Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer. IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.