Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing
Abstract Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs,...
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Nature Portfolio
2025-05-01
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| Online Access: | https://doi.org/10.1038/s41598-025-01905-3 |
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| author | Pawarisa Terbtothakun Suthida Visedthorn Pavit Klomkliew Prangwalai Chanchaem Vorthon Sawaswong Pavaret Sivapornnukul Samitanan Sunantawanit Ariya Khamwut Suwatchareeporn Rotcheewaphan Pornchai Kaewsapsak Sunchai Payungporn |
| author_facet | Pawarisa Terbtothakun Suthida Visedthorn Pavit Klomkliew Prangwalai Chanchaem Vorthon Sawaswong Pavaret Sivapornnukul Samitanan Sunantawanit Ariya Khamwut Suwatchareeporn Rotcheewaphan Pornchai Kaewsapsak Sunchai Payungporn |
| author_sort | Pawarisa Terbtothakun |
| collection | DOAJ |
| description | Abstract Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes. |
| format | Article |
| id | doaj-art-acea4dd035cd474cae41fb52026dbedd |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-acea4dd035cd474cae41fb52026dbedd2025-08-20T02:34:14ZengNature PortfolioScientific Reports2045-23222025-05-0115111210.1038/s41598-025-01905-3Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencingPawarisa Terbtothakun0Suthida Visedthorn1Pavit Klomkliew2Prangwalai Chanchaem3Vorthon Sawaswong4Pavaret Sivapornnukul5Samitanan Sunantawanit6Ariya Khamwut7Suwatchareeporn Rotcheewaphan8Pornchai Kaewsapsak9Sunchai Payungporn10Medical Biochemistry Program, Department of Biochemistry, Faculty of Medicine, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityDepartment of Biochemistry, Faculty of Science, Mahidol UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityFaculty of Medicine, Department of Biochemistry, Center of Excellence in Systems Microbiology, Chulalongkorn UniversityAbstract Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes.https://doi.org/10.1038/s41598-025-01905-3Mycobacterium tuberculosisMetagenomics16S rDNAInternal transcribed spacer (ITS)Oxford nanopore technologies (ONT) |
| spellingShingle | Pawarisa Terbtothakun Suthida Visedthorn Pavit Klomkliew Prangwalai Chanchaem Vorthon Sawaswong Pavaret Sivapornnukul Samitanan Sunantawanit Ariya Khamwut Suwatchareeporn Rotcheewaphan Pornchai Kaewsapsak Sunchai Payungporn Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing Scientific Reports Mycobacterium tuberculosis Metagenomics 16S rDNA Internal transcribed spacer (ITS) Oxford nanopore technologies (ONT) |
| title | Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| title_full | Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| title_fullStr | Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| title_full_unstemmed | Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| title_short | Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| title_sort | clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing |
| topic | Mycobacterium tuberculosis Metagenomics 16S rDNA Internal transcribed spacer (ITS) Oxford nanopore technologies (ONT) |
| url | https://doi.org/10.1038/s41598-025-01905-3 |
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