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.

全球两栖动物种群因真菌病原体引发衰退，这一现状推动了两栖动物保护应用研究的蓬勃发展。两栖动物皮肤相关细菌群落已被证实可介导真菌性皮肤感染的调控过程，而基于抗真菌细菌的益生治疗方案研发亦成为当前新兴研究热点。尽管探明保护性细菌的功能始终是两栖动物保护研究的核心方向，但本研究旨在拓展研究边界，对两栖动物皮肤群落中除细菌外的其他微生物（包括真菌与其他微真核生物）展开系统性研究。本研究采用非培养依赖型16S与18S rRNA标记基因测序技术，对喀斯喀特蛙（Rana cascadae）不同生命阶段个体的皮肤相关细菌与微真核生物多样性，及其栖息的水生环境进行表征分析。研究采样于北加州三一阿尔卑斯地区的一处喀斯喀特蛙种群，采样时段正处于蛙壶菌（Batrachochytrium dendrobatidis）的流行期，采样对象覆盖该蛙类的全部生命阶段。我们将获得的细菌序列与已发表的、经共培养实验证实可抑制蛙壶菌的细菌数据库进行比对筛选，以此估算皮肤细菌群落中具备潜在抗该蛙壶菌防御能力的菌群占比。数据分析结果显示，相较于亚成体与成年喀斯喀特蛙，蝌蚪样本中匹配到可抑制该蛙壶菌的细菌序列的占比显著更高。我们进一步采用网络分析方法，探究细菌类群与该蛙壶菌、以及微真核生物类群与该蛙壶菌之间的关联模式。结合上述已发表的抗该蛙壶菌细菌数据库，我们通过网络分析筛选出与该蛙壶菌呈显著负相关的细菌类群，这些类群有望成为喀斯喀特蛙保护体系中的优质益生候选菌株。