Global meta-analysis reveals the drivers of gut microbiome variation across vertebrates

Abstract Background Shifts in their gut microbial composition and diversity are a known mechanism vertebrates use to adapt to environmental conditions. However, the relative contribution of individual environmental factors to gut microbiota composition and diversity remains poorly understood. To understand the broad influence of different environmental factors on gut microbiome of vertebrates, we collected 6508 16S rRNA gene sequencing samples of gut bacterial communities from 113 host species, spanning seven different classes as well as different types of feeding behaviors and host habitats. Furthermore, we identified the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiomes (n = 489) and their sympatric soil environment samples (n = 203) using metagenomic sequencing analysis. Results We demonstrate that host diet patterns have a significant impact on changes in the gut microbiome. We reveal the phylum Fusobacteria is enriched in the gut of carnivorous vertebrates, while in the gut of herbivorous vertebrates there was a larger representation of Verrucomicrobia. Climate factors are also strongly associated with gut microbiome variation among vertebrates. We show that the abundance of Bacteroidetes increases gradually from high- to low-latitude zones, while Proteobacteria show a decreasing trend. In particular, we found that bacA and its flanking sequences are highly homologous among the genomes of mammals, avian gut communities, and sympatric soil biomes, suggesting that the bacA resistance gene may undergo horizontal transfer between vertebrates and sympatric environments. Conclusions Our findings show diet patterns and climatic factors play key roles in promoting specific taxa in vertebrate gut microbiota. In addition, we comprehensively decipher the common antibiotic resistance groups of wild vertebrates and their sympatric soil biological environment samples, and provide evidence of potential horizontal transfers of the bacA gene. These results significantly advance our knowledge of the diversity and structure of gut microbiomes in vertebrates and their association with environmental factors, and provide crucial insights to better manage the soil ARG pool.