{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T03:07:28Z","timestamp":1789441648460,"version":"build-2803163510"},"reference-count":70,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:00:00Z","timestamp":1755043200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>In pharmaceutical manufacturing, there is a significant need for the detection and identification of specified microorganisms (<jats:italic>i.e.<\/jats:italic>, <jats:italic>Burkholderia cepacia<\/jats:italic> complex (BCC), <jats:italic>E. coli, Pseudomonas aeruginosa<\/jats:italic>, <jats:italic>Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans,<\/jats:italic> and <jats:italic>Mycoplasma<\/jats:italic>), which are often missed or not identified by traditional culture-dependent methods. We employed a metagenomic analysis coupled with oligotrophic enrichment to identify specified microorganisms and evaluate tryptic soy broth (TSB) and 1\/10 strength TSB for the recovery of specific microorganisms in potable groundwater samples. A total of 589\u2013996 genera were identified in 12 water samples taken from a cold water fountain, with <jats:italic>Bacillus<\/jats:italic> spp. (97%) in TSB and <jats:italic>Stenotrophomonas<\/jats:italic> spp. (97%) in 1\/10 strength TSB, representing the primary recovered genera after a 72-h pre-enrichment at 23\u00b0C. Likewise, we also detected lower abundance of specific organisms, <jats:italic>Clostridium<\/jats:italic> spp., <jats:italic>Burkholderia<\/jats:italic> spp., and <jats:italic>Staphylococcus<\/jats:italic> spp. (0.04\u20130.07%) in TSB and <jats:italic>Burkholderia<\/jats:italic> spp., <jats:italic>Pseudomonas<\/jats:italic> spp., <jats:italic>Salmonella<\/jats:italic> spp., <jats:italic>Staphylococcus<\/jats:italic> spp. and <jats:italic>Escherichia<\/jats:italic> spp. (0.01\u20131.73%) in 1\/10 strength TSB. Co-inoculation with <jats:italic>Burkholderia cepacia<\/jats:italic> complex (BCC) yielded a higher recovery rate of <jats:italic>Pseudomonas<\/jats:italic> spp. compared to uninoculated controls in 1\/10 strength TSB. Further functional analyses indicated that, toluene degradation (PWY-5180 and PWY-5182) was chiefly contributed by BCC in co-cultures of TSB\u202f+\u202fBCC-24\u202fh and TSB\u202f+\u202fBCC-48\u202fh. Our results demonstrate the potential value of the metagenomic approach during enrichment in detecting specified microorganisms, including oligotrophs such as BCC in non-sterile pharmaceutical products.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1645324","type":"journal-article","created":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T14:13:16Z","timestamp":1755094396000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["A metagenomic analysis coupled with oligotrophic enrichment approach for detecting specified microorganisms in potable groundwater samples"],"prefix":"10.3389","volume":"16","author":[{"given":"Soumana","family":"Daddy Gaoh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Alusta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong-Jin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Hussong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Marasa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youngbeom","family":"Ahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,8,13]]},"reference":[{"key":"ref9001","doi-asserted-by":"publisher","first-page":"1305742","DOI":"10.3389\/fcimb.2024.1305742","article-title":"Defining a metagenomic threshold for detecting low abundances of Providencia alcalifaciens in canine faecal samples","volume":"14","author":"Aardal","year":"2024","journal-title":"Front. 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