Evaluation of the bacterial and fungal microbiome on the skin of Anaxyrus boreas, Rhinella marina, and Xenopus laevis and implications related to Batrachochytrium dendrobatidis susceptibility

ABSTRACTThe skin and its microbiome are the first lines of defense against environmental stressors and pathogens. The symbiotic relationships between the host and the microbiome and within the microbiome are critical to host health. In frogs, this research area is lacking especially in the context of their skin infection with Batrachochytrium dendrobatidis. B. dendrobatidis is a major fungal skin pathogen to amphibians that has caused the extinction of hundreds of amphibian species populations. While some frog species are known susceptible to B. dendrobatidis infections, and others are resistant, we hypothesized that the skin microbiome of frogs plays a role in the prevention of B. dendrobatidis infections that is yet unknown. Therefore, in this work we have examined the bacterial and fungal skin microbiome of one species that is sensitive to B. dendrobatidis infections, Anaxyrus boreas (formerly: Bufo boreas), and the resistant species, Xenopus laevis and Rhinella marina (formerly: Bufo marinus). This was accomplished using tag-encoded FLX amplicon pyrosequencing (bTEFAP) of the 16S rRNA and ITS DNA regions. Our results showed that the bacterial and fungal skin microbiome of A. boreas and R. marina were more similar than to that of X. laevis. We found distinct patterns between the skin microbiome of B. dendrobatidis sensitive and resistant frog species. For the bacterial microbiome, the most abundant bacterial genus observed in all frog samples was Microbacterium. The resistant species had higher abundance in the genera Pseudomonas, Sphingobium, Pedobacter, Variovorax, Morganella, Sphingomonas, Giesbergeria, and Agromyces. In contrast, they had lower abundance of Elizabethkingia (formerly: Flavobacterium), Enterobacter, Ochrobactrum, Arthobacter, Stenotrophomonas, Shinella, Klebsiella, Aeromonas, Comomonas, Chitinophaga, and Rhodococcus. Regarding the fungal microbiome, the resistant species showed higher abundance in the genera Aspergillus, Cladosporium, Elaphomyces, Monascus, Tritirachium, Ceratostomella, and Claviceps, while Asterotremella, Trichosporon, and Malasezzia genera were less represented in resistant species. We have also observed that in the resistant species, the skin microbiome had higher diversity in the fungal microbiota, but not in the bacterial microbiota. We speculate that those observed differences have implications in B. dendrobatidis susceptibility that are yet to be determined, possibly through competition for nutrients or the production of specific anti-fungal molecules.GRAPHICAL ABSTRACT