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In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome\u2019s taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436\u2013557 genera with <jats:italic>Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria,<\/jats:italic> and <jats:italic>Cyanobacteria<\/jats:italic> accounting for\u2009&gt;\u200995% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. <jats:italic>Escherichia<\/jats:italic> and <jats:italic>Salmonella<\/jats:italic> were mainly detected in Hot Springs, relative to Jefferson, while <jats:italic>Clostridium<\/jats:italic> and <jats:italic>Pseudomonas<\/jats:italic> were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.<\/jats:p>","DOI":"10.1007\/s00284-024-03791-w","type":"journal-article","created":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T06:02:25Z","timestamp":1721196145000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products"],"prefix":"10.1007","volume":"81","author":[{"given":"Soumana","family":"Daddy Gaoh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Alusta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1888-7322","authenticated-orcid":false,"given":"Yong-Jin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John J.","family":"LiPuma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Hussong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernard","family":"Marasa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youngbeom","family":"Ahn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,7,17]]},"reference":[{"key":"3791_CR1","doi-asserted-by":"publisher","DOI":"10.1201\/9781420025804.ch1","volume-title":"Effects and causes of contamination in sterile manufacturing","author":"N Halls","year":"2004","unstructured":"Halls N (2004) Effects and causes of contamination in sterile manufacturing. 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