A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples
Abstract The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders inves...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-024-84682-9 |
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| author | Xiangning Bai Simon Rayner Linda Ellevog Skuggen Kine Kragl Engseth Pål Marius Bjørnstad Marianne Dalland Gregor D. Gilfillan Magnar Bjørås Andreas Matussek |
| author_facet | Xiangning Bai Simon Rayner Linda Ellevog Skuggen Kine Kragl Engseth Pål Marius Bjørnstad Marianne Dalland Gregor D. Gilfillan Magnar Bjørås Andreas Matussek |
| author_sort | Xiangning Bai |
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| description | Abstract The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host 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 (n = 8), nasal swab (n = 8), and saliva samples (n = 8) were collected, nucleic acids were isolated using the NAxtra protocol, and 16 S 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. |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-0e3b0e1a9f424164b719cd55a1f0b1de2025-01-19T12:19:45ZengNature PortfolioScientific Reports2045-23222025-01-011511810.1038/s41598-024-84682-9A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samplesXiangning Bai0Simon Rayner1Linda Ellevog Skuggen2Kine Kragl Engseth3Pål Marius Bjørnstad4Marianne Dalland5Gregor D. Gilfillan6Magnar Bjørås7Andreas Matussek8Department of Microbiology, Division of Laboratory Medicine, Oslo University HospitalDepartment of Medical Genetics, Oslo University Hospital and University of OsloDepartment of Microbiology, Division of Laboratory Medicine, Oslo University HospitalFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU)Department of Medical Genetics, Oslo University Hospital and University of OsloDepartment of Medical Genetics, Oslo University Hospital and University of OsloDepartment of Medical Genetics, Oslo University Hospital and University of OsloDepartment of Microbiology, Division of Laboratory Medicine, Oslo University HospitalDepartment of Microbiology, Division of Laboratory Medicine, Oslo University HospitalAbstract The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota–host 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 (n = 8), nasal swab (n = 8), and saliva samples (n = 8) were collected, nucleic acids were isolated using the NAxtra protocol, and 16 S 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.https://doi.org/10.1038/s41598-024-84682-9MicrobiotaBacteria16S rRNA gene sequencingLow-microbial biomassRespiratory samplesNucleic acid extraction |
| spellingShingle | Xiangning Bai Simon Rayner Linda Ellevog Skuggen Kine Kragl Engseth Pål Marius Bjørnstad Marianne Dalland Gregor D. Gilfillan Magnar Bjørås Andreas Matussek A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples Scientific Reports Microbiota Bacteria 16S rRNA gene sequencing Low-microbial biomass Respiratory samples Nucleic acid extraction |
| 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 |
| title_full | A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples |
| title_fullStr | A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples |
| title_full_unstemmed | A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples |
| title_short | A preliminary evaluation of a fast, low-cost, and high-throughput nucleic acid extraction method for bacterial microbiota profiling in low-microbial biomass samples |
| title_sort | preliminary evaluation of a fast low cost and high throughput nucleic acid extraction method for bacterial microbiota profiling in low microbial biomass samples |
| topic | Microbiota Bacteria 16S rRNA gene sequencing Low-microbial biomass Respiratory samples Nucleic acid extraction |
| url | https://doi.org/10.1038/s41598-024-84682-9 |
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