The Human Microbiome Project : Implications for Probiotics

Transcription

1 The Human Microbiome Project : Implications for Probiotics James Versalovic, M.D., Ph.D. Associate Professor Departments of Pathology Baylor College of Medicine and Texas Children s Hospital Michael Hsieh, M.D., Ph.D. Fellow, Pediatric Urology Baylor College of Medicine and Texas Children s Hospital Therapeutic Microbiology Lab

2 (Glausiusz J. Discover June 2007) The Human Microbiome Project: Indigenous Microbiota and Microbiome P Eckburg et al. Science (2005) 308: >60% novel bacteria >80% nonculturable bacteria Mixed Microbial Communities Human Colon species Firmicutes Bacteroidetes Firmicutes include Lactobacillus spp. PJ Turnbaugh et al. Nature (2007) 449: S. Macfarlane et al. Appl Environ Microbiol (2005) 71:

3 HMP and MetaHit USA two sites St Louis and Houston Multiple sites Oral, nasal, vaginal, skin, and fecal Clinical sampling pending launch Nov/Dec 2008 Reference genomes component Healthy only in first phase Broad disease interests Europe two sites Barcelona and Copenhagen Gut (fecal) samples only Clinical sampling started in spring 2008 Reference genomes component Healthy subjects Disease focus on IBD and obesity IHMC Participants Australia: Commonwealth Scientific and Industrial Res. Organization Canada: Canadian Institutes of Health Research China: Meta-GUT project (Ministry of Science and Technology (MOST)) Sino-French collaboration; Human Gut Microbiome and Infections Human Gut Microbiome and Infections Europe: MetaHIT, European Commission France: Institut National de la Recherche Agronomique (INRA) Ireland: the DAFF/HRB elderly gut metagenomics project (ELDERMET) Japan: Human Metagenome Consortium Japan (HMGJ) Korea: Ministry for Health, Welfare and Family Affairs United States: HMP, National Institutes of Health

4 Reference Genomes Many commensal genomes including genomes of beneficial microbes Approximately genomes Lactobacillus and Bifidobacterium species are included Many other commensal bacterial genomes future candidate probiotics Reference dataset of genes / functions for metagenomics Reference Genomes, 16S, and True Metagenomics Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R. Curr Opin Chem Biol Feb;12(1): Epub 2008 Mar 5.

5 Overall Study Design and Study Population 250 individuals split evenly between Houston and Saint Louis Two samplings per person (within one year) Healthy adults years of age Equal number of males and females Minority Population Minimum 10% More ethnic diversity in Houston In-depth (invasive) sampling 10 individuals Future Core and Variable Microbiome : Implications for Probiotics Turnbaugh PJ et al. Nature 2007;449:

6 Microbial Composition Varies at Different Body Sites Oral Cavity dominance of Firmicutes Stomach Firmicutes about 50% Greater group diversity Small Intestine Paucity of Data Colon - Bacteroidetes and Firmicutes are most prominent Skin Proteobacteria and Actinobacteria are prominent Dethlefsen L, McFall-Ngai M, Relman DA. Nature Oct 18;449(7164): THREE PHYLA (OF 22 GROUPS) OF BACTERIA DOMINATE THE HUMAN INTESTINE Palmer et al. PLOS Biol 2007;5(7):e177

7 The Spatial Dimension along the Gut Axis Compositional differences in gut may reflect process of fecification Mucus-associated bacteria in feces may reflect mucosaassociated bacteria in gut Feces and Cecum Peterson DA, Frank DN, Pace NR, Gordon J Cell Host Microbe Jun Colonic Microbial Architecture : Differential Distribution of Bacteria Carnoy s Fixative Triple contrast: Bacteroides fragilis (Bfra Probe) yellow (Cy3) Eubacterium rectale group (Erec Probe) red (Cy5) Other bacteria (Eub338) green (FITC) Alexander Swidsinski, Berlin

8 The Time Dimension : Bacterial Colonization Patterns in Human Infants Antibiotic suppression of neonatal colonization No antibiotics in neonatal period Palmer et al. PLOS Biol 2007;5(7):e177 The Future of Probiotics: Going Beyond LAB, Bifidobacterium and Nissle The Story of Faecilibacterium prausnitzii Bacillus mucosus anaerobius" Prausnitz 1922 Firmicute C. leptum group

9 Faecilibacterium prausnitzii Commensal bacterium Fusobacterium prausnitzii Prominent member of human GI tract (feces) Healthy individuals Crohn disease Diminished quantities in patients with Crohn disease Sokol H et al PNAS 2008;105: Swidsinski A et al. F. prausnitzii a novel probiotic? Anti-inflammatory profile Enhanced IL-10/IL12 ratios with human PBMCs Suppress IL-8 by CaCo-2 intestinal epithelial cells Ameliorated disease and outcomes and TNBS murine colitis model Partially corrected dysbiosis by replacement therapy Sokol H et al PNAS 2008;105:

10 Beneficial Roles of Microbes (PROBIOTICS) in the Mammalian Intestine Pathogen Anti-Infective (Anti-Pathogenic) Probiotic Lactobacillus Amino Acids Polyphenols Vitamins Human Macrophages Immunomodulatory TNF, IL-8, IL-12, MCP-1 Anti-Diarrheal Anti-Nociceptive Antioxidants, nutrition Barrier function and integrity GUT LUMEN INTESTINAL EPITHELIUM MUCOSA Functional Genomics of Probiotics Understand traits that underlie probiotic function Identify genes responsible Compare strains at gene level and in vitro Derive robust mutants Designer strains improved alternatives Select natural strains for specific genes/gene products to improve probiotic function Natural, improved alternatives Pharma Clinical documentation Food

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