{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:19:11Z","timestamp":1760149151531,"version":"build-2065373602"},"reference-count":48,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2023,7,17]],"date-time":"2023-07-17T00:00:00Z","timestamp":1689552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Research and Development Program of Hubei Province","award":["2022BCA019","8200002","WSJKRC2022012"],"award-info":[{"award-number":["2022BCA019","8200002","WSJKRC2022012"]}]},{"name":"National Natural Science Foundation of China","award":["2022BCA019","8200002","WSJKRC2022012"],"award-info":[{"award-number":["2022BCA019","8200002","WSJKRC2022012"]}]},{"name":"2021 Hubei Provincial Leading Public Health Talents Project","award":["2022BCA019","8200002","WSJKRC2022012"],"award-info":[{"award-number":["2022BCA019","8200002","WSJKRC2022012"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower respiratory tract during viral infection. However, both bacterial and fungal microbiota in the lung of COVID-19 patients remained to be explored. Methods: In this study, we conducted nanopore sequencing analyses of the lower respiratory tract samples from 38 COVID-19 patients and 26 non-COVID-19 pneumonia controls. Both bacterial and fungal microbiome diversities and microbiota abundances in the lung were compared. Results: Our results revealed significant differences in lung microbiome between COVID-19 patients and non-COVID-19 controls, which were strongly associated with SARS-CoV-2 infection and clinical status. COVID-19 patients exhibited a notably higher abundance of opportunistic pathogens, particularly Acinetobacter baumannii and Candida spp. Furthermore, the potential pathogens enriched in COVID-19 patients were positively correlated with inflammation indicators. Conclusions: Our study highlights the differences in lung microbiome diversity and composition between COVID-19 patients and non-COVID-19 patients. This may contribute to predicting co-pathogens and selecting optimal treatments for respiratory infections caused by SARS-CoV-2.<\/jats:p>","DOI":"10.3390\/pathogens12070944","type":"journal-article","created":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T01:46:02Z","timestamp":1689644762000},"page":"944","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization"],"prefix":"10.3390","volume":"12","author":[{"given":"Linlin","family":"Xie","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangjun","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinran","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junying","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongpan","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4148-780X","authenticated-orcid":false,"given":"Zhiqiang","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yirong","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China"},{"name":"Wuhan Research Center for Infectious Diseases and Tumors, Chinese Academy of Medical Sciences, Wuhan 430071, China"},{"name":"Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan 430071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,7,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1001\/jamapediatrics.2020.1467","article-title":"Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review","volume":"174","author":"Castagnoli","year":"2020","journal-title":"JAMA Pediatr."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1016\/j.immuni.2020.04.023","article-title":"Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals","volume":"52","author":"Ni","year":"2020","journal-title":"Immunity"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/S0140-6736(20)30566-3","article-title":"Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective cohort study","volume":"395","author":"Zhou","year":"2020","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.jmii.2020.05.013","article-title":"Co-infections among patients with COVID-19: The need for combination therapy with non-anti-SARS-CoV-2 agents?","volume":"53","author":"Lai","year":"2020","journal-title":"J. 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