ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Aquatic Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1645324
This article is part of the Research TopicWater Resource Management Using Microbial SolutionsView all articles
A metagenomic analysis coupled with oligotrophic enrichment approach for detecting specified microorganisms in potable groundwater samples
Provisionally accepted
- 1National Center for Toxicological Research (FDA), Jefferson, United States
- 2Albany State University, Albany, United States
- 3Eagle Analytical Services, Houston, United States
- 4US Food and Drug Administration, Silver Spring, United States
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In pharmaceutical manufacturing, there is a significant need for the detection and identification of specified microorganisms (i.e., Burkholderia cepacia complex (BCC), E. coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma), 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 589-996 genera were identified in 12 water samples taken from a cold water fountain, with Bacillus spp. (97%) in TSB and Stenotrophomonas spp. (97%) in 1/10 strength TSB, representing the primary recovered genera after a 72-hour preenrichment at 23°C. Likewise, we also detected lower abundance of specific organisms, Clostridium spp., Burkholderia spp., and Staphylococcus spp. (0.04 -0.07%) in TSB and Burkholderia spp., Pseudomonas spp., Salmonella spp., Staphylococcus spp. and Escherichia spp. (0.01 -1.73%) in 1/10 strength TSB. Co-inoculation with Burkholderia cepacia complex (BCC) yielded a higher recovery rate of Pseudomonas 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 + BCC-24 h and TSB + BCC-48 h.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.
Keywords: Metagenomic analysis, oligotrophic enrichment, Specified microorganisms, Groundwater, Non-sterile pharmaceutical product
Received: 11 Jun 2025; Accepted: 22 Jul 2025.
Copyright: © 2025 daddy gaoh, Alusta, Lee, Hussong, Marasa and Ahn. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Youngbeom Ahn, National Center for Toxicological Research (FDA), Jefferson, United States
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