Change in the Fecal Microbiota of the Wild Cavy (Cavia tschudii) during the transition to captavity

This study investigated the effects of captivity and a controlled diet on the fecal microbiota of the wild guinea pig (Cavia tschudii), integrating forage nutritional analysis. Five wild-captured individuals were maintained for 21 days on an alfalfa and Brachiaria mutica diet. 16S rRNA sequencing yielded over one million reads and 4,131 ASVs, revealing reduced alpha diversity and distinct microbiota between wild and captive states. Dominant phyla were Bacteroidetes and Firmicutes, with notable shifts in Prevotellaceae and Ruminococcaceae. Functional predictions indicated metabolic changes related to DNA replication, repair, and energy metabolism. These findings highlight the significant impact of captivity and diet on microbial structure and function, with implications for the management, conservation, and domestication of wild species.