The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples.

ABSTRACT:

Background

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 mi

SUBMITTER: Gweon HS 

PROVIDER: S-EPMC8204541 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature