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Amphibian metagenome

ABSTRACT: Metagenome amplicon sequencing of amphibian skin bacteria

PROVIDER: PRJNA940133 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25610200.fastq.gz	Fastqsanger.gz
	SRR25610300.fastq.gz	Fastqsanger.gz
	SRR25610201.fastq.gz	Fastqsanger.gz
	SRR25610202.fastq.gz	Fastqsanger.gz
	SRR25610203.fastq.gz	Fastqsanger.gz

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Project description:Determining the mechanisms of host-pathogen interaction is critical for understanding and mitigating infectious disease. Mechanisms of fungal pathogenicity are of particular interest given the recent outbreaks of fungal diseases in wildlife populations. Our study focuses on Batrachochytrium dendrobatidis (Bd), the chytrid pathogen responsible for amphibian declines around the world. Previous studies have hypothesized a role for several specific families of secreted proteases as pathogenicity factors in Bd, but the expression of these genes has only been evaluated in laboratory growth conditions. Here we conduct a genome-wide study of Bd gene expression under two different nutrient conditions. We compare Bd gene expression profiles in laboratory growth media and in host tissue (i.e., frog skin). A large proportion of genes in the Bd genome show increased expression when grown in host tissue, indicating the importance of studying pathogens in their infection environment. A number of gene classes show particularly high levels of expression in host tissue, including three families of secreted proteases (metallo-, serine- and aspartyl-proteases), adhesion genes, lipase-3 encoding genes, and a group of phylogenetically unusual crinkler-like effectors. We discuss the roles of these different genes as putative pathogenicity factors and discuss what they can teach us about Bd's metabolic targets, host invasion, and pathogenesis. One 12-plex chip was analyzed from 12 RNA samples extracted from Batrachochytrium dendrobatidis grown in 2 substrates. Six biological replicates were used for each substrate - sterile frog skin and tryptone nutrient broth. The same dye, Cy5, was used for all samples.

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LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

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