How Host Phylogeny, Diet, and Habitat Affect Gut Microbial Diversity in Wild Snakes

Gut microbiota plays critical roles in host digestion, immune regulation, neurochemical signaling, and metabolic homeostasis. Based on wild snakes (73 individuals from 23 species) from China, we explored the composition, characteristics, and functions of gut microbes across different groups using fecal metagenomic samples; further we explored the relative contributions of host phylogeny, diet, and habitat to the microbial structure. Among 23 wild snake species, the dominant gut microbial phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with Bacteroides, Salmonella, Citrobacter, and Aeromonas comprising the major genera. Mantel test revealed a significant correlation (r = 0.3173, p = 0.0055) between microbial composition at the genus level and host genetic divergence (p-distance), indicating potential phylogenetic influence on gut microbial profiles. While α-diversity and principal coordinate analysis showed no marked differences across different subgroups. Linear discriminant analysis effect size demonstrated notable differences in the gut microbes of the terrestrial snakes with different diets and vertebrate-feeding snakes with different habitats. Functional annotation of microbial genes indicated enrichment in metabolic processes, as well as environmental and genetic information processing. Carbohydrate-active enzymes were predominantly from GT2, GT4, GT51, and GH23 families. Linear discriminant analysis effect size showed different diets and habitats had distinct differential taxa. Additionally, antibiotic resistance gene profiles varied across groups, with acrB, AcrF, MexB, acrD, and mdtF being most prevalent. Future studies should increase the samples and comprehensively consider different ecological factors to explore the impacts on the composition and functions of snake gut microbes on different evolutionary, which will provide a deeper understanding of the interrelationships between snake gut microbes and their hosts.