Host Phylogeny and Feeding Habit Jointly Govern Mammalian Gut Microbiota Composition

Host phylogeny and feeding habits constitute two fundamental determinants of gut microbiota composition. However, the differential impacts and interrelationships between these factors in shaping gut microbial communities across multispecies systems remain poorly understood. We systematically reviewed 10 974 published studies and identified 4987 qualified gut microbiota 16S rRNA sequencing samples from 60 wild mammal species, constructing an integrative multispecies database for analysis. Using this dataset, we analyzed the effects of host feeding habits and phylogeny on mammalian gut microbiota composition, and explored the relationship between phylogenetic distances among host species and the similarity in their gut microbiota composition. We found that herbivores exhibited significantly higher alpha diversity compared to carnivores and omnivores, while omnivores displayed the highest beta diversity; host phylogeny exerted stronger effects on gut microbiota composition in herbivores and omnivores compared to carnivores, as phylogenetic distance between animal species was positively correlated with microbial dissimilarity. These findings demonstrate that host phylogeny and feeding habits jointly determine mammalian gut microbiota composition. Our study highlights the synergistic effects of host phylogenetic relationships and feeding habits on the composition of gut microbial communities.