Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii).

Simple Summary: The Chinese three-keeled pond turtle is an endangered species in the wild but with large-scale farming. However, it is difficult to distinguish individuals belonging to different habitats from their appearance. The current study investigates intestinal microbial diversity, metabolic pathways, and resistance to various types of antibiotics among wild, farm, and released turtles. The results showed that at the phylum level, Bacteroidota, Firmicutes, Fusobacteriota, and Actinobacteriota were abundant in the wild group, but Chloroflexi was only dominant in the farm and released groups. In addition, most genera increased in the groups of farm and released turtles, while few were abundant in the wild group. A metabolic pathway analysis revealed heightened activity in the associated pathways in the wild turtles. The antibiotic resistance gene macB was higher in the farm turtle group, while tetA was more abundant in the wild turtles, and srpYmcr was abundant in the released group. These outcomes were deemed helpful for a better understanding of the relationship between the intestinal microbiota of Mauremys reevesii and its habitats and could be useful for tracking habitats to protect, manage, and conserve this endangered species. The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species. [ABSTRACT FROM AUTHOR]