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Cospeciation of gut microbiota with hominids

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Science  22 Jul 2016:
Vol. 353, Issue 6297, pp. 380-382
DOI: 10.1126/science.aaf3951

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Human-microbiota coevolution

The bacteria that make their home in the intestines of modern apes and humans arose from ancient bacteria that colonized the guts of our common ancestors. Moeller et al. have developed a method to compare rapidly evolving gyrB gene sequences in fecal samples from humans and wild chimpanzees, bonobos, and gorillas (see the Perspective by Segre and Salafsky). Comparison of the gyrB phylogenies of major bacterial lineages reveals that they mostly match the apehominid phylogeny, except for some rare symbiont transfers between primate species. Gut bacteria therefore are not simply acquired from the environment, but have coevolved for millions of years with hominids to help shape our immune systems and development.

Science, this issue p. 380; see also p. 350

Abstract

The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.

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