Rapid changes in the gut microbiome during human evolution.

Bibliographic Collection: 
Publication Type: Journal Article
Authors: Moeller, Andrew H; Li, Yingying; Mpoudi Ngole, Eitel; Ahuka-Mundeke, Steve; Lonsdorf, Elizabeth V; Pusey, Anne E; Peeters, Martine; Hahn, Beatrice H; Ochman, Howard
Year of Publication: 2014
Journal: Proc Natl Acad Sci U S A
Volume: 111
Issue: 46
Pagination: 16431-5
Date Published: 2014 Nov 18
Publication Language: eng
ISSN: 1091-6490
Keywords: Africa, Americas, Animals, Bacteria, Diet, Feces, Genetic Speciation, Genetic Variation, Hominidae, Humans, Intestines, Life Style, Microbiota, Phylogeny, Population Groups, Primates, Species Specificity, Urban Population, Venezuela

Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.

DOI: 10.1073/pnas.1419136111
Alternate Journal: Proc. Natl. Acad. Sci. U.S.A.
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