Dysbiosis and Accumulation of Antimicrobial Resistance in the Gut Bacterial Reservoir of Captive Sloth Bear (Melursus ursinus)

Captivity-associated conditions are major factors which modulate the gut microbiota in wild animals, as they receive several medications/ antibiotics, and are also exposed to various anthropogenic stressors throughout their captive lives. Our understanding of how these factors modify the gut microbiome, its resistome and associated mobile genetic elements (MGEs) is nascent at the very best. In this study, we analysed metagenomic data from 215 captive sloth bears in multiple facilities across India to describe their gut microbiota in association to age, gender, duration in captivity, health status and body condition, recent exposure to antibiotics/ other medications, and presence of chronic hepatic/ renal disorders and tuberculosis. Overall, we found low microbial diversity across all sampled locations, and this seems to decrease with age of animal and duration in captivity. Streptococcus , Sarcina , Escherichia , Clostridium and Klebsiella were the most abundant genera, richly populated with E. coli , E. faecium , K. variicola and S. alactolyticus . We observed a very diverse resistome, and almost all bears consistently showed high levels of antimicrobial resistance (AMR), even when not treated recently with antibiotics, indicating pleiotrophic effects in pathogenic bacteria adapting to captivity stress and horizontal gene transfer through MGEs. Abundances of Shigella , Escherichia , Salmonella , Citrobacter and Kluyvera positively correlated to ARG abundance and richness. We further observed that ARGs, which confer resistance to multiple drugs, were associated with plasmids and other MGEs making them highly virulent. In summary, our study highlights the importance of large scale metagenomic studies to understand the effects of captivity on the gut health of endangered animals, and to ultimately help improve conservation strategies.