Cospeciation of gut microbiota with hominids

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…

• NS
  National Science Foundation

  Award: 2011119472
• HU
  Harvard University
• AN
  Agence Nationale de Recherches sur le Sida et les Hépatites Virales

  Award: 12125/12182/12255/12325
• NI
  National Institutes of Health

  Awards: R01 AI120810, R01 GM101209, R37 AI050529, R01 AI091595, P30 AI045008