Antifungal isolates database of amphibian skin‐associated bacteria and function against emerging fungal pathogens

Abstract

Microbial symbionts of vertebrate skin have an important function in defense of the host against pathogens. In particular, the emerging chytrid fungus Batrachochytrium dendrobatidis, causes widespread disease in amphibians but can be inhibited via secondary metabolites produced by many different skin‐associated bacteria. Similarly, the fungal pathogens of terrestrial salamander eggs Mariannaea elegans and Rhizomucor variabilis are also inhibited by a variety of skin‐associated bacteria. Indeed, probiotic therapy against fungal diseases is a recent approach in conservation medicine with growing experimental support. We present a comprehensive Antifungal Isolates Database of amphibian skin‐associated bacteria that have been cultured, isolated, and tested for antifungal properties. At the start, this database includes nearly 2000 cultured bacterial isolates from 37 amphibian host species across 18 studies on five continents: Africa, Oceania, Europe, and North and South America. As the research community gathers information on additional isolates, the database will be updated periodically. The resulting database can serve as a conservation tool for amphibians and other organisms, and provides empirical data for comparative and bioinformatic studies. The database consists of a FASTA file containing 16S rRNA gene sequences of the bacterial isolates, and a metadata file containing information on the host species, life‐stage, geographic region, and antifungal capacity and taxonomic identity of the isolate.

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)

“…We utilized a concurrently developed database of cultured Bd-inhibitory bacteria (referred to here as the 'inhibitory database'), containing 1255 16S rRNA gene sequences isolated from amphibian skin (Woodhams et al, 2015). Many studies have tested these isolates for bioactivity against fungal pathogens including Bd, Mariannaea elegans and Rhizomucor variabilis in coculture challenge assays, summarized by Woodhams et al (2015).…”

“…Many studies have tested these isolates for bioactivity against fungal pathogens including Bd, Mariannaea elegans and Rhizomucor variabilis in coculture challenge assays, summarized by Woodhams et al (2015). From this database, we generated OTU lists by clustering sequences at 97% similarity using the Greengenes August 2013 reference.…”

“…(a) Mean percent of bacterial sequencing reads with Bd-inhibitory function, from boreal toad life-stages or environmental samples (across all sites, sample sizes in parentheses). Bd-inhibitory function was determined by matching OTUs to the database described in the methods and Woodhams et al, 2015. Four different bioinformatic algorithms were used to identify Bd-inhibitory OTUs as described in the methods section: exact match sequences, trimmed exact matches, exclusively inhibitory matches, and expected inhibitory matches.…”

“…After OTU filtering using the Bd-inhibitory bacterial OTUs database (Woodhams et al, 2015), we found 35 OTUs with exact matches and 85 OTUs with trimmed exact matches within the boreal toad data set, 495 expected inhibitory OTUs, and 479 exclusively inhibitory OTUs using the expanded phylogenetic estimation. We find a significant difference in the proportion of known inhibitory sequences by life stage, and the same pattern for all inhibitory data sets by Kruskal-Wallis test: exact match Po0.001, trimmed exact match Po0.001, expected inhibitory P = 0.005, and exclusively inhibitory P = 0.006, (Figure 5a).…”

“…These examples suggest that the assembly of microbial symbionts in early life stages may have adaptive significance for adult host health. The role of symbiotic microbes in defending against pathogens affecting amphibians is an area of intense interest (Harris et al, 2009;Woodhams et al, 2015), although studies to date have primarily focused on post-metamorphic amphibians. The process of symbiont community assembly through host development for both pre-and post-metamorphosis has not been explored and is the aim of the current study.…”