Metabolomics dataset of 44 Propionibacterium freudenreichii for Scoary2
44 yogurts were produced, each by combining a different (sequenced) Propionibacterium freudenreichii strain with the same starter culture (Yoflex® YC-381). The metabolomes of these yogurts were measured using liquid chromatography MS (LC-MS) and gas chromatography MS (GC-MS), the latter measuring the yogurt’s volatile metabolites (volatiles). The aim of this study was to investigate the effect of the pan-genome of the added bacterial strains on the phenotype of the yogurts. We discovered two genes affecting carnitine metabolism. This data was analyzed using Scoary2: https://github.com/MrTomRod/scoary-2/wiki/Output#example-output File descriptions: - traits_44_noraw.tsv: corrected and filtered metabolomics data. Includes lc-ms as well as gc-ms volatiles data - traits_info_44_noraw.tsv: metadata about the measured metabolites, e.g. m/z, retention times, descriptions, putative HMDB IDs, etc. - isolate_info_44.tsv: links each sample to its species, in this case, all samples are Propionibacterium freudenreichii. - N0.tsv: a list of Hierarchical Orthogroups (HOGs) that groups orthologous genes together. It was created using OrthoFinder v2.5.4 based on protein FASTA files. - N0_best_names.tsv: maps each HOG to a putative description
Steps to reproduce
See the paper about Scoary2.
Gebert Rüf Stiftung