Shared and genus-specific impact of domestication on mammal oral microbiomes revealed through museomics

Abstract

Animal domestication involves genetic, behavioural and ecological changes, all of which also impact the host-associated microbial communities. Early studies reported diversity loss in the gut microbiomes of domestic and captive animals, but comparisons across a wider diversity of host species showed that loss of microbiota does not always occur. For microbial communities other than the gut, comparisons of multiple domestic-wild pairs are lacking. Here, we use dental calculus metagenomics to investigate the impact of a domesticated lifestyle on the oral microbiome of three pairs of wild and domestic mammals from the genera Equus (plains zebra, horse), Ovis (argali, sheep) and Sus (wild boar, pig). We find that the oral microbiome of the three domesticates differs both in terms of taxonomic composition and functional capacity from their wild counterparts, but the change is smaller in Sus than the other two pairs. While the microbiomes of sheep and horses bear increased resemblance to those of humans compared to their wild relatives, this is unlikely to be due to colonisation by human-derived microbes, as our results suggest that ancestral lineages are mostly retained. Overall, the oral microbiome shows both a consistent signal of domestication, found across all three clades, and a host genus-dependent effect, which likely results from specific changes that underpinned each domestication event.