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The Human Microbiome: The Undiscovered Country

The Human Microbiome: The Undiscovered Country. Walter J. Coyle, MD, FACP,FACG. Movement of the Talk. Describe the Microbiome Microbiology 101 Review the diversity of human gut flora Understand how our bacteria influence our metabolism and obesity Review the plethora of probiotics

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The Human Microbiome: The Undiscovered Country

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  1. The Human Microbiome: The Undiscovered Country Walter J. Coyle, MD, FACP,FACG

  2. Movement of the Talk Describe the Microbiome Microbiology 101 Review the diversity of human gut flora Understand how our bacteria influence our metabolism and obesity Review the plethora of probiotics Describe prebiotics and their potential uses Conclusions and the Future

  3. The Human Microbiome • Definitions: • Microbiome: Aggregate of all gut species • Microbiota: Individual bacterial species in the biome • Over 100 trillion organisms (1014) • Passengers in the mobile colonic petri dish • Over 500 species identified so far (70 divisions) • 90% of the cells in our body our microbial! • 100 fold more genes in our gut then in us • Our flora are an integral part of our genetic landscape and evolution

  4. Anatomic Regions of the Gut • Upper GI tract: 102 – 104 cells/ml • Lactobacilli, streptococci, H pylori • Ileum: 106-1012 cells /ml, upper bacteria plus • Faculative anaerobes: Enterobacteriaceae • Obligate anaerobes: Bacteroides, Veillonella, FusobacteriumandClostridium species • Colon: distal human colon is the most biodense natural ecosystem known (1010-1012 cells/ml) • Complex and diverse • Comprise most of our bacterial biomass

  5. Microbes and Humans Dethlefsen Nature 2007; 449:812-818

  6. Micro 101 Pace in Science 1997 276:735-740

  7. The Human Gut Flora DiBiase, et al. Mayo Clin Proc 2008;83:460-469

  8. Mouse intestine, mucus gel layer Home to billions of organisms Sonnenburg J, et al. in Nature Immunology 2004:5

  9. The Microbiome: Who’s there? • Early gut colonization has four phases • Phase 1: Sterile gut • Phase 2: Initial acquisition: vagina, feces, hospital • Phase 3: Breast feeding or bottle-feeding (different) • Breast fed more bifidobacteria (up to 90% of flora) • Bottle fed more diverse; more Bacteroides , and Clostridial species • Phase 4: Start of solids; move to adult flora • Bifidobacteria remain key flora into adulthood Ley, Peterson, Gordon. Cell 2006 ;124:837 Ley, et al. PNAS. 2005, 102: 11070 Edwards, et al. Br J Nutr. 2002

  10. The Microbiome: Who’s there? • Adult Microbiome: • Increasing diversity of flora as we age • In some newer PCR (16S rRNA) studies, up to 92% of the flora in adults were “novel” species • Serial stool collections show remarkable stability by an individual • Greatest concordance with twins • Less concordance with households • Host genetic influence unexplored. McCartney and Gibson in Gastrointestinal Microbiology, 51-73, 2006

  11. The Microbiome: Who’s there? • Multiple species: eukaryotic, bacterial, archael • Firmicutes (Gram +/ motile) and Bacteroidetes (Gram -) : Majority • These two groups comprise > 90% • Anaerobes / aerobes: 1000:1 • Far fewer species than the environment • High levels of interpersonal diversity • My stool is not your stool Ley, Peterson, Gordon. Cell 2006 ;124:837 Ley, et al. Science 2005; 307: 1915

  12. Ley R, et al in Cell 2006:124:837-848

  13. Gut Flora and Metabolism

  14. Metabolomics • Study of the metabolites and small molecules that the body and gut bacteria produce. • New area of science • Broader than proteonomics • Includes bacteria products with our own genetic products • Pioneered by Jeremy Nicholson and Jeff Gordon

  15. Gut Flora and Metabolism • Microbial genomes enhance our metabolic activity • May indirectly or directly effect our metabolism • The colon is very active metabolically • 20-70 gms of carbos and 5-20 gms of protein/day • Over 100 kcal per day! • Mass of colonic microbiome = single kidney • Metabolically as active as the liver Hooper, et al. Annu Rev Nutr, 2002

  16. Gut Flora and Metabolism • Energy salvage: esp via the short-chain fatty acids • Acetate, butyrate, propionate (SCFAs) • Absorbed into body and used by liver and others organs • Acetate and propionate modulate glucose metabolism in the liver and adipocytes (glycemic index) • 50-70% of colonic cell energy derived from butyrate • Number and diversity of organisms key • Do we acquire flora that program us for obesity or normal weight? Mackowiak, NEJM, 1982; 307:83-93 Hooper, et al. Annu Rev Nutr, 2002

  17. Gut Flora Metabolic Reactions Metabolic reactions Goldin BR in Gastrointestinal Microbiology 138-154, 2006

  18. Gut Flora and the Brain Collins and Bercik in GASTRO 2009;136:2003–2014

  19. Obesity and the Gut Flora

  20. Ley, et al. PNAS. 2005, 102: 11070-75

  21. The Microbiome: Changes in flora • Mice and humans have different gut flora but the two largest divisions are shared in common • Bacteroidetes (Gram -) • Firmicutes (Gram +) • These flora change in response to diet and obesity of host Ley, et al. PNAS. 2005, 102: 11070-75

  22. Ley, et al. PNAS. 2005, 102: 11070-75

  23. The Microbiome: Changes in flora • Obesity changes the relative proportions of divisions. • Obese mice AND obese people have more Firmicutes than Bacteroidetes: dieting and weight gain shifts these proportions. • What are the implications of the change in our colonic metabolic machine • Chicken or the egg? Ley, et al. PNAS. 2005, 102: 11070-75

  24. Gut Flora and Obesity • Germ free mice studied by Gordon, et al • Control mice (remaining germ free) were changed from low fat diet to “Western” diet • Mice given normal gut flora (conventialized mice) also had same diet change. • Low fat diet: 5% lipids • “Western” diet: 41% lipids, 41% carbos (with simple sugars), 18% protein Gordon J, et al, PNAS 2007;104:983

  25. Gut Flora and Obesity • Mice then studied for change in weight and fat pad size • Assessed response to fatty meal loading • Assessed locomotion of mice via gastrocnemius muscle activity. • Results: See Figures Gordon J, et al, PNAS 2007;104:983

  26. Gut Flora and Obesity Gordon J, et al, PNAS 2007;104:983

  27. Gut Flora and Obesity • GF mice are “resistant” to the Western diet • Gut flora are responsible for increasing energy production from food • “Doctor, I don’t eat” May be partially true! • Gut flora also influence lipid production, adipose cell storage, and appear to influence mouse locomotor activity • “Couch potato” gut flora • My gut flora made me do it! Gordon J, et al, PNAS 2007;104:983

  28. “Let food be thy medicine and medicine be thy food.” Hippocrates

  29. The Microbiome: transplant experiments Ob Ob mouse Wild type mouse Turnbaugh, et al. Nature 2006; 444:1027

  30. The Microbiome: transplant experiments • Germ-free mice given ob/ob or wild-type flora • Chow consumption and exercise the same for both groups • Both sets had similar starting weight and % BF. • The ob/ob microbiota promote host adiposity Turnbaugh, et al. Nature 2006; 444:1027

  31. Human Flora and Obesity • Mice data links gut flora with obesity and diet • Studied 12 obese human subjects; low calorie diet for one year • Fat-restricted (FAT-R) • Carbohydrate restricted (CARB-R) • Microbiota studied for one year (16s rRNA) • Firmicutes and bacteroidetes dominated (92.6%) Ley R, et al in Nature 2006:444

  32. Human Flora and Obesity Ley R, et al in Nature 2006:444

  33. Human Flora and Obesity • Firmicutes dominate in obese subjects • All subjects (no diff with diet) had bloom of all Bacteroidetes with decline in Firmicutes • CARB-R: Change began at 2% wgt loss • FAT-R: Change began at 6% wgt loss • Dynamic link between obesity and gut flora exists in humans (proven 1st in mice) Ley R, et al in Nature 2006:444

  34. Proposed Mechanisms in Obesity DiBiase, et al. Mayo Clin Proc 2008;83:460-469

  35. Microbiome: regulators • Archae: 1-2 % of mouse and human flora • Represent a major microbial group in gut flora • Increased in obese mice • Many are methanogenic : Methanobactersmithii • Converts CO2 and H2 gas to methane • By decreasing the partial pressure of H2 gas these bacteria can drive bacterial metabolism • The flora of obese mice are more efficient at extracting energy: “The Energy Harvest”

  36. The Gut and Obesity: Options • Diet may manipulate flora • Low carbs, high fat • High carbs, low fat • Probiotics • Prebiotics • Stool transplants • “Guarantee weight loss with thin people’s feces!” • Could this be the future?

  37. Coyle’s Corollary It is better to be a stool donor than a recipient.

  38. Probiotics

  39. Probiotics • Definition: Live microorganisms which when ingested in adequate amounts confer a health benefit on the host. • Majority of probiotics are Gram +, lactic acid producers • Bifidobacterial species and Lactobacillus species • Survive transit through stomach and duodenum • Others include: non-pathogenic streptococci, enterococci, E coli Nissle 1917, Saccharomyces boulardii (yeast) Fooks, et al. Int Dairy J, 1999 Sheil, et al. In Gastrointestinal Microbiology, 2006

  40. Common Probiotics Khedkar and Ouwehand in GastrointestMicrobiology 315-334, 2006

  41. Probiotics • VSL #3 • 4 lactobacilli • L. plantarum, casei, acidopholus, delbrueckiispp • 3 bidifobacteria • B. infantis, breve, longum • 1 streptococcus • Streptococcus salivarius ssp. thermophilus Rand, PC studies have shown efficacy in pouchitis and IBS

  42. Probiotics • Digestive Advantage • Ganeden BC30 • Bacillus coagulans • Erythritol • Cellulose • Other minor ingredients

  43. Probiotics • Bifidobacteriuminfantis 35624 aka Bifantis • “Patented” strain of probiotic in Align • Decreased symptoms in two large trials in subjects with IBS* *Whorwell P, et al. Am J Gastro 2006; 101 O’Mahoney L, et al. Gastro 2005;128

  44. Probiotics • Saccharomyces boulardii • Other minor ingredients • Shown in Rand / PC trials to help prevent recurrent C. difficile infection

  45. Probiotics in Food (Actimel) • L. caseiImmunitas™ • Claim it is scientifically proven to be effective • “Each bottle contains 10 billion live” bacteria “that survive and remain active in the digestive tract.”

  46. Prebiotics

  47. Prebiotics • Ingested substances that selectively stimulate the proliferation and/or activity of desirable bacterial populations present in the host intestinal tract. • Usually target bifidobacteria and lactobacilli • Bifidogenic or bifidus factors explored in the 50s • Usually are non-digestible oligosaccharides (NDOs) • Lactulose, galacto-oligosaccharides, lactosucrose… Crittenden and Playne. In Gastrointestinal Microbiology, 2006, pg 285-314.

  48. Prebiotics • Inulin: plant polymers mainly comprising fructose units, use have a terminal glucose • Indigestable fiber • Gut flora produce H2, CO2, methane gas from inulin

  49. Prebiotics • Is is possible to design a food, sugar, protein, or fat that would alter your gut flora to promote weight loss? • More likely possibility is to give a prebiotic that decreases your “Energy Harvest” of colonic bacteria • ie. lose weight by making your gut flora less efficient at digesting your left over food

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