The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)


Metagenomic comparisons of gastrointestinal microbial function in hominoids

CARL J. YEOMAN2, REBECCA M. STUMPF1, BRYAN A. WHITE2, BRENDA A. WILSON2, KAREN E. NELSON3, MANOLITO TORRALBA3, MARCUS GILLIS3, LAWRENCE MUGISHA4 and STEVEN R. LEIGH1.

1Department of Anthropology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 2Institute for Genomic Biology, University of Illinois, 3J. Craig Venter Institute, 4Chimpanzee Sancutary & Wildlife Trust

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Dietary shifts are central to human evolution. Bacterial metabolic processes conducted by gut microbes may contribute to dietary adaptations, especially through digestion of resistant fiber. However, the contributions and significance of bacterial metabolic processes to human diet remain poorly understood.

We investigate bacterial metabolic contributions to diet analyzing fecal samples from 13 individuals, including wild gorillas (Gorilla gorilla) and free-ranging chimpanzees (Pan troglodytes), comparing these to published data from humans and captive gorillas and chimpanzees. We used high-throughput sequencing, attaining significant sequencing depth (>100 million reads), to describe microbial community structure and to identify functional genes in microbial samples. These data enable comparisons of microbial metabolic comparisons.

Substantial microbial differences characterize gorillas, chimpanzees, humans, and captive animals, revealing contrasts in both the structure and function of microbial ecosystems among groups. Protein metabolism prevailed in wild apes. Wild gorillas also harbored more microbial genes dedicated to polysaccharide and RNA metabolisms, while free-ranging chimpanzees were enriched for aromatic compounds, iron, virulence potential, and secondary metabolisms. Humans and captive apes were significantly enriched for central carbohydrate, fatty acid, and lipid metabolism genes. Humans were also enriched for sulfur metabolism.

Distinctions among microbial genomes may contribute to the evolution of host dietary differences. Microbial involvement in protein metabolism in noncaptive samples may be especially relevant to diet. We discuss computational challenges posed by metagenomic data, and consider the evolutionary significance of microbial community differences among host species.

This study was funded by the University of Illinois and NSF 0935374.

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