{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T05:51:07Z","timestamp":1788846667013,"version":"build-2803163510"},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004047","name":"Karolinska Institute","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004047","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota\u2013host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation of respiratory microbiota. Here, we performed a pilot study to assess the suitability of the NAxtra nucleic acid extraction protocol for profiling bacterial microbiota in respiratory samples. A small number of nasopharyngeal aspirate (<jats:italic>n<\/jats:italic>\u2009=\u20098), nasal swab (<jats:italic>n<\/jats:italic>\u2009=\u20098), and saliva samples (<jats:italic>n<\/jats:italic>\u2009=\u20098) were collected, nucleic acids were isolated using the NAxtra protocol, and 16\u00a0S rRNA gene sequencing was performed to characterize bacterial microbiota, which were compared to the same sample types from previous studies using other protocols. The bacterial composition in nasal and saliva samples were consistent with previous reports. Saliva microbiota was significantly richer than nasal microbiota and varied less among individual samples than nasal microbiota. Bacterial composition in nasal samples was distinct from nasopharyngeal aspirates, but closer to saliva samples. A sequencing depth of 50,000 reads\/sample was sufficient for microbiota profiling in low biomass respiratory samples. Our pilot study indicates the potential of the NAxtra protocol for bacterial microbiota characterization of low-microbial biomass samples and supports a more comprehensive study to fully evaluate the value of the NAxtra protocol in microbiota research and clinical diagnostics of respiratory pathogens.<\/jats:p>","DOI":"10.1038\/s41598-024-84682-9","type":"journal-article","created":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T07:24:22Z","timestamp":1736925862000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples"],"prefix":"10.1038","volume":"15","author":[{"given":"Xiangning","family":"Bai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Rayner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda Ellevog","family":"Skuggen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kine Kragl","family":"Engseth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e5l Marius","family":"Bj\u00f8rnstad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marianne","family":"Dalland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregor D.","family":"Gilfillan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magnar","family":"Bj\u00f8r\u00e5s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Matussek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,1,15]]},"reference":[{"key":"84682_CR1","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","volume":"7","author":"K Hou","year":"2022","unstructured":"Hou, K. et al. Microbiota in health and diseases. Signal. Transduct. Target. Ther. 7, 135. https:\/\/doi.org\/10.1038\/s41392-022-00974-4 (2022).","journal-title":"Signal. Transduct. Target. Ther."},{"key":"84682_CR2","doi-asserted-by":"publisher","unstructured":"Matijasic, M. et al. Gut microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and eukaryotic parasites in IBD. Int. J. Mol. Sci. 21 https:\/\/doi.org\/10.3390\/ijms21082668 (2020).","DOI":"10.3390\/ijms21082668"},{"key":"84682_CR3","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1264\/jsme2.ME17017","volume":"32","author":"ET Hillman","year":"2017","unstructured":"Hillman, E. T., Lu, H., Yao, T. & Nakatsu, C. H. Microbial ecology along the gastrointestinal tract. Microbes Environ. 32, 300\u2013313. https:\/\/doi.org\/10.1264\/jsme2.ME17017 (2017).","journal-title":"Microbes Environ."},{"key":"84682_CR4","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","volume":"15","author":"WH Man","year":"2017","unstructured":"Man, W. H., de Steenhuijsen Piters, W. A. & Bogaert, D. The microbiota of the respiratory tract: Gatekeeper to respiratory health. Nat. Rev. Microbiol. 15, 259\u2013270. https:\/\/doi.org\/10.1038\/nrmicro.2017.14 (2017).","journal-title":"Nat. Rev. Microbiol."},{"key":"84682_CR5","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1186\/s40168-022-01342-8","volume":"10","author":"C Merenstein","year":"2022","unstructured":"Merenstein, C., Bushman, F. D. & Collman, R. G. Alterations in the respiratory tract microbiome in COVID-19: Current observations and potential significance. Microbiome 10, 165. https:\/\/doi.org\/10.1186\/s40168-022-01342-8 (2022).","journal-title":"Microbiome"},{"key":"84682_CR6","doi-asserted-by":"publisher","first-page":"eabq5126","DOI":"10.1126\/scitranslmed.abq5126","volume":"15","author":"SK Di Simone","year":"2023","unstructured":"Di Simone, S. K., Rudloff, I., Nold-Petry, C. A., Forster, S. C. & Nold, M. F. Understanding respiratory microbiome-immune system interactions in health and disease. Sci. Transl. Med. 15, eabq5126. https:\/\/doi.org\/10.1126\/scitranslmed.abq5126 (2023).","journal-title":"Sci. Transl. Med."},{"key":"84682_CR7","doi-asserted-by":"publisher","unstructured":"Bai, X. et al. Characterization of the Upper Respiratory bacterial microbiome in critically ill COVID-19 patients. Biomedicines 10. https:\/\/doi.org\/10.3390\/biomedicines10050982 (2022).","DOI":"10.3390\/biomedicines10050982"},{"key":"84682_CR8","doi-asserted-by":"publisher","first-page":"11714","DOI":"10.1038\/s41598-023-38743-0","volume":"13","author":"E Ravlo","year":"2023","unstructured":"Ravlo, E. et al. A fast, low-cost, robust and high-throughput method for viral nucleic acid isolation based on NAxtra magnetic nanoparticles. Sci. Rep. 13, 11714. https:\/\/doi.org\/10.1038\/s41598-023-38743-0 (2023).","journal-title":"Sci. Rep."},{"key":"84682_CR9","doi-asserted-by":"publisher","first-page":"20836","DOI":"10.1038\/s41598-023-46868-5","volume":"13","author":"EJ Starheim","year":"2023","unstructured":"Starheim, E. J. et al. NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA. Sci. Rep. 13, 20836. https:\/\/doi.org\/10.1038\/s41598-023-46868-5 (2023).","journal-title":"Sci. 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