Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

A major theme in microbiome research is the strong effect of host diet on the composition and function of the gut microbiota. To this end, several studies have reported that hosts with similar evolutionary diet trends share key gut microbial traits that may facilitate the digestion of certain food resources. However, these studies rely heavily on samples from captive individuals and confound host phylogeny and gut morphology with diet. To more effectively test the impact of host evolutionary diet trends on the gut microbiota, we used 16S rRNA gene amplicon sequencing and shotgun metagenomics, comparing the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely-related non-folivores, evenly distributed throughout the primate Order and representing a range of gut morphological specializations. While folivory does result in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of diet. Our findings indicate that the gut microbiota is strongly constrained by evolutionary trends in host physiology and that its response to diet may be less dynamic than frequently described. More care must be taken to consider bidirectional interactions between host physiology and the gut microbiota when designing and interpreting microbiome studies, and common assumptions that specific host-gut microbe interactions can be extrapolated across a range of host species must be re-evaluated.