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 Describe prebiotics and their
potential uses Conclusions and the Future
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
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, Fusobacterium and Clostridium 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
Microbes and Humans
Dethlefsen Nature 2007; 449:812-818
Micro 101
Pace in Science 1997 276:735-740
The Human Gut Flora
DiBiase, et al. Mayo Clin Proc 2008;83:460-469
Mouse intestine, mucus gel layerHome to billions of organisms
Sonnenburg J, et al. in NatureImmunology 2004:5
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 ;124:837Ley, et al. PNAS. 2005, 102: 11070 Edwards, et al. Br J Nutr. 2002
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
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 ;124:837Ley, et al. Science 2005; 307: 1915
Ley R, et al in Cell 2006:124:837-848
Gut Flora and Metabolism
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
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 liverHooper, et al. Annu Rev
Nutr, 2002
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
Gut Flora Metabolic Reactions
Metabolic reactions
Goldin BR in Gastrointestinal Microbiology 138-154, 2006
Gut Flora and the Brain
Collins and Bercik in GASTRO 2009;136:2003–2014
Obesity and the Gut Flora
Ley, et al. PNAS. 2005, 102: 11070-75
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
Ley, et al. PNAS. 2005, 102: 11070-75
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
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
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
Gordon J, et al, PNAS 2007;104:983
Gut Flora and Obesity
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
Hippocrates
“Let food be thy medicine and
medicine be thy food.”
The Microbiome: transplant experiments
Turnbaugh, et al. Nature 2006; 444:1027
Ob Ob mouseWild type mouse
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
Ley R, et al in Nature 2006:444
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
Human Flora and Obesity
Ley R, et al in Nature 2006:444
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)
Proposed Mechanisms in Obesity
DiBiase, et al. Mayo Clin Proc 2008;83:460-469
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 :
Methanobacter smithii 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”
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?
Coyle’s Corollary
It is better to be a stool donor than a recipient.
Probiotics
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
Common Probiotics
Khedkar and Ouwehand in Gastrointest Microbiology 315-334, 2006
Probiotics
VSL #3 4 lactobacilli
L. plantarum, casei, acidopholus, delbrueckii spp
3 bidifobacteria B. infantis, breve,
longum 1 streptococcus
Streptococcus salivarius ssp. thermophilus
Rand, PC studies have shown efficacy in pouchitis and IBS
Probiotics
Digestive Advantage Ganeden BC30
Bacillus coagulans Erythritol Cellulose Other minor
ingredients
Probiotics
Bifidobacterium infantis 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; 101O’Mahoney L, et al. Gastro 2005;128
Probiotics
Saccharomyces boulardii
Other minor ingredients
Shown in Rand / PC trials to help prevent recurrent C. difficile infection
Probiotics in Food (Actimel)
L. casei Immunitas™
Claim it is scientifically proven to be effective
“Each bottle contains 10 billion live” bacteria “that survive and remain active in thedigestive tract.”
Prebiotics
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.
Prebiotics
Inulin: plant polymers mainly comprising fructose units, use have a terminal glucose
Indigestable fiber Gut flora produce
H2, CO2, methane gas from inulin
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
Designing Probiotics: The Future?
GASTROENTEROLOGY 2009;136:2015–2031
Conclusions
The human microbiome and the Microbiome Project: research just beginning…
Gut flora by their genes, by-products, and metabolic activity influence our metabolism, weight, activity, immunity, health and disease.
Manipulation of gut flora may be an integral part of weight loss programs and different disease treatments in the future.
Conclusions
Future studies must focus on the mechanisms of influence of our gut flora.
Studies must be placebo controlled and high quality.
Truly need translational science to work at the levels of the petri dish, genomics, and clinical outcomes.
Much more to come!
The Future
Define who is there: in healthy subjects and those with disease Study at Scripps in subjects with diet
change, NASH, and IBD Elucidate the gut flora host
interaction Design trials that truly assess the
potential for probiotics and prebiotics to make a difference in health and disease.
Questions