Rapid changes in the gut microbiome during human evolution

Andrew H. Moeller, Yingying Li, Eitel Mpoudi Ngole, Steve Ahuka-Mundeke, Elizabeth V. Lonsdorf, Anne E. Pusey, Martine Peeters, Beatrice H. Hahn, Howard Ochman

Research output: Contribution to journalArticlepeer-review

231 Scopus citations


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.

Original languageEnglish (US)
Article numberA54
Pages (from-to)16431-16435
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number46
StatePublished - Nov 18 2014
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General


  • Coevolution
  • Gastrointestinal tract
  • Gorilla
  • Microbiota
  • Pan


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