Data from: Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis

The introduction of next-generation sequencing has allowed for greater understanding of community composition of symbiotic microbial communities. However, determining the function of individual members of these microbial communities still largely relies on culture-based methods. Here, we present results on the phylogenetic distribution of a defensive functional trait of cultured symbiotic bacteria associated with amphibians. Amphibians are host to a diverse community of cutaneous bacteria and some of these bacteria protect their host from the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) by secreting antifungal metabolites. We cultured over 450 bacterial isolates from the skins of Panamanian amphibian species and tested their interactions with Bd using an in vitro challenge assay. For a subset of isolates, we also completed co-culture experiments and found that culturing isolates with Bd had no effect on inhibitory properties of the bacteria, but it significantly decreased metabolite secretion. In challenge assays, approximately 75% of the bacterial isolates inhibited Bd to some extent and these inhibitory isolates were widely distributed among all bacterial phyla. Although there was no clear phylogenetic signal of inhibition, three genera, Stenotrophomonas, Aeromonas, and Pseudomonas, had a high proportion of inhibitory isolates (100%, 77%, and 73%, respectively). Overall, our results demonstrate that antifungal properties are phylogenetically widespread in symbiotic microbial communities of Panamanian amphibians, and that some functional redundancy for fungal inhibition occurs in these communities. We hope that these findings contribute to the discovery and development of probiotics for amphibians that can mitigate the threat of chytridiomycosis.

下一代测序（next-generation sequencing）技术的问世，让学界得以更深入地解析共生微生物群落的组成结构。然而，要明确这些微生物群落中单个成员的功能，目前仍主要依赖基于纯培养的实验方法。本研究针对与两栖动物共生的已培养共生细菌的防御性功能性状的系统发育分布情况，展示相关研究成果。

两栖动物体表定殖着多样的细菌群落，其中部分细菌可通过分泌抗真菌代谢产物，帮助宿主抵御致命真菌病原体蛙壶菌（Batrachochytrium dendrobatidis, Bd）。我们从巴拿马两栖动物的皮肤样本中分离培养了450余株细菌分离株，并通过体外挑战实验（in vitro challenge assay）检测了这些菌株与Bd的相互作用。针对部分菌株，我们还开展了共培养实验，结果显示：与Bd共培养并不会影响细菌的抑菌活性，但会显著降低其代谢产物的分泌量。

在挑战实验中，约75%的细菌分离株可在一定程度上抑制Bd，且这些具有抑菌活性的菌株广泛分布于各个细菌门中。尽管未发现明确的抑菌活性系统发育信号，但寡养单胞菌属（Stenotrophomonas）、气单胞菌属（Aeromonas）和假单胞菌属（Pseudomonas）这三个属的抑菌菌株占比极高，分别为100%、77%和73%。总体而言，本研究结果表明，抗真菌活性在巴拿马两栖动物的共生微生物群落中具有广泛的系统发育分布特征，且该类群落中存在一定程度的真菌抑制功能冗余性。我们期望本研究结果能够助力两栖动物益生菌的开发与筛选，从而缓解壶菌病（chytridiomycosis）对两栖动物的生存威胁。