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. Files include: FF samples - Combined master sheet.tsv - metadata sheet for each sample, can be joined with other files based on the sample code with structure FF#### all-profiles-0.05x-covg-filtered-binary-matrix.tsv - Results table from sylph filtered for minimum effective coverage of 0.05X across the genome, and transformed to a binary 0/1 presence/absence matrix 2026-01-30-seqcoast-supermarket-sweep-profiles.tsv - Unfiltered sylph results table with all columns included