Presentation on theme: "Introducing the Microbiome"— Presentation transcript:
1 Introducing the Microbiome Dr Ailsa HartDirector IBD Unit, Consultant Gastroenterologist, St Mark’sHonorary Senior Clinical Lecturer, Imperial College
2 Introduction What is the gut microbiome? How does the gut microbiome play a role in disease?- role in inflammatory bowel diseaseHow can we modulate the gut microbiota as a therapy- faecal transplant
3 The gut microbiota 1014 gut bacteria and 1013 cells in body Most densely populated ecosystem on Earth4 major phyla (Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria)Provide traits we have not had to evolve on our own“Virtual” organGenes in gut flora 100 times our own genomeMostly anaerobic, steep stomach acid driven proximal distal gradient
4 Function of gut microbiota Germ-free animalsExist and surviveBut abnormalities of:Immune function (oral tolerance)Metabolic function (altered enzymes)Physiological function (altered motility)Trophic function (altered cell turnover)What is the function of the gut flora – well much can be deduced from studies in germ free animals – These animals exist and survive indicating that the gut flora is not a prerequisite for life but the animals do have profound abnormalities of immune function – reduced GALT, small PP, dec LP AND defective CMI and induction of oral tolerance.In addition these animals have abnormalities of…
5 Host – microbiota interactions Function of gut microbiotaHost – microbiota interactionsHooper et al. Science 2001A single commensal bacteria switches on genes involvingMucosal barrier functionNutrient absorption/ dietary energy extractionEnteric nervous systemIntestinal maturationImmune system developmentOne of the most illuminating studies assessing the function of the gut flora is this one by Hooper et al. reported in Science in This group introduced a single commensal bacteria into a germ free animal and assessed by gene array analysis the genes which were switched on. They found that a multitude of genes were switched on including …… Although clearly a reductionist model it does highlight the huge potential of the gut flora in its entirity to interact with and influence host physiology.
8 The human microbiome project 5 year project242 healthy men/women - samples from different body sites10,000 different types of organism foundIs there a core set of microbes that all humans share?Diversity of microbes across human beingsDiet, host genetics, early microbial exposureUnique communities of microbes at different body sitesAt specific body sites, many microbes had similar genes/functionsChallenges thinking of one-microbe model of diseaseMore likely “function” of group of microbes changes
9 Gut microbiota “pathology” e.g. inflammatory bowel diseasesfunctional bowel diseasegastrointestinal infectionsnon-GI diseases- obesity, metabolic syndrome, atopy/allergy
10 Genetics of IBD >160 independent IBD susceptibility loci 20012007200820112012For many loci fine mapping is underway as part of the Immunochip experiment
11 What has genetics taught us about IBD? > 75,000 cases & controlsInformation about pathways involved in disease processOver 2/3 of genes are shared between UC &CD30 CD-specific and 23 UC-specificParticular overlap between ankylosing spondylitis and psoriasis1Jostins et al Nature 491 (7422): ; 2Lees et al Gut 2011;60: (diagram)
12 Experimental models of colitis Germ-FreeNo ColitisAnimal modelsof colitisWhat is the evidence that the gut flora drives the inflammation in IBD. The best evidence comes from animal models
13 Experimental models of colitis Germ-FreeNo ColitisAnimal modelsof colitisBacterialColonisationColitis
14 In humans… Faecal stream diversion alleviates Crohn’s Reanastomosis triggers recurrenceInfusion of luminal contents into excluded normal bowel induces inflammation
15 What part of the gut microbiota drives inflammation? Single organism?Expansion or relative contraction?“Functional” changes?
18 - Reduction of a major member of Firmicutes, F - Reduction of a major member of Firmicutes, F. prausnitzii, associated with higher risk of postoperative recurrence of ileal CD.Experimental replacement of F. prausnitzii had anti-inflammatory effects
19 But changes in “function” of microbiota…. Mucosa/stool samples from 231 IBD patients & controls16S gene pyrosequencing/shotgun metagenomicsMajor shifts in oxidative stress pathwaysDecreased carbohydrate metabolismDecreased amino acid synthesisIn ileal Crohn’s, increases in virulence and secretion pathwaysOverall CD is not caused by diminished diversity alone – but requires a susceptible genotype – as confirmed by research in mice with human relevant susceptibility mutationsMucin, which is rich in cysteine and glycosylated sugars, is abundant in the intestinal epithelium, and it isupregulated during inflammation. The increases in cysteine metabolism and N-acetylgalactosaminetransporters may reflect a shift in the microbiome towards greater abundance of microbes that usemucin as a primary energy source (Figure 6). This functionality suggests activity at the mucosa and thismay be problematic for a damaged IBD epithelium with compromised barrier function.Thisraises the interesting possibility that E. coli or related species in IBD may be highly represented becausethey gain a competitive advantage from oxidative stress and are better able to compensate for it withglutathione production.Microbial function more consistently altered than microbial compositionMorgan et al. Genome Biology Sept 2012
20 Challenges Clinical phenotype confounders “healthy” controls Sampling age, gender, smokingethnicity, diet, surgerymedications“healthy” controlsSamplingfaeces v mucosaaxial and longitudinal variationreplicationmultiple samples from same regionlongitudinal samplingCommunicationcliniciansmicrobial ecologistsbioinformaticsstatisticiansTechnical16S sequencemetagenomicsmetatranscriptomicsmetabonomics… economics
21 Can the gut microbiota be modified? If so, how?
22 Faecal transplantation - history 1600s – “transfaunation” – gastric contents transplanted into animals unable to ruminateBedouin of northern Africa – “coprphagia” – ingestion of camel dung as treatment for dysenteryWWII – same practice in soldiers – led to Bacillus subtilis as probioticFaecal transplant (FT ) - treatment in humans for pseudomembranous colitis in1958Landy et al. Aliment Pharmacol Ther 2011; 34:
24 Faecal transplantation in C. difficile Over 376 cases of faecal transplant (FT) for C. diff infection17/22 studies of FT are in refractory/fulminant C. diffEnemas; via duodenal tubes; via colonoscopesOverall success rates of >90%Landy et al. Aliment Pharmacol Ther 2011; 34:
25 Faecal transplantation in C. difficile First randomised controlled trialAimed to recruit 120 patients – stopped early13/16 (81%) in FT group – resolution of diarrhoea4/13 (31%) in vancomycin group3/13 (23%) in vancomycin + bowel lavageAfter FT, ↑diversity (similar to healthy donors)Van Nood et al. NEJM January 2013
26 Faecal transplantation in IBD 41 patients with IBD (27 UC; 12 CD; 2 indeterminate)Majority (19/25) had reduction in symptoms/ 15/24 remissionResolution of C. diff infection in 15/15Damman et al. Am J Gastro. 2012; 107: ; Anderson et al. APT Sept 2012
27 with faecal transplantation may be effective in refractory pouchitis Faecal transplantation in pouchitisHypothesis – increasing diversity and altering selection of resistant bacteriawith faecal transplantation may be effective in refractory pouchitisPilot study of faecal transplantation in patients with chronic pouchitisMicrobiological; immunological; histological & clinical assessmentpre and post transplant
28 Faecal transplantation in pouchitis PDAI CGQoL score pouch frequencyNo major adverse events; 3 patients reported adverse effects nausea (n=3); bloating (n=2)Landy et al. ECCO 2013
31 Unresolved issues… Can microbiota be altered in IBD with FT? If so, does genetic pressure / indigenous bacteria affect ability to change?Donor - mixture of phylogenetically diverse bacteria – which?Frequency and route of administration?Use of concomitant treatment?Fresh versus frozen (banks)?Safety?
32 Altering microbiota - beyond IBD ….. Other gastrointestinal disordersFunctional bowel disordersGastrointestinal infections e.g. Clostridium difficile, rotavirusNon-intestinal disordersAtopic diseasesType I diabetes/ metabolic syndromeObesity ……
34 Could manipulation of gut microbiota influence obesity? Calorie extraction from food variesdepending on gut flora“Obese flora” more effective atextracting energy from foodCould manipulation of gut microbiota influence obesity?
35 Could manipulation of gut microbiota influence malnutrition? Calorie extraction from food variesdepending on gut flora“Obese flora” more effective atextracting energy from foodCould manipulation of gut microbiota influence malnutrition?
36 Summary Gut microbiota – virtual organ; microbiome; metobonome Role of microbiota in IBDModulation of gut flora as a therapeutic interventionMechanistic approachFar reaching potential in GI (and non-GI) disease