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ABSTRACT: DNA extraction for fungal and bacterial targeted metagenomics

PROVIDER: PRJNA548447 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9277350_1.fastq.gz	Fastqsanger.gz
	SRR9277350_2.fastq.gz	Fastqsanger.gz
	SRR9277351_1.fastq.gz	Fastqsanger.gz
	SRR9277351_2.fastq.gz	Fastqsanger.gz
	SRR9277352_1.fastq.gz	Fastqsanger.gz

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Project description:BackgroundAntibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over three months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. ResultsWhile the bacterial community recovered mostly over three months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared three months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrate in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.ConclusionsWe demonstrate that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Linked data:Metagenomics has been submitted to NCBI SRA repository as projects PRJNA573821, PRJNA573905 and PRJNA579284.

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