The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data.

Eria A Rebollar,Elhanan Borenstein,Lisa K Belden,Myra C Hughey,Ana Gutiérrez-Preciado,Cecilia Noecker,Daniel Medina,Roderick V Jensen,Jenifer B Walke,Reid N Harris,Alexander Eng

doi:10.3389/fmicb.2018.00466

Abstract

Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog, Craugastor fitzingeri. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found that Pseudomonas was a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found genes enriched either in Sapo or Sob. We then focused our study on five functional classes of genes: biosynthesis of secondary metabolites, metabolism of terpenoids and polyketides, membrane transport, cellular communication and antimicrobial drug resistance. These gene classes are potentially involved in bacterial communication, bacterial-host and bacterial-pathogen interactions among other functions. We found that C. fitzingeri metagenomes have a wide array of genes that code for secondary metabolites, including antibiotics and bacterial toxins, which may be involved in bacterial communication, but could also have a defensive role against pathogens. Several genes involved in bacterial communication and bacterial-host interactions, such as biofilm formation and bacterial secretion systems were found. We identified specific genes and pathways enriched at the different sites and determined that gene co-occurrence networks differed between sites. Our results suggest that skin microbiomes are composed of distinct bacterial taxa with a wide range of metabolic capabilities involved in bacterial defense and communication. Differences in taxonomic composition and pathway enrichments suggest that skin microbiomes from different sites have unique functional properties. This study strongly supports the need for shotgun metagenomic analyses to describe the functional capacities of skin microbiomes and to tease apart their role in host defense against pathogens.

Highlights

Microbial symbiotic communities are ubiquitous in animals and plants
Our results indicate that both methods gave similar results when trying to define the dominant groups present on amphibian skin bacterial communities (PROTEST nperm = 999 p = 0.0069)
We described the taxonomic and functional diversity of C. fitzingeri skin metagenomes, and we compared these microbiomes between two populations, one being from a Bd-endemic site (Sob) and the other from a Bd-naïve site (Sapo)

Summary

Introduction

Microbial symbiotic communities are ubiquitous in animals and plants. For decades, most of the studies in animals have focused on insect endosymbionts, which generally involve only a few bacterial species (Dale and Moran, 2006), whereas more recent studies, mainly in humans, have revealed a complex community of microbes coexisting with their host (Turnbaugh et al, 2007; Grice, 2014; Jorth et al, 2014). Recent studies have determined that the skin of amphibians harbors bacterial communities that are unique to different species (McKenzie et al, 2012; Kueneman et al, 2014; Walke et al, 2014; Belden et al, 2015; Costa et al, 2016; Rebollar et al, 2016; Bletz et al, 2017a) and might play an important role in protecting the host against Batrachochytrium dendrobatidis, Bd (Harris et al, 2009; Becker et al, 2011; Kueneman et al, 2016). Skin bacterial community structure before infection can predict mortality and morbidity after infection (Becker et al, 2015a; Walke et al, 2015)

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Conclusion