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They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an <jats:italic>Enterococcus faecium<\/jats:italic> strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in <jats:italic>E. faecium<\/jats:italic> QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.<\/jats:p>","DOI":"10.1007\/s10482-024-01938-0","type":"journal-article","created":{"date-parts":[[2024,2,23]],"date-time":"2024-02-23T15:02:28Z","timestamp":1708700548000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression"],"prefix":"10.1007","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4300-9279","authenticated-orcid":false,"given":"Daniel","family":"Acero-Pimentel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diana I.","family":"Romero-S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sac Nict\u00e9","family":"Fuentes-Curiel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0247-4774","authenticated-orcid":false,"given":"Maricarmen","family":"Quirasco","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,2,23]]},"reference":[{"key":"1938_CR1","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.2147\/IDR.S358248","volume":"15","author":"AHM Alduhaidhawi","year":"2022","unstructured":"Alduhaidhawi AHM, AlHuchaimi SN, Al- Mayah TA, Snr A-O, Alkafaas SS, Muthupandian S, Saki M (2022) Prevalence of CRISPR-Cas systems and their possible association with antibiotic resistance in Enterococcus faecalis and Enterococcus faecium collected from hospital wastewater. 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