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The Gastrointestinal Microbiome in Ulcerative Colitis. Susan V. Lynch, PhD Associate Professor of Medicine Director Colitis and Crohns Disease Research.

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Presentation on theme: "The Gastrointestinal Microbiome in Ulcerative Colitis. Susan V. Lynch, PhD Associate Professor of Medicine Director Colitis and Crohns Disease Research."— Presentation transcript:

1 The Gastrointestinal Microbiome in Ulcerative Colitis. Susan V. Lynch, PhD Associate Professor of Medicine Director Colitis and Crohns Disease Research Core Division of Gastroenterology, Department of Medicine, University of California San Francisco. BROAD FOUNDATION Investigator Meeting. LA, March 7-8, 2013

2 The Human Microbiome

3 Culture-independent microbial profiling CompositionFunction Microbiome dysbiosis associated with chronic inflammatory/autoimmune diseases Contribute functions critical to host health: Metabolism of indigestible carbohydrates Vitamin and hormone production Immune development Immune homeostasis Ancillary mucosal protection Spor, A. et al. Nat Rev Microbiol Apr;9(4):

4 Selective Pressures Shaping the Microbiome Host Genetics Gut Microbiome Immune response Environment

5 Relationship between IBD and GI Microbiome Antibiotic use can reduce or prevent inflammation both in patients and in murine models of disease Kang SS, et al. PLoS Med. 2008;5:e41. Swidsinski A, et al, J Clin Microbiol. 2005;43:3380–3389. Depleted microbiome diversity – a hallmark of both Crohns disease and Ulcerative colitis Walker A. et al. BMC Microbiol Jan 10;11:7. Fecal transfer - disease remission within a week; complete recovery noted after 4 months. No clinical, colonoscopic, or histologic evidence of UC in any patient (1-13 years later). Borody, T.J. et al., J Clin Gastroenterol Jul;37(1):42-7. Mutations in NOD2 and ATG16L1 associated with shifts in the relative abundance of members of the Faecalibacterium and Escherichia genera. Frank, D. et al. Inflamm Bowel Dis Jan;17(1):

6 Role of Gut Microbes in Immunomodulation Th17 deficient Th17 sufficient ~100 taxa significantly altered in relative abundance Jackson Taconic Ivanov et al. Cell. 139: Mice from Jackson or Taconic labs had marked differences in Th17 cell numbers in Fecal transfer or co-housing induced Th17 phenotype.

7 Ivanov et al. Cell. 139: Role of GI microbes in immunomodulation

8 Segmented Filamentous Bacterium Segmented Filamentous Bacterium (SFB) Uncultured, commensal, gram-positive,anaerobic, spore-forming bacteria Adhere tightly to epithelium in the ileum Abundance correlates with reduced colonization and growth of pathogenic bacteria Garland et al., Microb Ecol, (198) ; Heczko et al., The Journal of infectious diseases (2000) 181, IL-17 IL IL-17IL-22 Jax + SFB Jax + SFB JaxJax + SFB Colonization of Jackson B6 mice with SFB leads to IL-17 and IL-22 expression in TCR+CD4+ small intestine lamina propria lymphocytes Other bacteria do not induce IL-17

9 Corynebacteriaceae Fusobacteriaceae Relatively even community Bacteriodales Pseudomonaceae Staphylococcaceae Sinotypes p=0.001 Sinus mucosal microbiota cluster by dominant pathogen Distinct co-colonization patterns Opportunity to clinically characterize patients by microbiotype Tailored treatment

10 Prevalence of IBD is higher in migrant populations Microbiome perturbation Adoption of a Western Diet? Genetically predisposed to disease? Relationships between the microbiome (bacterial and fungal), host risk gene profile and diet IBD Microbiome Host Genetics Gut Microbiome Immune response Environment

11 Study Cohort Examine a cohort of (first generation) migrant South Asian and European UC patients 120 UC subjects: 60 European descent 60 South Asian 30 control subjects UC patients - Stable disease – gradient of disease severity Controls – family members not known to have UC Stool samples (Microbiome – bacterial and fungal species) Saliva collection (Risk allele SNP profile) Long-term dietary information (Block Food Frequency Questionnaire)

12 Do distinct disease sub-enterotypes exist? Which microbial species (bacterial or fungal) dominate these communities? What are the patterns of microbial co-colonization? Do relationships exist between sub-enterotypes and disease severity/distinct phenotypes How is the intestinal microbiome related to host genetics, long-term dietary habits? Determine whether an ulcerative colitis microbial enterotype exists across migrant populations of distinct ethnic backgrounds compared to control populations Aims

13 To date Study commenced in May 2012 Enrolled 47 subjects to date Paired stool and saliva samples and FFQs received from 30 participants Extracted nucleic acids from 25 paired samples – quantified Q-PCR for bacterial burden Bacterial microbiome profile – PhyloChip 60,000 bacterial taxa in a single assay Fungal profiling - MiSeq Risk allele sequencing commenced for 8 loci Study Subjects Enrolled to Date UC patientsHealthy subjects South Asian EuropeanSouth Asian European Index SNPGene/Locus of interest Rs RNF186 Rs IL23R Rs FCGR2A Rs PUS10 Rs CEP72 Rs CARD9 Rs LOC Rs971545IL26

14 Bacterial Burden is lower in UC Patients Anova P < 0.09 P < 0.16

15 Extracted total DNA from a bacterial community 16S rRNA gene is amplified using universal primers in 12 replicate reactions across a gradient of annealing temperatures Amplicon pool fragmented, biotin labeled and hybridized to PhyloChip Microarray stained, washed and scanned Fluorescently labeled 16S fragments hybridize to complementary probes on the array surface Fluorescence data analyzed and microbes identified 16S rRNA PhyloChip Analysis 15 All 25 samples amplified across a gradient of annealing temperatures Pooled, quantified, labeled and applied to PhyloChip

16 Next Steps Continue enrollment – currently on target Microbiome analysis PcoA - disease enterotypes Multi-variate regression (Adonis) Diet Host risk allele profile Disease severity Specific taxa related to variables Co-colonization patterns Dietary comparisons across ethnic groups and patients vs controls Risk allele comparisons across ethnic groups and patients vs controls

17 Acknowledgements Uma Mahadevan Michelle Nazareth Morgan McCormick Jordan Mar Mark Seielstad Mark Segal Broad Foundation


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