Impact of captivity on gut microbiota, tracheal microbiota and metabolic pathways in wild chipmunks

Understanding the effects of captivity on wild animals is essential, as it helps to improve the physical health and welfare of captive wild animals. The changes in environment, diet and other factors during the captivity may reshape their internal microbiota and affect the body’s metabolism. Using 16S rRNA gene sequencing, we analyzed gut and tracheal microbiota from wild and captive chipmunks, and examined differences in serology, histopathology, fat metabolism, and muscle quality. The dominant bacterial phyla in the gut and tracheal microbiota of chipmunks are Firmicutes, Bacteroidota, and Proteobacteria, with the gut and tracheal microbiota of captive chipmunks showing an increase in the Spirochaetota and Patescibacteria at the phylum level. No major organ (the heart, lung, colon, muscle and kidney) damage was observed in captive chipmunks. Fat metabolism analysis revealed increased expression of genes related to fat processing (PPARG, ACACA, FASN, ELOVL1, LPL, and SCD). Muscle gene expression analysis showed higher levels of MYH1, MYH2, and MYH7, in captive chipmunks. These findings suggest that core bacterial types remained largely stable, but there were shifts in bacterial types that aid digestion during the laboratory captivity. Meanwhile, the fat metabolism of the captive chipmunks also changed, which supports muscle fatty acid absorption, and shifts muscle fiber types from fast to slow, promoting muscle synthesis and energy efficiency in captive chipmunks. Our study provides new insights into the influence of laboratory captivity on wild animals, establishes a foundation for facilitating the transformation of wild chipmunks into experimental animals.