GOING TO MOVE QUICKLY TO THE Q&A SESSION BUT I WANTED TO ENCOURAGE EVERYONE TO THINK ABOUT SUBMITTING YOUR BEST IDEAS IN MICROBIOME RESEARCH AS IT RELATES TO MINORITY HEALTH AND HEALTH DISPARITIES. WE ARE AGGRESSIVELY GROWING OUR PORTFOLIOY OF INVESTIGATOR INITIATED RESEARCH PROJECTS SO NOW SAY GOOD TIME TO THINK ABOUT NI PH.D. I SHOULD SAY WE ARE VERY INTERESTED IN PRECISION MEDICINE. LAST YEAR WE FUNDED A MAJOR CENTER GRANT TO STAMFORD UNIVERSITY AND MIKE SNYDER IS LEADER OF ONE OF THE SUBPROJECTS ON THAT GRANT AND THE PI IS MARK CULLEN. SO, WE ARE OPEN FOR BUSINESS AND LOOKING FOR YOUR GOOD IDEAS. THANK YOU.>>SO HERE IS THE EXPERIMENTAL PART. I THINK WHAT I WANT TO DO IS HAVE ONE OR MORE OF YOU ELABORATE ON THE OBSTACLES YOU NAMED VERY QUICKLY IN YOUR INTRO. PARTICULARLY AS YOU HEARD THE GAPS NEEDS AND CHALLENGES ALSO VOICED BY THE AUDIENCE. LIKE WHAT RESONATED WITH YOU WHEN YOU WERE LISTENING TO THE TALKS OVER THE LAST FEW DAYS? OR HAVE YOU IDENTIFIED AN OBSTACLE YOU HADN’T HEARD YET? ANYBODY? FOR THOSE OF YOU WHO ARE HERE? GO AHEAD, LINDA JUMP IN.>>YES, SO LINDA CHRISY FROM THE DEPARTMENT OF DEFENSE. SO I WASN’T HERE FOR THE FIRST TWO DAYS. I DID APPRECIATE THE COMMENTS ON GAPS AND CHALLENGES FROM THE SPEAKERS TODAY. ONE CHALLENGE I’D SAY THAT I SEE AS A FUNDER OF RESEARCH FOR THE DEPARTMENT OF DEFENSE IN THIS AREA IS WHEN WE GO TO OUR OPERATIONAL COMMUNITIES, THEY ASK US, WHAT ARE YOU GOING TO DO TO HELP US? AND FOR MANY OF THE AREAS THAT I’M INTERESTED IN, WE HAVE ANIMAL STUDIES BUT THERE AREN’T ANY HUMAN STUDIES AND YET IT IS VERY HARD TO CONTEMPLATE TAKING PEOPLE OUT OF A MISSION AND DOING RESEARCH STUDIES ON THEM. SO IS THAT IS A QUESTION I HAVE A HARD TIME ANSWERING. WHAT AM I GOING TO DO FOR THE OPERATIONAL FOLKS WITH STUDIES THAT ARE STILL AT THE ANIMAL RESEARCH STAGE AT BEST?>>COULD I ASK SOMEONE TO JUST TURN ON THE HOUSE LIGHTS? THERE IS NO REASON FOR THEM TO BE DOWN. ANYBODY WHO IS IN THE BOOTH IN THE BACK?>>CAN I JUMP IN WITH A GAP.>>PLEASE DO.>>SO, WHO HERE IN THE AUDIENCE IN THE LAST COUPLE OF WEEKS IN NATURE READ THE PAPER ON ECOSYSTEM ON ON A LEASH TALKING ABOUT MICROBIOME? AND IT WAS REALLY INTERESTING BECAUSE IT WAS THE CONCEPT OF THE FACT THAT MICROBIOME BOTH IN OUR GUT AND THE MICROBIOME THAT EXISTS IN THE SOIL IS THAT INTERACTS WITH CROP PLANTS FOR EXAMPLE, IS REALLY ITSELF AN ECOSYSTEM THAT IS IN THIS VERY COMPLICATED RELATIONSHIP, OBEYING COMPLICATED RULES OF THE ROAD WITH EITHER ITS HOST OR THE PLANTS THAT IS NEARBY. AND THOSE RULES OF THE ROAD STRIKE ME TO BE A GAP SPACE. AKIN TO THE RULES OF THE GAME OF CHESS BUT THE RULES OF THE ROAD BY WHICH THAT MASSIVE ECOSYSTEM INTERACTS WITH HOST STRIKES ME AS A BIG GAP AREA THAT IS WORTHY OF ALL OF OUR AGENCIES FOCUSING ON.>>I’D LIKE TO SECOND THAT AND JUST FROM THE PERSPECTIVE OF — AN ORGANISM WE THINK OF HEALTH CARE ASSOCIATED PATHOGENS BUT WE REALIZE IT IS REALLY RESERVOIRS IN THE COMMUNITY AND WE REALLY DON’T KNOW WHERE IT DIVERSIFIES OUT OF THE HUMAN HOST. AND SO IT’S JUST PERPLEXING QUESTION AND YOU CAN ALSO BRING IT TO WHEN YOU DON’T HAVE A SOIL AROUND, I THINK WE HEARD THAT TODAY. IN HEALTH CARE, FOR EXAMPLE, WE HAVE MICROBIOME SYSTEM IN HEALTH CARE THAT ARE SEPARATED FROM THE SOIL BUT THEY DEVELOP SOME CHARACTERISTICS OF THAT INTERACTION BETWEEN HUMAN AND SOIL AND NOW HUMAN AND HEALTH CARE FACILITY, THE DRAINS, THE SURFACES, AND THE PEOPLE COMING IN AND OUT.>>SO ONE POSSIBLE APPROACH TO SOME OF THESE AREAS IS, ONE APPROACH MIGHT BE TO TRY TO DEVELOP SOME MODELS AND I THINK AT NIH I DON’T SEE AS MUCH MODEL BUILDING AS I DID WHEN I WAS AT NSF. SO, ANY THOUGHTS, JIM, ABOUT WHAT IS HAPPENING IN THE MODEL DEVELOPMENT AREA AT NSF AND WHAT ELSE IS NEEDED?>>WELL, MODELS ARE REALLY IMPORTANT TO US. AND NOT USING THE OPERATIONAL DEFINITION OF MODEL ORGANISMS BUT MODELS ARE REALLY IMPORTANT TO US. AND BASICALLY, WHAT THAT GETS AT IS A THEORETICAL FRAMEWORK. SO GETS US OUT OF THE STAMP COLLECTING AND INTO THE PREDICTIVE SCIENCE. WE DO SUPPORT THAT. WE ARE VERY ENTHUSIASTIC ABOUT SUPPORTING THAT AND WHATILATED SAY IS I THINK A LOT OF OUR SISTER AGENCIES ARE INTERESTED IN THAT ALSO. I’LL JUST NOTE THAT ANOTHER CHARTER CREATION OF THE DEPARTMENT OF AGRICULTURE IS THE FOUNDATION FOR FOOD AND AGRICULTURE RESEARCH WHICH I SIT ON THE BOARD OF AND IS ABLE TO ACTUALLY INVEST DIRECTLY INTO BASIC RESEARCH ALONG THOSE LINES ALSO, SALLY ROCKEY FORMERLY OF NIH IS THE EXECUTIVE DIRECTOR OF THAT ORGANIZATION. THEY HAVE A BANK ACCOUNT OF 200 MILLION DOLLARS COURTESY OF THE FARM BILL OF 2013. SO, I THINK THERE IS A LOT OF POTENTIAL IN THIS AREA AND I’D LIKE TO SEE SOME CREATIVE IDEAS COME OUT.>>SO I THINK FOR HIV RESEARCH SOME OF THE GAPS THAT I SEE, ONE IS ANIMAL MODELS, WE DO A LOT OF OUR RESEARCH IN NON-HUMAN PRIMATES, WHICH IS THE BEST MODEL FOR HIV HOWEVER THERE ARE SMALL ANIMAL MODELS WE COULD EXPLORE BECAUSE NON-HUMAN PRIMATES ARE QUITE EXPENSIVE. ANOTHER GAP, I THINK IS SORT OF THE MULTIDISCIPLINARY RESEARCH. WE HAVE A LOT OF HIV EXPERTISE. WE DON’T HAVE A LOT OF MICROBIOME EXPERTISE. SO I THINK TRYING TO LINK THE TWO COMMUNITIES IS SOMETHING THAT NIH SHOULD BE PROMOTING. AND I THINK MAYBE THE THIRD GAP WOULD BE — IT JUST WENT OUT OF MY HEAD. IT WILL COME BACK TO ME. SORRY.>>SCOTT JACKSON FROM NIST. I WASN’T ABLE TO ATTEND THE FIRST DAY OF THIS CONFERENCE BUT IN 2015, THE WHITE HOUSE OFFICE OF SCIENCE AND TECHNOLOGY POLICY HOSTED THE FAST TRACK ACTION COMMITTEE ON MAPPING THE MICROBIOME. THAT COMMITTEE WAS TASKED WITH IDENTIFYING GAPS AND ONE OF THE UNANIMOUS GAPS THAT WAS IDENTIFIED BY THAT COMMITTEE WAS THE NEED FOR STANDARDS FOR MICROBIOME REFERENCE MATERIALS, REFERENCE DATA, ET CETERA. SO NIS HAS PERKED THEIR EARS UP. WE HAVE WORKSHOPS TO BRING IN THE STAKEHOLDER COMMUNITY AND SAY, WHAT DOES THAT MEAN? A THOUGHT EXERCISE I LIKE TO DO WHEN I HAVE PEOPLE GATHERED LIKE THIS IS ASK, IN YOUR MIND, WHAT IS A STANDARD FOR MICROBIOME MEASUREMENT? WHAT DOES THAT LOOK LIKE? AND THERE IS NO RIGHT OR WRONG ANSWER. SOME PEOPLE SAY IT’S A MOCK COMMUNITY. SOME PEOPLE SAY IT’S A PROCEDURE. IT’S A PROTOCOL. MAYBE DATA. AND THESE THINGS ARE ALL CORRECT SO, WE HAVE BEEN WORKING TOWARDS DELIVERING STAKEHOLDER COMMUNITY NEEDS BOTH IN THE DIAGNOSTIC SIDE AS WELL AS THE THERAPEUTIC SIDE. SO, ONE OF THE THINGS I AM MOST PASSIONATE AND INTERESTED ABOUT IS THE EMERGING FIELD OF LIE MICROBIAL BIOTHERAPEUTICS BECAUSE THE DEVELOPMENT OF THESE NEXT GENERATION THERAPEUTICS ARE HELD TO THE MOST STRINGENT REGULATORY LEVELS. SO MEASUREMENT SCIENCES IS CRITICAL? THAT FIELD DEMONSTRATING PURITY, STABILITY, IDENTITY, VIABILITY OF YOUR NEW MICROBIAL THERAPEUTIC. THESE ARE MEASUREMENT CHALLENGES AND WE TRADITIONALLY DEVELOP NEW MEASUREMENTS IN ADDITION TO DEVELOPING STANDARDS. SO THAT IS SOMETHING WE THINK A LOT ABOUT AND ON THE OTHER SIDE, NIST HAS LOTS OF ENGINEERING AND PHYSICS EXPERTISE AND WE TYPICALLY BUILD NEW DEVICES, NEW INSTRUMENTS. WE HAVE STARTED A NEW RESEARCH PROGRAM THAT IS BUILDING IN-VITRO TOOLS TO MODEL AND UNDERSTAND MICROBIAL COMMUNITY RESILIENCE. SO MY CROW FLUIDIC DEVICES THAT ALLOW US TO INOCULATE SMALL NUMBERS OF BACTERIA AND THEN WATCH HOW THEY BECOME A COMMUNITY AND HOW THEY STABILIZE SO, WE ARE JUST BEGINNING THIS BUT WE HAVE A LOT OF MICROFLUIDIC ENGINEERING EXPERTISE WE ARE LEVERAGING TO BEGIN TO UNDERSTAND HOW MICROBIAL COMMUNITIES BECOME ROBUST OR UNSTABLE OR STABLE AND
–>>THOSE KINDS OF RESEARCH ACTIVITIES THOUGH, BECAUSE YOU’RE PRIMARILY INTRAMURAL ORGANIZATION, YOU DON’T GIVE OUT GRANTS OR — HOW DO YOU PARTNER WITH ACADEMICS AND MEDICAL RESEARCHERS?>>SO, WE OFTEN PARTNER WITH INDUSTRY THROUGH CRADAS. WE PARTNER WITH FDA. A LOT OF US BIOLOGICAL STANDARDS THAT HAVE BEEN DEVELOPED LIKE OUR HUMAN GENOME IN A BOTTLE HAVE BEEN FUNDED BY THE FDA CENTER FOR DEVICES. SO THEY NEED STANDARDS TO HELP THEM REGULATE INDUSTRIES, TYPICALLY DIAGNOSTICS AND THERAPEUTICS SO THEY FUND US TO DEVELOP THOSE STANDARDS. ACADEMIA IS TYPICALLY AN INFORMAL COLLABORATION. ACTUALLY THE GROUP THAT DEVELOPED THE HUMAN GENOMIC REFERENCE MATERIAL, THEY ACTUALLY MOVED THEIR LAB FROM NIST GAITHERSBURG TO STANFORD UNIVERSITY SOY THEY HAVE A NIST LAB ON STANFORD CAMPUS AND IT WAS SPECIFICALLY DONE TO ALLOW YOUNG RESEARCHERS TO ENGAGE WITH NIST EARLY ON THROUGHOUT THEIR CAREER THEY UNDERSTAND WHAT NIST AND IT HAS BEEN VERY SUCCESSFUL SO FAR.>>I HAVE A QUESTION. SO I HAVE HEARD A LOT OF FROM INVESTIGATORS IN ACADEMIA THAT SAY IT IS VERY DIFFICULT TO GET STANDARDS FROM NIS IS T BECAUSE THEY ARE VERY EXPENSIVE AND BUDGE UT DOES NOT NAKE MUCH MONEY FOR GETTING THOSE STANDARDS. THEY WANT TO USE THEM BUT THE COST A MAIN FACTOR. HOW DO YOU DEAL WITH THAT?>>SO TYPICALLY, OUR STANDARDS ARE DEVELOPED FOR INDUSTRY AND INDUSTRY USUALLY DOESN’T HAVE THOSE FINANCIAL CHALLENGES, I GUESS. AS FAR AS THE PRICE GOES, I CAN JUST TELL YOU THAT IT MAY TAKE US 10 YEARS TO DEVELOP A STANDARD REFERENCE MATERIAL. BUT THE PRICE IS BASED ON HOW MUCH IT COST TO MANUFACTURE THAT MATERIAL. SO FOR EXAMPLE, WE ARE MAKING A MIXED PATHOGEN DNA REFERENCE MATERIAL NOW. IT’S COSTING US UNDER $100,000 TO MAKE IT BUT WE’LL SPEND THE NEXT FIVE YEARS CHARACTERIZING IT. SO THE PRICE OF THE MATERIAL IS BASED ON HOW MUCH IT WAS COST TO MANUFACTURE NOT THE R AND D THAT GOES INTO THE CHARACTERIZATION OF THE MATERIAL. THAT’S THE MODEL THAT NIST USED WHEN PRICING. YES, WE HAVE SOME REFERENCE MATERIALS THAT ARE 50,000 DOLLARS FOR A SINGLE UNIT AND SOME THAT ARE MUCH CHEAPER THAN THAT. ANY ACADEMICS WHO HAVE AN ISSUE OF NEEDING A REFERENCE MATERIAL THEY CAN’T GET THEIR HANDS ON. CONTACT A RESEARCHER AT NIST. I’LL MAIL YOU THE MATERIAL. I DIDN’T SAY THAT OUT LOUD. BUT WE WANT PEOPLE UTILIZE OUR MATERIALS AND DON’T WANT TO IMPEDE RESEARCH BECAUSE YOU CAN’T AFFORD T THAT’S THE LAST THING WE WANT TO DO. SO, YES. SO CONTACT A RESEARCHER AT NIS IS T. IF YOU NEED SOMETHING PARTNER WITH THAT RESEARCHER AND COLLABORATE AND I NEED HELP CHARACTERIZING THE REFERENCE MATERIAL THAT WE ARE MAKING SO WHAT WE ARE DOING IS SELECTIVELY GIVING THAT — IT’S A RESEARCH WELL MATERIAL UNTIL WE STAMP IT REFERENCE MATERIAL. SO WE ARE SENDING THAT RESEARCH OUT RESEARCH MATERIAL OUT TO COLLABORATORS AND SAYING, IF YOU SEQUENCE IT, SHARE YOUR DATA WITH US AND THEN THAT’S A CROWD SOURCING WAY OF HELPING US BUILD CONFIDENCE IN WHAT THE MATERIAL IS. IT’S AN INFORMAL INTERLAB STUDY IS WHAT IT IS. SO IT HELPS US BUILD CONFIDENCE IN OUR REFERENCE MATERIALS.>>I WANT TOED SOMETHING. I DON’T KNOW — ERYNN AND MARCUS IS STILL IN THE HOUSE. COULD YOU JUST TAKE A MOMENT AND LET US KNOW IF ANYONE HAS COME IN THROUGH OUR LIVE TWEET? HERE IS JEN. OR GMAIL. ANY QUESTIONS FOR THE PANEL? [ OFF MICROPHONE ] IT’S INTERESTING. IF ANYONE IS STILL ON TWITTER AND IS LISTENING, I HAVE THE FEED IN FRONT OF ME AND I’M HAPPY TO PICK UP A QUESTION.>>I WANT TO MAKE SURE, THANK YOU. I THINK STACEY REMEMBERED HER THIRD THING.>>ACTUALLY IT WAS AS SOON AS SCOTT STARTED TALKING BECAUSE IT WAS ON STANDARDS. SO STANDARD METHODS, STANDARD WAYS OF DOING RESEARCH AND HIV IN THE MICROBIOME I THINK IS AN IMPORTANT AREA THAT WE NEED TO FOCUS ON AS WELL.>>SO JACK HERE AGAIN. I WANT TO ECHO JEN’S SUGGESTION FOR MODELS. SO WE THINK WHERE WE WANT TO BE 5, 10 YEARS FROM NOW IN TERMS OF BETTER BEING ABLE TO ENSURE HUMAN HEALTH, SAFETY, THE SAFETY AND SECURITY OF OUR AGRICULTURE MODELS FOR WHERE ARE THE SOURCES, RESERVOIRS OF THE PATHOGENS, IN THE WILD OR IN OUR AGRICULTURAL SYSTEMS AND HOW DO HUMAN ACTIVITIES, HOW DO NATURAL ACTIVITIES EFFECT THOSE MICROBIOMES AND EFFECT THE STRUCTURES OF THE COMMUNITIES SO WE CAN BETTER MANAGE THE RISKS AND NOT WORRY ABOUT THE NEXT OUTBREAK OF ZIKA OR EBOLA OR SOME OF THESE OTHER THINGS. SO I THINK MODELS ARE VERY IMPORTANT.>>GO AHEAD.>>SO I WAS REALLY STRUCK BY THE THEME THAT CAME OUT TO MANY OF THE TALKS ABOUT THE NEED FOR MORE UNDERSTANDING OF FUNCTIONAL INTERACTIONS BETWEEN MICROBIAL COMMUNITIES AND WITH THE HOST IN THE HUMAN HOST IN PARTICULAR. SO, FROM THE PERSPECTIVE OF MINORITY HEALTH AND HEALTH DISPARITIES, THE HUMAN RESEARCH IS GOING TO BE CRITICAL. AND ONE THING I WOULD SEE AS A GAP FOR US IS UNDER REPRESENTATION OF MINORITY POPULATIONS IN HUMAN MICROBIOME RESEARCH AND THIS IS ALWAYS BEEN A PROBLEM WITH OMICS RESEARCH IN GENERAL. BUT WE WOULD LIKE TO SEE A GREATER REPRESENTATION OF MINORITY POPULATIONS BECAUSE WE KNOW THERE ARE SOME DIFFERENCES IN MICROBIAL THAT MAP TO CONTINENTAL ANCESTRY FOR EXAMPLE. SO EPIDEMIOLOGIC STUDIES, MECHANISTIC STUDIES, PATIENT-ORIENTED STUDIES, ALL OF IT. WE WOULD LIKE TO ENCOURAGE RECRUITMENT OF MINORITIES.>>JUST AS AN OBSERVATION, MAYBE I’M TALKING OUT OF SCHOOL HERE, BUT WHEN THE HMP HAD A SMALL COHORT, 300 PEOPLE, I THINK 10% OR SO WERE HISPANIC AMERICANS AND MAYBE ANOTHER 10 OR 5 OR 10% WERE AFRICAN-AMERICANS. BUT THERE WAS A VERY CLEAR MEAT GENOMIC SIGNAL IN THAT POPULATION BUT THERE WAS A LOT OF PUSH BACK FROM NIH IN GENERAL ABOUT HIGHLIGHTING OR REPORTING THOSE DATA. THERE WAS A SUGGESTION THAT MAYBE WE DIDN’T HAVE ENOUGH POPULATION SCIENCE TO MAKE THESE DECLARATIONS BUT THE SCIENTIFIC DATA WAS VERY CLEAR. SO, PART OF WHAT IS HAPPENING IS I THINK AT NIH MIGHT BE GIVING OUT TWO MESSAGES. DO THESE STUDIES BUT YOU HAVE TO BE SUPER CAREFUL BECAUSE A PRESUMED IT WAS POLITICAL SENSITIVITIES. SO I WANTED TO JUST MAKE THAT COMMENT AS AN NIH PERSON TALKING TO ANOTHER NIH PERSON. SO, I KNOW NOT EVERYBODY AT THE TABLE HERE IS A FUNDING AGENCY. AND I DID PROMISE YOU WE WEREN’T GOING TO TALK ABOUT MONEY, BUT IS THERE ANY — ARE THERE MAJOR OBSTACLES TO TRY TO DEVELOP — JIM GAVE WONDERFUL JOINT AGENCY ACTIVITIES. LIKE THE ECOLOGY OF INFECTIOUS DISEASE. BEEN OUT FOR A LONG TIME. ARE THERE MAJOR OBSTACLES TO BUILDING MORE JOINT AGENCY ACTIVITIES OR IS THAT THE WAY TO GO TO SPAN THIS VERY LARGE FIELD?>>SO, I THINK IT IS THE WAY TO GO. AND I THINK THERE ARE PLENTY OF EXAMPLES. I LOOK AT THE PARTNERSHIPS THAT HAVE COME OUT OF THE BRAIN PROJECT BETWEEN MULTIPLE AGENCIES. WE JUST HAD A MEETING YESTERDAY HERE ON CAMPUS. THE MULTI-COUNCIL WORKING GROUP. AND THE SYNERGIES HAVE BEEN INCREDIBLE. AND I THINK WE CAN DO THAT IN MICROBIOME ALSO. AND I THINK IT’S ALSO A WAY TO CATCH THE IMAGINATION OF THE AMERICAN PUBLIC TO GET DIFFERENT AGENCIES WITH DIFFERENT STAKEHOLDERS WORKING TOGETHER. SO I THINK THAT CAN BE VERY POWERFUL. BUT MOST IMPORTANTLY, I THINK WE HAVE AN OBLIGATION TO LEVERAGE OUR FINITE FUNDS TO MOVE THE SCIENTIFIC NEEDLESS AS EFFECTIVELY AS POSSIBLE AND THE WAY TO DO THAT IS TO WORK TOGETHER.>>AND I WANT TO GIVE THE AUDIENCE AN OPPORTUNITY TO ASK ANY QUESTIONS OF THE PANEL. AGAIN, THIS WAS NOT MEANT TO BE JUST A DISCUSSION AMONG PANELISTS. SO, AS WE CONTINUE OUR CONVERSATION, PLEASE STAND UP AND ASK YOUR QUESTION. JEN?>>THIS IS A QUESTION FROM NATASHA SHELBY. SHE WOULD LIKE TO ASK, WHY ARE THERE SO MANY EXPERIMENTAL DIETS LABELED HIGH-FAT INSTEAD OF HIGH-PROCESSING OR LOW-FIBER? IT MAY SEEM LIKE A MATTER OF SEMANTICS. IT EFFECTS OUR INTERPRETATIONS, MEDIA FALL OUT AND HUMAN ACTION. THERE IS A GREAT BODY OF RESEARCH THAT HIGH-FAT DIETS RESULT IN HIGHLY BENEFICIAL HEALTH 0U9 COMES TREATING EPILEPSIES ONE SPECIFIC EXAMPLE THAT IS WELL PUBLICIZED. WHAT IF THE RESULTS WE SEE IN THESE SO-CALLED HIGH-FAT DIETS ARE THE RESULTS OF HIGH-PROCESSING LOW FIBER AND ARE NOT THE CONTENT OF FAT? IS THERE VALUE IN BEING MORE CAREFUL WITH HOW WE LABEL THESE TREATMENTS AND INTERPRET THESE RESULTS?>>I’M NOT SURE IT’S NECESSARILY A QUESTION FOR THE PANEL SO MAYBE I’LL JUST RESPOND TO IT QUICKLY. I THINK THERE ARE OTHER STUDIES LOOKING AT OTHER DIETARY COMPONENTS OF A NORMAL DIET. HIGH-FAT SEEMS TO BE ONE OF THE MORE COMMON ONES. SO WHOMEVER ASKED THE QUESTION, I THINK YOU CAN TAKE HEART THERE ARE MANY OTHER KINDS OF DIET AND MICROBIOME STUDIES.>>LISTENING TO YOU TALK IT’S COOL SEEING ALL THE COMMON INTERESTS ACROSS THESE VARIOUS AGENCIES AND THINGS. IT ALSO SEEKS LIKE AN AMAZING OPPORTUNITY TO LAUNCH PROJECTS THAT MAYBE WOULDN’T BE SO EASIED AND ONE I THINK I’M INVOLVED IN, NASA PROJECT WHERE THEY ARE PROFILING TWO TWINS, ONE ON SPACE AND ONE ON THE GROUND AND SPACE STATION IS VERY CONTROLLED ENVIRONMENT. SO LISTENING TO THE SUBMARINE ENVIRONMENT IS A PRETTY COOL OPPORTUNITY TO BE SOME NOT OPEN-ENDED IN THE NEW TRICIAN SIDE OF THINGS IN THE FOOD SIDE. SO, IT DOES SEEM TO THE EXTENT THAT WE CAN TAKE MORE ADVANTAGE OF THOSE SITUATIONS AND I DON’T KNOW IF YOU ACTIVELY SEEK IS THAT OUT OR HOW DOES THAT WORK? PROBABLY FOR EACH OF THESE AGENCIES THERE MUST BE SOME NICHE THAT IS VERY SPECIAL THAT MAKES A VERY INTERESTING EPERIMENTAL SITUATION THAT WE SHOULD TRY TO CAPTURE. I USE THE SUBMARINE AND I THOUGHT IT WAS A GREAT IDEA.>>WE PROBABLY WON’T BE ABLE TO DO THAT BUT WE THINK OF DOING — FOR EXAMPLE, HAVING A RESEARCH STUDY ON A SUBMARINE DURING A MISSION IS NOT GOING TO HAPPEN FOR OBVIOUS REASONS. BUT WE DO THINK ABOUT EXPOSURE CHAMBERS WHERE YOU CAN CONTROL DIFFERENT PARAMETERS OF THAT ENVIRONMENT AND SORT OUT THOSE DIFFERENT STRESSORS. THEY ARE VERY EXTENSIVE STUDIES AND WE ARE AT THE FRONT END OF TRYING TO FIGURE OUT WHAT WE MIGHT WANT TO DO IN THAT SPACE AND IT WOULD PROBABLY BE ACROSS SERVICE EFFORT BECAUSE THE DIFFERENT AGENCIES FOR EXAMPLE WE MAY BE INTERESTED IN HIGH OXYGEN AND ELEVATED CO2 AND ANOTHER AGENCY OR PART OF THE DEPARTMENT OF DEFENSE MIGHT BE INTERESTED IN LOW OXYGEN SO WE PROBABLY WILL FORMULATE A SUITE OF STUDIES THAT COULD LOOK AT THESE THINGS IN CONTROLLED ENVIRONMENTS.>>SURE. THAT WOULD BE TERRIFIC AND FYI, ONE OF THE THINGS WE DISCOVERED IS THAT PEOPLE’S BLOOD OXYGEN DROPS ON AIRPLANES AND SO THAT IS VERY INTERESTING OPPORTUNITY AS WELL WHERE YOU MIGHT HAVE A WHOLE BUNCH OF PEOPLE. I DON’T SEE THE AIR FORCE REPRESENTED HERE BUT AGAIN ANOTHER VERY – AUDIO YOU REPRESENT THAT TOO? COOL. AGAIN, THERE IS SOME VERY INTERESTING SITUATIONS THAT COULD HAVE IMPLICATIONS FOR THE GENERAL POP UPON POPULATION AS WELL.>>SO THROUGHOUT THE MEETING, WE TOUCHED ON TOPICS REGARDING ETHICS OF MICROBIOMES BASED THERAPEUTICS AND YOU MENTIONED NEED TO SAMPLE UNDER REPRESENTED GROUPS AND POPULATIONS AND SO ON IN THESE STUDIES. I’M WONDERING IF IN THE BUDGET OR PLANNING OF THIS PROTECT JEC, YOU ARE TRYING TO IN CORPORATE 8 THE POTENTIAL ETHICAL IMPACTS OF THE TECHNOLOGIES THAT ARE BEING DEVELOPED?>>SO LITTLE SAY IN FM26789 YOU HAVE A STOOL COLLECTION COMING FROM ALL THESE PEOPLE AND THEN PEOPLE DOING IT AT HOME BECAUSE WE HAVE A TECHNOLOGY THAT IS BEING DAWNED AND IS BEING PROVEN TO BE VERY EFFICIENT AND NO INFRASTRUCTURE IN THE RESEARCH TO LIKE QUICKLY IMPLEMENT IT OR MAKE SURE IT IS REGULATED IN AN EASY WAY. SO I DON’T KNOW WITH THE PROJECTS BEING FUNDED YOU’RE FORESEEING THE POTENTIAL IMPACT OF SOME OF THESE THINGS THAT ARE BEING PRODUCED.>>SO I’M GOING TO STOP YOU THERE. JUST FOR A MINUTE. I HAVE NOTHING TO SAY ABOUT FUNDING. WE DON’T FUND BUT FMT IS BEING REGULATED. AND WE ARE DOING A LOT OF THINGS. WE SEE A LOT OF FMT FILES COMINGS IN. I HEARD IT ONCE BEFORE AND YOU JUST SAID IT NOW THAT FMT IS NOT BEING REGULATED AND THAT’S NOT TRUE. IN TERMS OF C.DIFF AND MANY OTHER APPLICATIONS. FOR C.DIFF WE HAVE POLICY ENFORCEMENT DISCRETION BUT THAT DOESN’T MEAN PEOPLE AREN’T DOING STUDIES FOR THAT INDICATION AS WELL.>>IF I COULD SAY MORE ABOUT THAT TOO. THAT IS AN ENFORCEMENT DISCRETION FOR MULTIPLY RECURRENT C.DIFF ONLY IN WHICH THE PATIENT SHOULD BE CONSENTED AND EXPLAINED THAT IT IS EXPERIMENTAL AND ANY OTHER USE EVER FMT, IT IS A DRUG AND IND SHOULD BE OBTAINED AND I KNOW THAT WE FUNDED A COUPLE OF PROJECTS WHERE AN IND WAS OBTAINED TO DO A STUDY SPECIFICALLY WITH FMT. BUT I THINK THE QUESTION AT LARGE IS STILL A GOOD ONE THAT IN THE GENERAL SENSE YOU’RE TRYING TO SAY THESE THINGS ARE AVAILABLE. IT’S A LITTLE DIFFERENT FROM THATS SINCE WITH A DRUG. MOST OTHER DRUGS YOU CAN’T MAKE UP IN YOUR KITCHEN OR CAN’T GO TO THE BATHROOM AND PRODUCE IT. SO, AND THEN ALSO JUST THE VERY FACT THAT THERE IS MICROBES ALL AROUND AND SO, THAT TOUCHES ON IP ISSUES AND ALSO TOUCHES ON REGULATION ISSUES AND IT IS PROBABLY BEYOND THE SCOPE OF THIS MEETING. BUT THERE ARE — I KNOW THAT NIH FUNDED AND I DON’T KNOW WHICH GROUP. I CAN’T REMEMBER. SOMEONE ELSE CAN SPEAK UP TO IT. BUT AS FUNDED ALSO LOOK AT THE ETHICAL OR NOT THE — REGULATORY FRAMEWORK OF PROBIOTICS FOR EXAMPLE, AND FMT. AND THERE IS OTHERS IN THE AUDIENCE WHO CAN TELL US.>>I THINK IT MIGHT BE — SO THERE IS A ETHICAL, LEGAL SOCIETAL IMPLICATION PROGRAM IN MY INSTITUTE, NATIONAL HUMAN GENOME RESEARCH INSTITUTE. AND THEY DID THE REGULATORY FRAMEWORK OF PROBIOTICS FUNDED NETWORK AND I KNOW THERE ARE GROUPS WITHIN THE LC. THE LC COMMUNITY THAT ARE STUDYING THOSE VERY TOPICS. IT MAY BE ALSO BEING FUNDED BY OTHER INSTITUTES LIKE NIAID BUT I’M AWARE OF SEVERAL INVESTIGATORS WITHIN THE MC PROGRAM AT MY INSTITUTE. MIKE?>>SO, WE FUNDED FIVE CENTERS LAST YEAR AND FOCUS ON VARIOUS ASPECTS OF PREDICTION MEDICINE. ONE I MENTIONED STANFORD. ALL OF THEM, ONE OF THE PRIORITIES OF THE INITIATIVE WAS TO LOOK AT THE ETHICS AND ACCEPTABILITY AND FEASIBILITY OF IMPLEMENTING PRECISION MEDICINE APPROACHES IN DISADVANTAGED POPULATIONS, MINORITY POPULATIONS. SO THEY ARE ALL LOOKING AT THAT IN VARIOUS WAYS. THAT SELL VERY IMPORTANT POINT.>>THANK YOU.>>I HAVE A COMMENT. SO I THINK THE BIGGEST CHALLENGE OR THE GAP IS ACTUALLY FIND OUT HOW THE MICROBIOME SHOULD LOOK LIKE. WE KNOW THERE IS FOR CHRONIC DISEASES RELATED TO THIS BIOLOGIC GUT MICROBIOTA, IT’S NOT GAIN OF FUNCTION LIKE INFECTION. IT IS ACTUALLY A LOSS OF FUNCTION. SO YOU HAVE LOST THE PROTECTIVE MICROBIOTA SO THAT YOU MAY HAVE SOME PATHOGENIC OR DETRIMENTAL BACTERIA OVER GROWING AND YOU NEED THIS ANTIBIOTIC AND IT MAY BE DRIVING VARIOUS CHRONIC DISEASES OR CONTRIBUTING TO IT. SO WE SHOULD PROBABLY CHANGE OR SHIFT FROMCENTRIC TO HEALTHCENTRIC. SO LOOK AT HOW FROM THE VERY BEGINNING OF LIFE, AND AT VARIOUS STAGE, HOW MICROBIOTA SHOULD LOOK LIKE AND WHAT IS THE NORMAL VARIATION OF THE STRUCTURE AMONG CLINICALLY DEFINED HEALTHY PEOPLE? AND THEN USING THAT AS A STANDARD OR REFERENCE. AND THEN COMPARE THAT WITH THE DISEASE POPULATIONS AND IDENTIFY TARGETS.>>SO, NSF’S SBE DIRECTORATE ASSOCIATE BEHAVIORAL AND ECONOMIC SCIENCES, IS VERY INTERESTED IN THAT SO OUR PERSPECTIVE ON A LOT OF THESE ISSUES IS UNDERSTANDING THE HEALTHY. AND THAT’S QUITE DIFFERENT FROM THE DISEASE PERSPECTIVE BUT IT’S VERY COMPLEMENTARY TO WHAT GOES ON AT NIH. AND IT CERTAINLY FALLS INTO THE NOTION OF WHAT WE SEE AS OUR WHEEL HOUSE IN TERMS OF UNDERSTANDING BASIC MECHANISMS.>>THANK YOU VERY MUCH. AND ANOTHER VERY QUICK COMMENT IS THE WHOLE FIELD PROBABLY NEED TO BRING MORE MY CROW BIOLOGISTS AND PARTICULARLY MICROBIAL ECOLGISTS INTO THE MICROBIOME RESEARCH. THAT WILL BENEFIT A LOT.>>TWO QUESTIONS. SO, ONE IS THAT A LOT OF INDIVIDUALS SHOWED THAT A BIG GAP IS BEING ABLE TO BRING A LOT OF THIS MICROBIOME RESEARCH TO HUMANS. AND PART OF THAT PROBLEM — I MEAN THERE ARE LOTS OF CHALLENGES TO THAT BUT PART OF THAT PROBLEM IS THAT THE PRO DIFFERENT FROM WHAT ANOTHER LAB WILL USE WHICH MAY BE DIFFERENT FROM ANOTHER LAB. ALTHOUGH WE HAVE RELEGATED PROBIOTICS TO THE REALM OF SUPPLEMENTS, IS IT TIME TO CHANGE THAT AND MAKE THAT MORE STANDARD? SO WE CAN GET SOME ANSWERS? THAT’S NUMBER 1. AND NUMBER 2, A LOT OF — ANOTHER GAP PEOPLE BROUGHT UP IS SHOWING MECHANISTIC RELATIONSHIPS. AND A LOT OF INDIVIDUALS WHO SPOKE ARE SHOWING THAT THROUGH ENGINEERED BACTERIA, IN WHICH CASE THE QUESTION IS, HOW WILL THAT FINALLY TRANSLATE INTO HUMANS? IS THERE A PLAN FOR — LIKE WHAT DOES ENGINEERED BACTERIA THERAPY LOOK LIKE IN HUMANS IN TERMS OF WHAT REGULATIONS THEY HAVE TO GO THROUGH?>>SO I CAN TAKE THE SECOND ONE. I THINK IT’S GOING TO DEPEND ON WHAT THE ORGANISM IS AND WHAT THE MODIFICATION IS. BUT EVERYTHING WILL BE REVIEWED BASED ON THE SCIENCE. THERE IS NOT — NO DIRECTIVE THAT SAYS NO, WE CAN’T HAVE GENETICALLY MODIFIED ORGANISM. THERE MIGHT BE A LITTLE MORE WORK THAT HAS TO BE DONE DEPENDING ON WHAT THE MODIFICATIONS ARE. BUT I DON’T SEE ANY MAJOR BABEIERS TO GETTING SOMETHING THROUGH.>>AND THOSE ARE NOT REALLY — THE IL10 PRODUCING — HAS BEEN AROUND A LONG TIME AND SOME OF ISSUES HAVE BEEN ADDRESSED. INITIALLY BUT –>>I CAN TAKE A STAB AT THE FIRST QUESTION TOO. REGARDING REGULATION OF PROBIOTICS. SO, ONE OF THE THINGS THAT I WANT TO POINTS OUT JUST SOME PEOPLE IT’S NOT CLEARS AS YOU MENTIONED PRO BY OATICS AND SUPPLEMENTS ARE REGULATED BY THE CENTER FOR FOOD SAFETY FDA. AS OOH POSED TO THESE EMERGING LIVE MICROBIAL THERAPEUTICS, WHICH IS REGULATED AT A MUCH HIGHER STRIPIGENCEY BY THE CENTER FOR BIOLOGICS THAT PAUL REPRESENTS. — STRINGENT SEE. ONE OF THE THINGS THAT — SO IN A PREVIOUS LIFE BEFORE I JOINED NI ST, I WORKED FOR — FOR 11 YEARS. ONE OF THE THINGS WE LOOKED AT 2014, IS LOOKING AT PROBIOTICS MORE CLOSELY THEIR IDENTITY AND THEIR VIABILITY. WHAT WE FOUND IS THAT OFTEN TIMES THEY WEREN’T WHAT THEY WERE LABELED. SO 10 TO THE 10th ACTIVE CULTURE WAS SOMETIMES 10 TO THE 6th AND SOMETIMES THERE WEREN’T THE SPECIES THEY WERE LABELED ON THE SIDE OF THE TUBE. BECAUSE THERE WERE NO CLAIMS BEHIND PROBIOTICS, THEN AS LONG AS THEY ARE SAFE, THAT’S REALLY THE ONLY REGULATORY CRITERIA. PAUL IS LOOKING SIDEWAYS AT ME.>>SO THE ONE THING I’LL ADD IS THAT IF YOU’RE USING AN OFF THE SHELF PRO BIOTIC TO TREAT A DISEASE INDICATION, IF IT’S BEING USED AS A DRUG, THAT STILL HAS TO BE DONE UNDER IND. JUST BECAUSE IT’S AVAILABLE AT WHOLE FOODS AND IT’S OUT THERE AS A SUPMINUTE DECENT MEAN YOU CAN JUST GO AHEAD AND USE IT IN A TRIAL AGAINST C.DIFF OR AGAINST SOMETHING ELSE. SO IF IT IS USED TO TREAT, PREVENT, CONTROL, MITIGATE DISEASE IN HUMANS, IT IS CONSIDERED A DRUG. SO IT DOES STILL HAVE TO COME THROUGH AND GO UNDER IND.>>I GUESS I WAS REFERRING DAILY USE OF PROBIOTICS, LIKE I TAKE A PILL EVERY MORNING. IT’S JUST A SUPPLEMENT. THE LAST THING I’LL SAY, IS U.S. PHARMACOPEIA DEVELOPS STANDARDS FOR THE PHARMACEUTICAL INDUSTRY STARTED A PANEL ON PROBIOTICS ON THE DEVELOPMENT OF PROBIOTICS STANDARDS. HOW DO YOU DEMONSTRATE PURITY,ITEY STABILITY OF YOUR PROBIOTICS AND VIABILITY. THESE THINGS WERE REALLY UNWRITTEN PREVIOUSLY AND I KNOW WHEN THESE FLEW PHARMACEUTICAL COMPANIES CAME IN TO EXISTENCE, THEY LOOKED TOWARDS THE PRO BIOTIC INDUSTRY FOR STANDARDS. HOW DID YOU ENSURE YOUR MANUFACTURING PROCESSES AND THINGS DIDN’T REALLY EXIST AT LEAST NOT IN A WELL DEFINED WAY. SO U.S. S DEVELOPING NEW STANDARDS FOR THE MANUFACTURING AND PROBIOTICS AND I KNOW TO A HIGHER REGULATORY LEVEL SIEBER IS AS WELL.>>AND MUCH MORE MUNDANE LEVEL, STANDARDS OF COURSE ARE EXTREMELY IMPORTANT BUT IN CLINICAL RESEARCH WE CAN’T EVEN GET BLOOD PRESSURE MEASURED THE SAME WAY IN TWO DIFFERENT SEATTLE ASY EN WHITE POINTED OUT IN HIS PRESENTATION. — IN TWO DIFFERENT SEATTLE. OWEN WHITE. IN ORDER TAKE THIS INTO HUMANS, IT HAS TO GET DISCIPLINED ABOUT MEASURING ALL KINDS OF THINGS.>>WE’RE NOT COLLECTING OR AGREEING ON THE SAME TERM FOR COMMON PROPERTIES SO IF YOU WANT TO DO COMPARATIVE STUDIES YOU CAN’T DO IT BECAUSE YE ARE FLOTUSING THE SAME TERMINOLOGY FOR A PARTICULAR PROPERTY THEY IS TRUE FOR OCEAN STUDIES, TRUE FOR SOIL STUDIES AND TRUE FOR HUMAN STUDIES. I CHAIR A GROUP THAT HELPED TO BUILD THIS WORKSHOP, TRANS-NIH MICROBIOME WORKING GROUP AND I WANT TO START A DIALOGUE WITH THEM ABOUT ENCOURAGING THEIR PIs AND PUTTING IN THEIR RFAs REQUEST, MAYBE NOT REQUIREMENT BUT REQUEST THEY INCLUDE A MINIMUM SET OF METADATA WITH THESE COMMON STANDARDS AND MAYBE THAT WILL HELP TO START TO BUILD THE ETHIC OF UTILIZING COMMON TERMS ACROSS COMMON STUDIES.>>I WONDER IF WE COULD GET NCATS TO PARTNER ON THAT THROUGH THEIR CTS.>>LET’S DO THAT. I’LL FIND A WAY TO GET THAT INFORMATION OUT. THANK YOU. AND ROB WAS IN LINE.>>STOW ROB, BAYLOR COLLEGE OF MEDICINE. SO HMP2 KICK OFF I MADE A PLUG FOR EPIGENETICS. AND I THINK THE COMMENT REALLY IS METAGENOMICS, REALLY NEAT ASSOCIATION ASSOCIATIONS AND NEW GENES WE ARE FINDING TO GET TO THE MECHANISM YOU NEED GENETICS IT’S ALMOST LIKE MICROARRAYS 20 YEARS AGO. PEOPLE WRITING PARENTS AND MAKING CONCLUSIONS AND FINDING OUT LATER WHEN THEY DID THE FOLLOW-UP EXPERIMENTS THEY WERE WRONG. AND I FEEL LIKE WE REALLY ARE GOING TO NEED TO HAVE A COMMUNITY-BASED EFFORT NOT JUST PEOPLE LIKE ME WHO DEVELOP IT FOR MY ONE BUG BUT REALLY IDENTIFY THE 20, 40, 50 ORGANISMS WE WANT TO DEVELOP GENETIC TOOLS. THERE IS ENOUGH TALENT IN THIS LOOM AND IN THIS FIELD IF WE HAD A CONCERTED EFFORT WE COULD BUILD THE TOOLS THAT WOULD REALLY HELP US MOVE FROM REALLY INTERESTING AND NEAT ASSOCIATIONS FROM ALL THIS TECHNOLOGY WE BUILD AROUND SEQUENCING AND GET US TOW THE FUNCTION. BECAUSE THAT’S WHAT YOU ALL WANT TO PUT IN PEOPLE BUT WE REALLY — WE DON’T NEED TO KNOW THE FUNCTION FOR EVERY DRUG WE FAKE BUT THAT WILL HELP US GET TO ANSWERS IN THE MICROBIOME FIELD BECAUSE THESE ARE LIVING ENTITIES NOT CHEMICALS.>>AND JACK, THE AG ROW NOMIC FIELD WITH LOOKING NOW TRYING TO REDISCOVER WHAT THE MICROBIOME IS OF CROP PLANTS, THAT SAME ARGUMENT MUST BE MADE IN YOUR COMMUNITY AS WELL.>>AND THE ADVANTAGE EVER WORKING AGRICULTURALLY IS WE CAN DO THE EXPERIMENT OVER AND OVER AGAIN AND CHANGE THE VARIABLES SO THE ADVANTAGE OF USING GENETICS AND GERM PLASM OF DIFFERENT ENVIRONMENTS OF MANIPULATING CULTURES IS VERY POWERFUL. SO THINK ABOUT ANIMAL AND CROP SYSTEMS.>>SO MATT IN SERIES THERAPEUTICS. I GUESS I HAVE MORE OF A COMMENT THAN A QUESTION. SOMETHING I HAVE BEEN REALLY STRUCK BY OVER THE PAST THREE DAYS IN LISTENING TO PEOPLE EXPLAIN GAPS AND THIS CONVERSATION IT’S COME — I REALIZED THERE IS A BIGGER GAP HERE THAT I HAVEN’T HEARD BROUGHT UP WHICH IS HOW WE ACTUALLY WORK TOGETHER. AND WHAT I MEAN BY THAT IS THAT THE GAPS THAT WE ARE HEARING ABOUT WE HAVE BEEN HEAR BEING FOR YEARS. I HAVE BEEN ON THE ACADEMIC SIDE FOR THE MAJORITY OF MY CAREER. I HELPED LAUNCH SERIES ABOUT FIVE YEARS AGO. SO I HAVE BEEN ON THE INDUSTRY SIDE NOW FOR A HAND 68 OF YEARS AND I CAN TELL YOU THAT ALL THESE THINGS WE HEARD OVER THE PAST SEVERAL DAYS ARE GAP THAT IS JUSTED KEEP COMING UP. AND I THINK THE REASON WE ARE NOT SOLVING THIS IS FOR A COUPLE OF REASONS. NUMBER 1 I THINK WE HAVE TO GET GOOD GOVERNMENT ACADEMIC AND INDUSTRY PARTNERSHIPS GOING BECAUSE THESE ARE HUGE PROBLEMS THAT REQUIRE A LARGE AMOUNT OF MONEY AT NO ENTITY ON ITS OWN CAN SUPPORT INDEPENDENTLY. BUT TO MAKE THAT SUCCESSFUL, WE NEED TO STOP TALKING ABOUT THE GAPS AND DEFINE ATTAINABLE MILESTONES AND STEPS TO MOVE THE PROGRESS FORWARD THAT WE CAN BEVERAGE MARK OURSELVES AGAINST BECAUSE THAT IS WHAT I’M NEVER HEARING IN ANY CONVERSATIONS IS WHAT ARE THE SPECIFIC MILESTONES WE WANT TO ACHIEVE AND ACCOMPLISH AS WE MOVE THE BALL FORWARD. SO I GUESS I’D PUT A CHALLENGE OUT TO THIS WHOLE GROUP TO SAY, CAN WE GET A FORUM TOGETHER? CAN WE GET SOME WORKING GROUPS TOGETHER TO WORK TO DEFINE VERY TANGIBLE ATTEMPTS OR MILESTONES THAT WE WANT TO ACHIEVE? THAT IS HOW YOU’RE GOING TO GET ALIGNMENT OF EVERYBODY AND HOW YOU’RE GOING TO GET THE INVESTMENT FROM ALL THE DIFFERENT SECTORS TO MOVE THE BALL FORWARD. SO THAT’S IT.>>I MEAN, I THINK YOU’RE DEAD RIGHT. YOU MIGHT DECIDE THIS IS LIKE A GOVERNMENT JARGON OR WHATEVER, BUT THIS MORNING AT 9:42, I GOT AN E-MAIL STATING THAT THERE IS A GROUP THAT FORMED AMONG THE GOVERNMENT SIDE OF THE NATIONAL MICROBIOME INITIATIVE, THE INNER AGENCY WORKING GROUP. I MENTIONE THEM. MANY OF THE PEOPLE HERE AT THE TABLE ARE MEMBERS. I GOT AN E-MAIL THIS MORNING SAYING WE NEVER GLOTT OUR STRATEGIC PLAN APPROVED BY OSTP BECAUSE OF CHANGE IN ADMINISTRATION BUT THE E-MAIL SAID OUR CHARTER HAS BEEN EXTENDED TO THE END OF DECEMBER. WHICH IS GREAT BECAUSE THAT MEANS IT GIVES US MORE TIME TO GET THE PLAN APPROVED AND THE REASON YOU SHOULD CARE IS IN ORDER FOR US TO WORK TOGETHER, WE HAVE TO HAVE THE CHARTER. WE HAVE TO HAVE LIKE PERMISSION IF YOU WILL, OR THE WAY PAVED. AND I THINK NOW MAYBE WE ARE CLOSER TO WORKING TOGETHER AS AGENCIES AROUND THIS COMMON NEED. SO, THAT ACTUALLY IS A GOOD THING THAT JUST HAPPENED TODAY.>>SO I KNOW THAT ONE OF THE PASSIONS OF MY BOSS, DR. FRANCE CORDOVA, IS PUBLIC PARTNERSHIPS. AND IN BIOLOGICAL SCIENCES DIRECTORATE AT NSF, WE ARE PROUD AND HAVE A LOT OF THEM. THE ONE I’D LIKE TO TALK ABOUT THE BREAD PROGRAM THAT WE DO WITH THE BILL AND MELINDA GATES FOUNDATION. WHERE WE ARE PARTNERING IN PRACTICAL APPLICATIONS OF RELEVANT PLANT BIOLOGY, AGRICULTURE APPLIED SCIENCE FOR DEVELOPING COUNTRIES THAT ARE IN DISTRESS WITH REGARD TO FOOD BUT THESE PARTNERSHIPS, THERE IS A LOT OF HOUSE OF NO IN GOVERNMENT ABOUT MAKING THOSE WORK. AND WHAT I’M REALLY PLEASED ABOUT IS THAT MORE RECENTLY, THERE IS A TENDENCY TO SAY, OKAY, LET’S FIGURE OUT WHAT WE NEED TO TWO TO GET THOSE PARTNERSHIPS TO WORK. NOT ONLY BETWEEN GOVERNMENT AND PRIVATE PHILANTHROPIC FOUNDATIONS BUT GOVERNMENT AND INDUSTRY. SO I’M CAUTIOUSLY OPTIMISTIC WE MAY BE TURNING THE CORNER THERE.>>I WANTED TO ECHO THE COMMENTS ON THE PANEL JUST THE LAST FEW MINUTES ACTUALLY. I LEAD THE PROGRAM AT MICROBIOME PROGRAM AT D-NA GENOTECH AND ONE ROLE FOR INDUSTRY POTENTIALLY IS IN THE CREATION AND BROAD DISSEMINATION OF TOOLS. A LOT OF THE ACADEMICS AND PIs AREN’T FUNDED TO DEVELOP THESE THINGS AND GET THEM BROADLY AVAILABLE BUT THAT IS IT A ROLE INDUSTRY IS KEEN TO PLAY AND I’M GLAD WE ARE HAVING THIS DIALOGUE NOW ON THAT THEME. MAYBE A PROVOCATIVE QUESTION FOR THE GROUP. DO YOU THINK IT IS READY TO ELEVATE MICROBIOME TO A LEVEL ALL OF US KIND OF STUDY OR ALL OF OUR BUGS STUDY?>>LIKE WE WERE TALKING ABOUT A FOOD-OHM PROJECT WHICH WOULD UNDER SECRETARY THERE. I SUSPECT WE WILL GO IN THAT DIRECTION WITH ALL OF US — I SUSPECT F A LARGE NATIONAL RESEARCH CORE WAS TO BE MOUNTED IS AND THEY WANTED TO INCLUDE A MICROBIOME COMPONENT, THE QUESTION TO ME WAS, WHAT SAMPLE, WHAT SHOULD THEY COLLECT? THEY ARE NOT SURE WHAT THEY WOULD DO IT WITH IT YET BUT THEY DON’T WANT TO MISS AN OPPORTUNITY TO HAVE A SAMPLE FROM THE SUBJECTS TO BE ABLE TO DO A MICROBIOME ANALYSIS. THE FIRST ONE THAT WAS POSED WAS SALIVA AND I SAID, NO. I SAID SA LEAVA IS EASY. BECAUSE DEPENDING ON YOUR AGE, GENDER, WHAT YOU EIGHT HOW DEHYDRATED YOU ARE, HOW WELL YOU BRUSHED YOUR TEETHED, THAT SALIVA SAMPLE WILL HAVE A LOT OF NOISE IN IT. BUT THEY — THE IT’S EASY, WE ARE ALREADY PLANNING. CAN WE JUST DO LEVERAGE ON MICROBIOME COMPONENT. SO ANYBODY CAN ANSWER THIS QUESTION. SO IF YOU WERE TO MOUNT A NATIONAL RESEARCH COHORT, AND YOU WANTED TO HEAD YOUR BET AND BANK A BODY SAMPLE TO BE ABLE TO DO MICROBIOME ANALYSIS DOWN THE ROAD AND ALL THESE AGENCIES ARE THINKING ABOUT THIS. WHAT WOULD BE THE MOST USEFUL ONE? IT SOUNDS SIMPLE BUT WHEN YOU THINK ABOUT IT, IT GETS VERY COMPLICATED. ANYBODY WANT TO TACKLE THAT ONE? LET’S START WITH HUMANS. THIS IS THE HUMAN MICROBIOME WORKSHOP. S IS AUTOMATICALLY SAY STOOL? AUTOMATICALLY SAY STOOL.>>I JUST HAD A STUDY MEETING ON TUESDAY WEDNESDAY AND THAT WAS RELATED WITH ENVIRONMENTAL INFLUENCES ON CHARITABLE OUTCOMES WHICH IS 165 MILLION DOLLAR PROGRAM BY NIH FOR 7 YEARS AND LOOKING FOR THE OUTCOME OF CHILDREN WHO HAVE NEURODEVELOPMENT PROBLEMS OR ANY OTHER KINDS OF PROBLEMS AND LOOKING FOR MICROBIOME, THE ONLY CENTER WHICH SHOULD BE COLLECTED FROM PRENATAL AS WELL AS POSTNATAL DIFFERENT STAGES IS THE STOOL SAMPLE.>>THAT WAS EASIER THAN I EXPECTED.>>I STUDY THE ORAL MICROBIOME AND I WANT TO CHAMPION SALIVA AS BEING MICROBIAL SAMPLE AND IT HAS SERUM AND OTHER BIOMARKERS. THERE IS A LOT OF WORK ALREADY USING SALIVARY SAMPLES AS BIOMARKERS FOR ALL KINDS OF DISEASES SO THERE IS A LOT OF EFFORT ALREADY PUT INTO THAT ALREADY. SO, AND IT’S EASY TO COLLECT. SO –>>BUT IF WE HAD SOMEBODY HERE FROM NIDCR, HE WOULD TOTALLY SHOOT THAT DOWN AND THEY RESPONDED JUST LIKE YOU DO. SO I’LL REPORT BACK THAT WE HAVE A CHAMPION FOR SALIVA AND APARENTEDLY MORE CHAMPIONS FOR STOOL. I THINK I SHOULD WRAP IT UP IF YOU DON’T MIND. I’M NOT SURE I’LL BE ABLE TO RECOLLECT EVERYTHING THAT I HEARD BUT I HEARD A LOT ABOUT THE NEED FOR MORE TRAINING, MORE TRAINEES, MORE RESEARCHERS IN THIS FIELD. I HEARD THE NEED FOR TRYING TO MOVE TO UNDERSTANDING THE FUNCTIONAL PROPERTIES OF THE MYCOBIOME AND THAT WOULD REQUIRE DEEPER DIVES INTO THE MICROBIAL MEMBERSHIP THROUGH UNDERSTANDING THE INDIVIDUAL MEMBERS OF THE MICROBIOME THROUGH HAVING GENETIC TESTS OR GENETIC MODELS FOR UNDERSTANDING THESE MICROBES. HELP ME RECOLLECT ALL THE MAJOR THEMES THAT CAME OUT HERE. MODELING WAS A BIGGIE AND THAT MIGHT BE A REALLY REAL OPPORTUNITY BETWEEN NS. AND NIH BECAUSE THERE IS NOT A LOT OF MODELING THAT HAPPENS AT NIH AND I THINK THE NIH COMMUNITY COULD BENEFIT FROM MODELING APPROACHES. AND TALKING ABOUT COINING A MODEL, THERE IS A CALL FOR ALTERNATE MODELS BESIDES MOUSE OR MACAQUE. I THINK THERE WAS A LOT OF DISCUSSION YESTERDAY ABOUT THAT. THE NEED FOR STANDARDS. THEY NEED TO BE MORE INCLUSIVE IN OUR FORWARD STUDIES BY GENDER OR BI-RACIAL AND ETHNIC GROUPS. HAVE I COVERED THE MAIN THEMES?>>CAN I ADD ONE THING I DIDN’T SEE IN THE PRESENTATIONS, THE REPORTING OF THE SEX IN THE DATA. BECAUSE ONLY FEW PRESENTERS SAID THEY MENTIONED LIKE WHAT KIND OF SECTION –>>YES.>>LIKE ONE PERSON MENTIONS AND A FEW OTHER BUT OTHERWISE PEOPLE ARE STILL NOT REPORTING AND AS I HAVE SHOWED YOU IN MY PRESENTATION THERE IS A BIG DIFFERENCE BETWEEN MALES AND FEMALES.>>UH-HUH. AND I WOULD AGREE WITH THAT AND I WOULD ALSO AGREE THAT MAYBE ANOTHER GAP THAT SHOULD BE ADDRESSED IS AGREEING AS A COMMUNITY TO WHAT WE CALL A PARTICULAR PROPERTY SO WE COULD COMPARE ACROSS STUDIES. THAT’S A BIG CHARGE TOO. I’M PROBABLY MISSING A BIG ONE. ANYBODY WANT TO CALL IT OUT? NO? THANK YOU EVERYBODY. REALLY APPRECIATE IT.


5 thoughts on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century (Day 3)

  1. at birth: HEP B shot against sexual diseases and for IV drug users … WHAT THE FXxx
    + antibiotics in the EYES !

    do parents know this ?

    population control from birth

  2. is this 5 hours of problems and ZERO SOLUTIONS ? every speaker brings an aspect but nothing what to do about it …. is this a funding charity video ?

Leave a Reply

Your email address will not be published. Required fields are marked *