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Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16431-5. doi: 10.1073/pnas.1419136111. Epub 2014 Nov 3.

Rapid changes in the gut microbiome during human evolution.

Author information

1
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511; Department of Integrative Biology, University of Texas, Austin, TX 78712;
2
Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
3
Institut de Recherches Médicales et d'Études des Plantes Médicinales, Prévention du Sida au Cameroun, BP 906 Yaoundé, Republic of Cameroon;
4
Institut National de Recherche Biomedicale, BP 1197 Kinshasa, Democratic Republic of the Congo; Institut de Recherche pour le Développement, University of Montpellier, 34396 Montpellier, France;
5
Department of Psychology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA 17603; and.
6
Department of Evolutionary Anthropology, Duke University, Durham, NC 27708.
7
Institut de Recherche pour le Développement, University of Montpellier, 34396 Montpellier, France;
8
Departments of Medicine and bhahn@upenn.edu howard.ochman@austin.utexas.edu.
9
Department of Integrative Biology, University of Texas, Austin, TX 78712; bhahn@upenn.edu howard.ochman@austin.utexas.edu.

Abstract

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.

KEYWORDS:

Gorilla; Pan; coevolution; gastrointestinal tract; microbiota

PMID:
25368157
PMCID:
PMC4246287
DOI:
10.1073/pnas.1419136111
[Indexed for MEDLINE]
Free PMC Article

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