Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids

Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (Gorilla gorilla gorilla, Gorilla beringei beringei), three chimpanzee subspecies (Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii), and bonobos (Pan paniscus), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family Dialisteraceae, though we find that overall, co-phylogeny patterns are frequently disrupted in humans. ### Competing Interest Statement The authors have declared no competing interest.