Comparative analysis of gut microbiota and fecal metabolites in captive and wild Gansu red deer

Gut microbiota is the largest and most complex micro-ecosystem in animals, influenced by the host’s dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Nevertheless, the composition of Gansu red deer (Cervus elaphusKansuensis) gut bacteria is not known. In this study, the composition and diversity of gut microbiome and fecal metabolomics of C. elaphusKansuensis were identified and compared for the first time using 16S-rRNA gene sequencing, metagenomic sequencing and a combination of untargeted liquid chromatogram-mass spectrometry (LC-MS). There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphusKansuensis. At the genus level, UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD), andBacteroidales_RF16_group was dominant in CRD, whereas Bacillus was dominant in WRD. Metagenomic sequencing showed similar results to 16s rRNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rRNA sequencing and metagenomic datasuggested that Bacteroides and Bacillusmight serve as a marker microbiota for both CRD and WRD. LC-MS/MS results showed that 520 significantly different metabolites were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggest that the large differences in gut microbiota composition and fecal metabolites between CRD and WRD may be due to the fact that different diet habits and living environments over time have developed their own stable gut microbiome characteristics to meet their respective survival and reproduction needs.