Metagenomic profiling of commercially available fermented food samples

Metagenomic profiling of commercially available fermented foods using Illumina shotgun metagenomic sequencing. Using a curated database of fermented food-associated microbial genomes and a Nextflow workflow for profiling the presence of micobial genomes in metagenomic reads, we profiled our ~100 fermented food samples and kept genomes that had at least 0.05X coverage in a sample.