Shotgun metagenomics and isolate sequencing for environmental microbial communities

In this pilot study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to help establish optimum protocols and approaches for sample processing. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced these samples with shotgun metagenomics at high depth (~200 million reads per sample). Alongside this, we cultured multiple single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data.