Our 'metagenome'is a composite of H. sapiens genes and genes present in the genomes of the trillions of microbes that colonize our adult bodies. 'Our'microbial genomes (microbiome) encode metabolic functions we have not had to evolve on our own, but remain largely unexplored: they include degradation of otherwise indigestible components of our modern diet. Our studies of gnotobiotic mice and humans have revealed a dynamic linkage between adiposity and gut microbial ecology, and provided evidence that the gut microbiota of obese mice is more efficient at harvesting energy than the microbiota of lean animals. This interdisciplinary program project application, involving three groups with a history of close interactions and a unique combination of expertise, seeks to provide new insights about the role of the gut microbiota in regulating energy balance in humans, and to help lay experimental and computational foundations for the human microbiome project, with the ultimate goal of establishing new strategies for targeting the microbiota to help treat obesity. Monozygotic (MZ) twin pairs, who represent an ideal design for testing key program hypotheses about the concordance of the microbiota and microbiome with obesity, will be recruited by one of the world's foremost twin researchers from his ongoing study of a mid-western cohort of female like-sex twin pairs. Project 1 uses comparative metagenomics (16S rRNA enumerations, sequencing of total fecal microbial community DNA and expressed cDNAs, measurement of metabolites), plus computational approaches developed from metagenomic studies of obese and lean mice, to examine whether there is a set of shared organisms and gene lineages present in the microbiota and microbiomes of obese (BMI=35) versus lean (BMI 18.5-25) MZ and dizygotic European-ancestry and African-American twin pairs and their mothers. Project 2 combines comparative genome hybridization and large-scale DNA sequencing to determine the extent of inter-individual variation in the pan-genomes of two prominent members of the human gut microbiota that play an important role in polysaccharide fermentation, in obese vs. lean MZ twins. Project 3 uses new/powerful statistical tools, together with Project 1-2 datasets, to test whether there are systematic differences in human gut communities related to host genetics and obesity, and whether strong selective pressure in the gut environment results in adaptation through the acquisition of genes with specific functions (e.g. carbohydrate metabolism) through lateral gene transfer. It will also relate the gut microbiota of lean and obese individuals to gut communities in other mammals and different physical environments, to trace the provenance of genes and genomes that contribute key metabolic capabilities to the human gut. A Biospecimen Collection Core will recruit twins and collect fecal samples. A Microbiome Data Management Core will serve as a central data repository. An Administrative Core will facilitate communications between projects and personnel.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Program Projects (P01)
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Study Section
Special Emphasis Panel (ZDK1-GRB-6 (M1))
Program Officer
Karp, Robert W
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Washington University
Schools of Medicine
Saint Louis
United States
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Seedorf, Henning; Griffin, Nicholas W; Ridaura, Vanessa K et al. (2014) Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159:253-66
Faith, Jeremiah J; Ahern, Philip P; Ridaura, Vanessa K et al. (2014) Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med 6:220ra11
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory et al. (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814-21
Ridaura, Vanessa K; Faith, Jeremiah J; Rey, Federico E et al. (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341:1241214
Smith, Michelle I; Yatsunenko, Tanya; Manary, Mark J et al. (2013) Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339:548-54
Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J et al. (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57-9
Faith, Jeremiah J; Guruge, Janaki L; Charbonneau, Mark et al. (2013) The long-term stability of the human gut microbiota. Science 341:1237439
Rey, Federico E; Gonzalez, Mark D; Cheng, Jiye et al. (2013) Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc Natl Acad Sci U S A 110:13582-7
Ravussin, Yann; Koren, Omry; Spor, Ayme et al. (2012) Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity (Silver Spring) 20:738-47
Kau, Andrew L; Ahern, Philip P; Griffin, Nicholas W et al. (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327-36

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