Comparative Profiling of the Fecal Bacteriome, Mycobiome, and Protist Community in Wild Versus Captive (Cervus canadensis)

Diet and living environments exert a profound influence on gut microbiota composition. This study presents the first comprehensive characterization of fecal bacteria, fungi, and protozoa in wild (WA) (<i>n</i> = 10) and captive (DA) (<i>n</i> = 11) wapiti (Cervus canadensis) in China. Results reveal distinct microbial profiles between the two groups. In wild wapiti, <i>Escherichia-Shigella</i> and <i>UCG-005</i> were the dominant bacterial genera, while <i>Succinivibrio</i> and <i>Treponema</i> predominated in captive individuals. Among fungi, <i>Agaricus</i> and <i>Preussia</i> were most abundant in wild wapiti, whereas <i>Xeromyces</i> was identified in captive ones. For protozoa, <i>Heteromita</i> was the primary genus in wild wapiti, while <i>Heteromita</i>, <i>Entamoeba</i>, and <i>Eimeria</i> were the main genera in captive wapiti. Functional predictions further underscored these differences. In wild wapiti, bacterial and fungal functions were primarily associated with carbon metabolism and the pyruvate cycle, with mutualistic interactions prevailing among bacteria, fungi, and protozoa. Conversely, captive wapiti exhibited functional profiles centered on lipopolysaccharide and amino acid metabolism, also characterized by mutualistic coexistence among microbial communities. These findings highlight the significant impact of dietary composition on the gut microbiome. In summary, wild wapiti appear to possess a superior capacity for plant fiber utilization. These findings provide valuable data for the health management of farmed wapiti and their adaptability in natural habitats.