Gut Microbiome Community Assembly Across Three Snake Communities

Microbial communities associated with vertebrate hosts (microbiomes) play crucial roles in host physiology including nutrient acquisition and the immune response. Microbiomes are structured by host ecology and evolution, yet gut microbiome studies of wild reptile hosts are lacking. This study investigated the gut microbiome of wild snakes across three geographically distinct regions (tropical, subtropical, and temperate), revealing that snake gut microbiome is generally conserved at the host family level. Core bacterial taxa identified in snake gut communities include Gammaproteobacteria, Bacilli, Bacteroidia, Betaproteobacteria, Alphaproteobacteria, Clostridia, and Flavobacteria, aligning with previous findings. Despite this broad conservation across the snake gut microbiome, geographic locality significantly influenced bacterial community structure and diversity. Host phylogeny, physiological traits, and factors related to host ecological niche further shaped the gut microbiome structure within each regional community, as with patterns reported for other ectotherms. Foraging mode exerted a strong influence on bacterial composition, likely because of its influence on feeding frequency and meal size. Habitat use significantly impacted microbiome structure in two of the three host communities, suggesting a link to foraging strategy and diet. Broadly, snake gut microbiome composition is conserved despite thousands of kilometers of separation between host communities, and the snake gut microbiome is largely reflective of host niche and phylogeny.