Data from: Widespread extinctions of co-diversified gut bacterial symbionts from humans

Humans and other primates harbour complex gut bacterial communities that
influence health and disease, but the evolutionary histories of these
symbioses remain unclear due to a lack of information about the state of
the microbiota in ancestral primates. Here we show that hundreds of gut
bacterial lineages co-diversified with primate species over millions of
years, but that nearly half of these ancestral symbionts have been lost
from humans. Analyses of thousands of metagenome-assembled genomes from
humans, chimpanzees, bonobos, and other non-human primates revealed
significant co-diversification within ten gut bacterial phyla. Remarkably,
44% of the co-diversifying clades detected in African apes were absent
from available human metagenomic data. In contrast, only ~3% of the clades
displaying the weakest evidence for co-diversification and detected in
African apes were absent from humans. This study identifies bacterial
symbioses that predate hominid diversification, revealing accelerated
extinctions of ancestral, co-diversifying symbionts from human
populations.