Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.

由于广泛的偷猎和全球贩运，穿山甲是最濒危的动物之一。圈养繁殖被认为是保护它们和增加种群规模的一种方式。然而，在肠道微生物群背景下对圈养和野生穿山甲的比较研究很少见。在这里，比较了圈养和没收获救的野生穿山甲的肠道微生物组，并考虑了不同时期的圈养和圈养与抗生素治疗的影响。我们表明，不同的饮食和圈养时期，以及抗生素治疗的应用，可以改变穿山甲的肠道群落组成和丰度。与野生穿山甲相比，圈养穿山甲对甲壳素和纤维素/半纤维素降解、脂肪酸代谢、和短链脂肪酸合成，但代谢外源物质的能力降低。除了增加圈养肠道微生物群代谢营养物质的能力外，圈养繁殖还会导致圈养穿山甲的抗生素抗性基因和毒力因子比野生穿山甲更丰富，从而给生存带来一些风险。我们的研究对于制定穿山甲保护指南非常重要，包括健康评估、疾病预防和野生穿山甲种群的康复。圈养繁殖会导致圈养穿山甲比野生穿山甲拥有更多丰富的抗生素抗性基因和毒力因子，从而给生存带来一些风险。我们的研究对于制定穿山甲保护指南非常重要，包括健康评估、疾病预防和野生穿山甲种群的康复。圈养繁殖会导致圈养穿山甲比野生穿山甲拥有更多丰富的抗生素抗性基因和毒力因子，从而给生存带来一些风险。我们的研究对于制定穿山甲保护指南非常重要，包括健康评估、疾病预防和野生穿山甲种群的康复。