The number of microorganisms residing in our intestines is 10 times the number of our somatic and germ cells.

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2 The number of microorganisms residing in our intestines is 10 times the number of our somatic and germ cells.

3 The number of microorganisms residing in our intestines is 10 times the number of our somatic and germ cells. But the bugs are not distributed equally Stomach: relatively few Small Intestine: more Cecum & colon: lots & lots

4 What s the cecum all about? material undigested by the host (coarse, fibrous foods) passes slowly through the cecum longer residence time = more complete microbial degradation = nutritional benefit to the host animals which lack a cecum are largely able to use their own enzymes to digest their food

5 Herbivores Carnivores Omnivores Source:

6 Herbivores Carnivores Omnivores Source:

7 Herbivores Carnivores Omnivores Source:

8 Herbivores Carnivores Omnivores Source:

9 Herbivores Carnivores Omnivores Source:

10 Herbivores Carnivores Omnivores Source:

11 Herbivores Carnivores Omnivores Source:

12 Who makes up our intestinal microbiota? - Bacteria, archaea and eukarya - Only 8 of 55 bacterial divisions - Cytophaga-Flavobacterium-Bacteroides (CFB), Firmicutes, Proteobacteria and 5 rare divisions - Coevolution - mammalian associated CFB members are most derived - CFB subgroups are divided among different mammalian species, suggests subgroups coevolved with their hosts

13 The 55 bacterial divisions Red: common in intestine Green: rare Black: not detected Note: evolutionary distance of divisions marked in red

14 Phylogenetic tree of CFB division based on 16S rrna gene sequences graphical symbols represent the source of the sequences Ratio: number of sequences derived from human gut relative to total number in the subgroup red: majority of sequences derived from human gut yellow: minority black: absence

15 Who makes up our intestinal microbiota? - Few divisions, but high strain and species diversity

16 Who makes up our intestinal microbiota? - Few divisions, but high strain and species diversity - although genus and species not precisely defined for microbes

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18 Few divisions, but many strains... a result of host-selection? - Natural selection at two levels (at least) - competition among individual microbes - integrated microbiota do not harm the host - So...is there a mechanism to promote cooperation and functional stability? - bacteria must break down nutrients and provide the host with energy - cooperation...group selection (ambiguous) - functional stability...redundancy of key processes distributed among many strains

19 How stable is our gut microbiota? i.e. can functional stability be maintained among strains - stability was shown for ~6 months with TGGE

20 What is responsible for maintaining stability? - Physical factors - ph, oxygen tension, temperature, peristalsis, bile acids* - Our immune system - IgA in mice ** - Also shown that gut microflora are unable to induce antibodies, especially when present in GI tract * - These microbes often share antigens with the mucosa of the gut (recognized as self) * * **

21 What is responsible for maintaining stability? (cont.) - Phage attack - is there enough strain diversity to withstand phage attack and maintain functional stability? - could we recruit phage to help shape our microbiota? - Influence of host genotype vs. type of food consumed - adult monozygotic twins living apart have flora more similar than unrelated individuals - marital partners, consuming the same food, do not

22 What is responsible for maintaining stability? (cont.)

23 What is responsible for maintaining stability? (cont.) But... - were the twins fed the same way as infants? - do they have similar eating habits?

24 How are we colonized? - GI tract sterile in normal fetus - Colonization occurs during suckling - Lactobacillus sp. predominate in formula-fed infants (Firmicutes division) - Bifidobacterium sp. predominate in breast-fed infants (Actinobacteria division)

25 A model organism: Bacteroides thetaiotaomicron - Habitat is distal intestine - Genome reflects towering ability to digest otherwise indigestible polysaccharides paralogs of outermembrane proteins involved in starch binding and uptake - 15 polysaccharide lyases predicted glycoside hydrolases (we have 98) - 64 predicted enzymes involved in the degradation of dietary fiber (we have one)

26 How is the carbohydrate foraged? - Gnotobiotic mice colonized exclusively with B. thetaiotaomicron - Communities of bacteria assemble on: - undigested food particles, shed mucosa, exfoliated epithelial cells - actively degrade food particle, and release SCFA, CO and H - Methanogenic archaea improve transformation efficiencies by converting CO and H to CH B. thetaiotaomicron lacks adhesive organelles - relies on outer membrane glycan binding proteins - binding protein expression is diet dependent 2 2

27 What to do when there are no food particles? - B. thetaiotaomicron is able to turn to host glycosides when diet is scarce - glycans on host mucosa and epithelial cells - depend on host genotype and microbial regulation of host glycosyltransferase gene expression - maintain gut ecosystem stability during starvation - may avoid immune response by - ability to change carbohydrates on surface (recognized epitopes) in response to glycans in the gut - ability to alter its genome content (63 transposases, 43 integrases, 4 homologs of a conjugative transposon) but growth rate?

28 1) no adhesive organelles 2) glycan specific binding on food platform 3) methanogens drive carbohydrate utilization 4) bind to host glycans in absence of food

29 1) no adhesive organelles 2) glycan specific binding on food platform 3) methanogens drive carbohydrate utilization 4) bind to host glycans in absence of food

30 1) no adhesive organelles 2) glycan specific binding on food platform 3) methanogens drive carbohydrate utilization 4) bind to host glycans in absence of food

31 1) no adhesive organelles 2) glycan specific binding on food platform 3) methanogens drive carbohydrate utilization 4) bind to host glycans in absence of food

32 What is the difference between germ-free and conventionally raised mice? from Table S-2 GF mice have 40% less body fat than CONV-R animals fed same polysaccharide rich diet - CONV-R eat less food - innoculating GF adults with CONV-R cecal contents increases body fat

33 Why does gut microflora result in body fat? - Colonization increases glucose uptake and elevates serum glucose, SCFA, and insulin levels - induces lipogenesis (fat production) from liver - Triglycerides from liver taken up by adipocytes (fat storage cells) via lipoprotein lipase (LPL) - microbiota suppress expression of LPL inhibitor

34 Why does gut microflora result in body fat? - Colonization increases glucose uptake and elevates serum glucose, SCFA, and insulin levels - induces lipogenesis (fat production) from liver - Triglycerides from liver taken up by adipocytes (fat storage cells) via lipoprotein lipase (LPL) - microbiota suppress expression of LPL inhibitor White Adipocyte Brown Adipocyte

35 How does this impact nutrition fact labeling? - Our intestinal microbiota dictate (in part) how efficiently we produce and store fat - Could individual gut microflora efficiency really make a difference? - microflora dependent on host genotype - small but chronic difference between energy produced: consumed can make a significant difference (ambiguous) - microbes themselves consume a lot of energy - obese mice study

36 image credit: Ralph House

37 - ob/+ mothers produce obese (ob/ob), lean (ob/+) and wild type (+/+) offspring - all mice fed the same diet since birth - Analyzed 5,088 cecal-micobiota 16S rdna sequences - Obese mice have a 50% reduction in the abundance of Bacteroides and a proportional increase in Firmicutes - Mouse and human gut microconsortia are similar at the division level, but not at the species level - Could this be why domestic animals gain weight more efficiently when fed antibiotics?

38 Future Work - Focus on contribution from archaea - Metagenome sequencing - identify gene content (extension of HGP) - characterize difference between healthy and sick ethnically diverse groups - characterize difference between lean and obese individuals - monitor changes in microflora with weight loss - How do metabolites from the microbial consortia influence host physiology

39 in the end...

40 in the end... You are what you eat!