{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T16:30:28Z","timestamp":1783441828602,"version":"3.54.6"},"reference-count":40,"publisher":"Maad Rayan Publishing Company","issue":"2","content-domain":{"domain":["bi.tbzmed.ac.ir"],"crossmark-restriction":false},"short-container-title":["Bioimpacts"],"published-print":{"date-parts":[[2021,10,9]]},"abstract":"<jats:p>Introduction: With the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the interaction between the host and SARS-CoV-2 was widely studied. However, it is unclear whether and how SARS-CoV-2 infection affects lung microflora, which contribute to COVID-19 complications.  Methods: Here, we analyzed the metatranscriptomic data of bronchoalveolar lavage fluid (BALF) of 19 COVID-19 patients and 23 healthy controls from 6 independent projects and detailed the active microbiota landscape in both healthy individuals and COVID-19 patients. Results: The infection of SARS-CoV-2 could deeply change the lung microbiota, evidenced by the \u03b1-diversity, \u03b2-diversity, and species composition analysis based on bacterial microbiota and virome. Pathogens (e.g., Klebsiella oxytoca causing pneumonia as well), immunomodulatory probiotics (e.g., lactic acid bacteria and Faecalibacterium prausnitzii, a butyrate producer), and Tobacco mosaic virus (TMV) were enriched in the COVID-19 group, suggesting a severe microbiota dysbiosis. The significant correlation between Rothia mucilaginosa, TMV, and SARS-CoV-2 revealed drastic inflammatory battles between the host, SARS-CoV-2, and other microbes in the lungs. Notably, TMV only existed in the COVID-19 group, while human respirovirus 3 (HRV 3) only existed in the healthy group. Our study provides insights into the active microbiota in the lungs of COVID-19 patients and would contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. Conclusion: SARS-COV-2 infection deeply altered the lung microbiota of COVID-19 patients. The enrichment of several other pathogens, immunomodulatory probiotics (lactic acid or butyrate producers), and TMV in the COVID-19 group suggests a complex and active lung microbiota disorder.<\/jats:p>","DOI":"10.34172\/bi.2021.23378","type":"journal-article","created":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T04:57:14Z","timestamp":1638334634000},"page":"139-146","update-policy":"https:\/\/doi.org\/10.34172\/crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis"],"prefix":"10.34172","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0034-5848","authenticated-orcid":true,"given":"Yang","family":"Han","sequence":"first","affiliation":[{"name":"Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 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