Ecological and Environmental Factors Influence the Gut Microbiome Structure in Wild Mammals

The mammalian gut microbiome represents a critical symbiotic ecosystem influencing host metabolism, immunity, and ecological adaptation, yet comprehensive understanding of how ecological and environmental factors shape microbial diversity across mammalian species remains limited, constraining our ability to predict microbiome responses to global environmental change and inform conservation strategies. This study addresses this knowledge gap through an integrative meta-analysis of 1,443 high-quality gut microbiome samples from 173 wild mammalian species spanning diverse global habitats, integrating high-resolution climate data (temperature and precipitation), ecological variables (diet type, habitat range, and body mass), IUCN conservation status, and advanced metagenomic analyses using QIIME 2 with phylogenetic diversity metrics and multivariate statistical models. Diet type emerged as the dominant ecological determinant, with herbivores harbouring significantly higher microbial diversity than carnivores (Faith PD approximately 2.1-fold higher; 95% CI: 1.86–2.31), reflecting diet-specific selection. Habitat area and host taxonomic order were also robust predictors of microbial diversity, with smaller-ranging species and several mammalian orders supporting distinctly higher diversity, while body mass was significantly associated with phylogenetic diversity but not with evenness, indicating a metric-dependent rather than uniform relationship with host body size. Precipitation showed a non-monotonic relationship with microbial evenness, with both very-low and very-high precipitation zones supporting greater evenness than intermediate zones, whereas temperature and IUCN conservation status were not significant predictors of microbial diversity. These findings establish that ecological and environmental factors collectively govern mammalian gut microbiome assembly through complex multidimensional interactions, with profound implications for understanding host-microbe co-evolution, predicting microbiome vulnerability to climate change and anthropogenic pressures, and designing microbiome-based conservation strategies to safeguard both mammalian and microbial biodiversity.