Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors

The lability of the gut microbiome has been posited as an additional axis of animals' phenotypic plasticity. However, whether and how such plasticity varies across hosts with different biological features remains unclear. Usinggenome-resolved metagenomics coupled joint-species distribution modelling, we compared how the taxonomic, phylogenetic and functional microbial dynamics varied across a series of disturbances in two mammals: the insectivorous-specialist Crocidura russula and the omnivorous-generalist Apodemus sylvaticus. Although microbiome alpha diversity of both species remained stable, C. russula exhibited substantially higher variability and directionality of microbial responses than A. sylvaticus. Our results indicate that the intrinsic properties (e.g., diversity, functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.