{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:52:45Z","timestamp":1791363165172,"version":"4.3.1"},"reference-count":144,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre, Poland","doi-asserted-by":"publisher","award":["2022\/45\/B\/NZ9\/04254"],"award-info":[{"award-number":["2022\/45\/B\/NZ9\/04254"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2022\/45\/B\/NZ9\/04254"],"award-info":[{"award-number":["2022\/45\/B\/NZ9\/04254"]}],"id":[{"id":"https:\/\/ror.org\/03ha2q922","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Food-associated microorganisms represent a diverse reservoir of bacterial strains with functional traits potentially relevant to host\u2013microbiome interactions, stress resilience, metabolic processes, and microbial competition. In this study, we performed a multi-omics characterization of food-origin bacterial isolates to identify a potential candidate strain for further studies on microbiome\u2013microgreens interactions. Over one hundred bacterial isolates were initially recovered from various food products and subjected to molecular screening, followed by whole-genome sequencing, metabolic profiling, transcriptomic characterization and morphological analysis of selected strains. Comparative characterization revealed significant differences among the strains. Among the tested isolates, strain B107\/23, identified as Priestia megaterium (formerly Bacillus megaterium), showed consistently high numbers of genes associated with stress responses, nutrient uptake, plant growth-promoting traits, and colonization mechanisms. Phenotypic characterization later demonstrated high metabolic flexibility and a low substrate stress index, while transcriptomic profiling revealed the expression of genes associated with stress responses and metabolic activity. Overall, the integration of genomic, phenotypic, and transcriptomic results distinguished B107\/23 as the most promising candidate among the tested isolates and revealed the molecular traits potentially relevant to interactions between the microbe and the host. These findings provide a basis for the validation of the selected strain in microgreens systems, including studies addressing plant stress resilience and post-harvest quality.<\/jats:p>","DOI":"10.3390\/ijms27198734","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:25:42Z","timestamp":1790760342000},"page":"8734","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3063-8648","authenticated-orcid":false,"given":"Daria","family":"Bara\u0144ska","sequence":"first","affiliation":[{"name":"Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9217-5902","authenticated-orcid":false,"given":"Jacek","family":"Panek","sequence":"additional","affiliation":[{"name":"Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1636-3765","authenticated-orcid":false,"given":"Giorgia","family":"Pertile","sequence":"additional","affiliation":[{"name":"Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agata","family":"Gryta","sequence":"additional","affiliation":[{"name":"Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1695-5154","authenticated-orcid":false,"given":"Sylwia","family":"R\u00f3\u017calska","sequence":"additional","affiliation":[{"name":"Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9437-3139","authenticated-orcid":false,"given":"Magdalena","family":"Fr\u0105c","sequence":"additional","affiliation":[{"name":"Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"eadn3747","DOI":"10.1126\/science.adn3747","article-title":"Climate Change Exacerbates the Environmental Impacts of Agriculture","volume":"385","author":"Yang","year":"2024","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Pylak, M., Oszust, K., and Fr\u0105c, M. 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