Captivity Reduces Gut Microbial Diversity and Metabolic Pathway Abundance Across Mammals with Different Diet and Gut Fermentation Types

Captivity has a large impact on mammalian microbiomes, which play vital roles in host digestion and immune function. Captivity introduces environmental changes, such as altered diets and reduced species exposure, that often lead to decreased microbial diversity. Recent research has shown that diet type and gut fermentation strongly influence beta diversity differences in captive populations, but a knowledge gap exists on how these factors influence the gut microbial composition and metabolic functions. Using paired wild and captive samples from over 40 mammalian species, we examined how captivity affects gut microbiome composition and metabolic pathways across diet and gut fermentation types. Differential expression analysis showed an overall reduction in microbial abundance for captive mammals, highlighting the phyla, Bacillota and Bacteroidota, as key contributors. The largest difference between wild and captive populations was observed for foregut fermenters and herbivores. Furthermore, indicator species analysis revealed that wild mammals consistently harbored more unique microbial taxa, primarily from Bacillota and Bacteroidota once again. Wild foregut fermenters and omnivores exhibited the highest number of indicator species among their respective categories. Lastly, functional analysis with PICRUSt2 revealed that captivity was associated with widespread downregulation of metabolic pathways across all diet and gut fermentation types, with carnivores and non-fermenters most affected. Our findings demonstrate that captivity profoundly alters the gut microbiome through a reduction in diversity and metabolic function, underscoring the importance of mitigating microbiome disruption in conservation efforts.