Data from: Composition of micro-eukaryotes on the skin of the Cascades frog (Rana cascadae) and patterns of correlation between skin microbes and Batrachochytrium dendrobatidis

Global amphibian decline linked to fungal pathogens has galvanized research on applied amphibian conservation. Skin-associated bacterial communities of amphibians have been shown to mediate fungal skin infections and the development of probiotic treatments with antifungal bacteria has become an emergent area of research. While exploring the role of protective bacteria has been a primary focus for amphibian conservation, we aim to expand and study the other microbes present in amphibian skin communities including fungi and other micro-eukaryotes. Here, we characterize skin-associated bacteria and micro-eukaryotic diversity found across life stages of Cascades frog (Rana cascadae) and their associated aquatic environments using culture independent 16S and 18S rRNA marker-gene sequencing. Individuals of various life stages of Cascades frogs were sampled from a population located in the Trinity Alps in Northern California during an epidemic of the chytrid fungus, Batrachochytrium dendrobatidis. We filtered the bacterial sequences against a published database of bacteria known to inhibit B. dendrobatidis in co-culture to estimate the proportion of the skin bacterial community that is likely to provide defense against B. dendrobatidis. Tadpoles had a significantly higher proportion of B. dendrobatidis-inhibitory bacterial sequence matches relative to subadult and adult Cascades frogs. We applied a network analysis to examine patterns of correlation between bacterial taxa and B. dendrobatidis, as well as micro-eukaryotic taxa and B. dendrobatidis. Combined with the published database of bacteria known to inhibit B. dendrobatidis, we used the network analysis to identify bacteria that negatively correlated with B. dendrobatidis and thus could be good probiotic candidates in the Cascades frog system.

与真菌病原体相关的全球两栖动物种群衰退，催生了两栖动物应用保护领域的研究热潮。两栖动物的皮肤共生细菌群落可调控真菌性皮肤感染的发生发展，而基于抗真菌细菌的益生菌疗法研发也已成为新兴研究热点。尽管保护性细菌的功能研究已成为两栖动物保护的核心方向，但本研究旨在拓展研究范畴，对两栖动物皮肤群落中包括真菌与其他微型真核生物在内的其他微生物展开系统调查。本研究依托免培养16S与18S rRNA标记基因测序技术，对喀斯喀特蛙（Rana cascadae）不同生活史阶段个体及其关联水生环境中的皮肤共生细菌与微型真核生物多样性进行了表征分析。研究样本采集自北加州三一阿尔卑斯地区的喀斯喀特蛙种群，采样期间正值蛙壶菌（Batrachochytrium dendrobatidis，简称Bd）的流行暴发期。我们将测序得到的细菌序列与已发表的、经共培养实验验证可抑制B. dendrobatidis的细菌数据库进行比对，以此估算皮肤细菌群落中具备抵御B. dendrobatidis潜力的菌群所占比例。相较于亚成体与成体喀斯喀特蛙，蝌蚪样本中匹配到可抑制B. dendrobatidis的细菌序列的比例显著更高。我们采用网络分析方法，探究了细菌类群、微型真核生物类群分别与B. dendrobatidis之间的关联模式。结合上述已发表的抗B. dendrobatidis细菌数据库，我们通过网络分析筛选出与B. dendrobatidis呈负相关的细菌类群，这些类群有望成为喀斯喀特蛙保护体系中的潜在益生菌候选菌株。