Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics
Abstract The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bron...
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Nature Portfolio
2025-05-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08234-1 |
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| author | Denian Wang Yishang Duan Lijuan He Juan Jiang Jinghong Xian Ke Yuan Rui Zhang Huohuo Zhang Jing Wang Nan Li Min Huang Chenggong Hu Sifeng Lu Zhiheng Luo Taibing Deng Zhongwei Zhang Bojiang Chen Weimin Li |
| author_facet | Denian Wang Yishang Duan Lijuan He Juan Jiang Jinghong Xian Ke Yuan Rui Zhang Huohuo Zhang Jing Wang Nan Li Min Huang Chenggong Hu Sifeng Lu Zhiheng Luo Taibing Deng Zhongwei Zhang Bojiang Chen Weimin Li |
| author_sort | Denian Wang |
| collection | DOAJ |
| description | Abstract The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression. |
| format | Article |
| id | doaj-art-dbcc9c2ef834409d95fccad3a87fd879 |
| institution | DOAJ |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-dbcc9c2ef834409d95fccad3a87fd8792025-08-20T03:22:12ZengNature PortfolioCommunications Biology2399-36422025-05-018111210.1038/s42003-025-08234-1Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomicsDenian Wang0Yishang Duan1Lijuan He2Juan Jiang3Jinghong Xian4Ke Yuan5Rui Zhang6Huohuo Zhang7Jing Wang8Nan Li9Min Huang10Chenggong Hu11Sifeng Lu12Zhiheng Luo13Taibing Deng14Zhongwei Zhang15Bojiang Chen16Weimin Li17Precision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityDepartment of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityBGIPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityBGIGeneral Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan UniversityDepartment of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityBGIBGIDepartment of Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He StreetPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityDepartment of Respiratory Medicine, Guang’an People’hospitalDepartment of Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He StreetPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityPrecision Medicine Research Center, Precision Medicine Key Laboratory of Sichuan Province, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityAbstract The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.https://doi.org/10.1038/s42003-025-08234-1 |
| spellingShingle | Denian Wang Yishang Duan Lijuan He Juan Jiang Jinghong Xian Ke Yuan Rui Zhang Huohuo Zhang Jing Wang Nan Li Min Huang Chenggong Hu Sifeng Lu Zhiheng Luo Taibing Deng Zhongwei Zhang Bojiang Chen Weimin Li Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics Communications Biology |
| title | Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics |
| title_full | Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics |
| title_fullStr | Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics |
| title_full_unstemmed | Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics |
| title_short | Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics |
| title_sort | altered microbiota of the lower respiratory tract and its association with covid 19 severity analysed by metagenomics and metatranscriptomics |
| url | https://doi.org/10.1038/s42003-025-08234-1 |
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