Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas, across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd-inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd-inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd-inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.

宿主相关微生物组（Host-associated microbiomes）具有诸多有益功能，包括抵御病原体以及训练免疫系统。本研究表明，人工饲养环境下发育的两栖动物会丧失大量皮肤细菌多样性，这主要源于环境来源的持续输入量减少。本研究结合了野生与人工饲养两栖动物的研究，同时使用包含逾1000株菌株的数据库，得以深入分析皮肤微生物组（skin microbiome）的抗真菌功能。我们对62只濒危北方蟾蜍（*Anaxyrus boreas*）的皮肤细菌群落进行了18个时间点的追踪，涵盖4种益生菌处理方案，以及两次在人工饲养条件下暴露于致死性真菌病原体蛙壶菌（*Batrachochytrium dendrobatidis*, Bd）的实验，并将这些数据与同期同生命阶段野生种群采集的33份样本进行对比。随着人工饲养的两栖动物随时间推移逐渐丧失可抑制Bd的细菌，暴露于Bd的个体感染率从首次暴露时的33%升至第二次暴露时的100%。接种可抑制Bd的益生菌詹氏杆菌（*Janthinobacterium lividum*）后，第二次Bd攻毒实验中的存活率提升了40%，这表明通过恢复可抑制Bd的细菌，微生物组耗竭带来的负面影响是可逆的。综上，本研究阐明了皮肤相关细菌的持续环境输入在抵御破坏性两栖动物病原体中的功能作用，并证实长期人工饲养会削弱这一防御功能。