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

## TL;DR

This study compares gut microbes in wild and captive wapiti, finding that captivity changes microbial composition and function, affecting metabolism and interactions.

## Contribution

The study provides the first comprehensive profiling of bacteria, fungi, and protozoa in wild and captive wapiti gut microbiomes.

## Key findings

- Captive wapiti gut microbes are enriched in amino acid and fatty acid metabolism, with mutually exclusive microbial interactions.
- Wild wapiti gut microbes are associated with fiber utilization and mutualistic coexistence among microbes.
- Diet and environment significantly alter gut microbiome composition and function in wapiti.

## Abstract

Diet and living environments can profoundly influence the composition of animal gut microbiota. Current research primarily focuses on detecting bacterial communities in animal intestines, with less attention paid to fungi and protozoa. This study comprehensively characterized bacteria, fungal and protozoan communities in fecal samples from wild and captive Chinese wapiti. Results revealed significant differences in gut microbial communities and functional characteristics between captive and wild wapiti. Fecal microbiota in captive wapiti was enriched with microbes involved in amino acid and fatty acid metabolism, exhibiting predominantly mutually exclusive interactions between bacteria, fungi, and protozoa. Conversely, wild wapiti harbored an abundant fecal microbiota associated with fiber utilization, characterized by largely mutualistic coexistence among bacteria, fungi, and protozoa. These findings suggest that domestication leads to alterations in the intestinal microbiota of wapiti.

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) (n = 10) and captive (DA) (n = 11) wapiti (Cervus canadensis) in China. Results reveal distinct microbial profiles between the two groups. In wild wapiti, Escherichia-Shigella and UCG-005 were the dominant bacterial genera, while Succinivibrio and Treponema predominated in captive individuals. Among fungi, Agaricus and Preussia were most abundant in wild wapiti, whereas Xeromyces was identified in captive ones. For protozoa, Heteromita was the primary genus in wild wapiti, while Heteromita, Entamoeba, and Eimeria 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.