{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:17:09Z","timestamp":1789996629499,"version":"4.0.1"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T00:00:00Z","timestamp":1697068800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Lung infection is a global health problem associated with high morbidity and mortality and increasing rates of hospitalization. The correlation between pulmonary microecology and infection severity remains unclear. Therefore, the purpose of this study was to investigate the differences in lung microecology and potential biomarkers in patients with mild and severe pulmonary infection.<\/jats:p><\/jats:sec><jats:sec><jats:title>Method<\/jats:title><jats:p>Patients with pulmonary infection or suspected infection were divided into the mild group (140 cases) and the severe group (80 cases) according to pneomonia severity index (PSI) scores. Here, we used metagenomic next-generation sequencing (mNGS) to detect DNA mainly from bronchoalveolar lavage fluid (BALF) collected from patients to analyze changes in the lung microbiome of patients with different disease severity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Result<\/jats:title><jats:p>We used the mNGS to analyze the pulmonary microecological composition in patients with pulmonary infection. The results of alpha diversity and beta diversity analysis showed that the microbial composition between mild and severe groups was similar on the whole. The dominant bacteria were <jats:italic>Acinetobacter<\/jats:italic>, <jats:italic>Bacillus<\/jats:italic>, <jats:italic>Mycobacterium<\/jats:italic>, <jats:italic>Staphylococcus<\/jats:italic>, and <jats:italic>Prevotella<\/jats:italic>, among others. Linear discriminant analysis effect size (LEfSe) results showed that there were significant differences in virus composition between the mild and severe patients, especially Simplexvirus and Cytomegalovirus, which were prominent in the severe group. The random forest model screened 14 kinds of pulmonary infection-related pathogens including <jats:italic>Corynebacterium<\/jats:italic>, <jats:italic>Mycobacterium<\/jats:italic>, <jats:italic>Streptococcus<\/jats:italic>, <jats:italic>Klebsiella<\/jats:italic>, and <jats:italic>Acinetobacter<\/jats:italic>. In addition, it was found that <jats:italic>Rothia<\/jats:italic> was negatively correlated with <jats:italic>Acinetobacter<\/jats:italic>, <jats:italic>Mycobacterium<\/jats:italic>, <jats:italic>Bacillus<\/jats:italic>, <jats:italic>Enterococcus<\/jats:italic>, and <jats:italic>Klebsiella<\/jats:italic> in the mild group through co-occurrence network, while no significant correlation was found in the severe group.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Here, we describe the composition and diversity of the pulmonary microbiome in patients with pulmonary infection. A significant increase in viral replication was found in the severe group, as well as a significant difference in microbial interactions between patients with mild and severe lung infections, particularly the association between the common pathogenic bacteria and <jats:italic>Rothia<\/jats:italic>. This suggests that both pathogen co-viral infection and microbial interactions may influence the course of disease. Of course, more research is needed to further explore the specific mechanisms by which microbial interactions influence disease severity.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2023.1227581","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:29:42Z","timestamp":1697131782000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection"],"prefix":"10.3389","volume":"13","author":[{"given":"Danting","family":"Zhan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihua","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijuan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiacheng","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingwei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,10,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.541092","article-title":"Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples","volume":"11","author":"Chen","year":"2021","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.7189\/jogh.12.05040","article-title":"The role of respiratory co-infection with influenza or respiratory syncytial virus in the clinical severity of COVID-19 patients: A systematic review and meta-analysis","volume":"12","author":"Cong","year":"2022","journal-title":"J. Glob Health"},{"key":"B4","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1586\/ers.13.24","article-title":"The role of the bacterial microbiome in lung disease","volume":"7","author":"Dickson","year":"2013","journal-title":"Expert Rev. Respir. Med."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1016\/S0140-6736(20)30925-9","article-title":"Global burden of 369 diseases and injuries in 204 countries and territorie-2019: a systematic analysis for the global burden of disease study 2019","volume":"396","year":"2020","journal-title":"Lancet"},{"key":"B6","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1186\/s13054-022-04068-z","article-title":"Composition and diversity analysis of the lung microbiome in patients with suspected ventilator-associated pneumonia","volume":"26","author":"Fenn","year":"2022","journal-title":"Crit. Care"},{"key":"B7","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1056\/nejm199701233360402","article-title":"A prediction rule to identify low-risk patients with community-acquired pneumonia","volume":"336","author":"Fine","year":"1997","journal-title":"N Engl. J. Med."},{"key":"B8","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.chest.2021.07.035","article-title":"Treatment of mycobacterium abscessus pulmonary disease","volume":"161","author":"Griffith","year":"2022","journal-title":"Chest"},{"key":"B9","doi-asserted-by":"publisher","first-page":"10480","DOI":"10.1080\/21655979.2021.1997563","article-title":"Characteristics of the lung microbiota in lower respiratory tract infections with and without history of pneumonia","volume":"12","author":"Hong","year":"2021","journal-title":"Bioengineered"},{"key":"B10","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s40168-022-01437-2","article-title":"Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health","volume":"10","author":"Huang","year":"2022","journal-title":"Microbiome"},{"key":"B11","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1186\/s12967-021-03159-9","article-title":"Virus infection induced pulmonary fibrosis","volume":"19","author":"Huang","year":"2021","journal-title":"J. Transl. Med."},{"key":"B12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.jaci.2014.11.011","article-title":"The microbiome in asthma","volume":"135","author":"Huang","year":"2015","journal-title":"J. Allergy Clin. Immunol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"255","DOI":"10.3760\/cma.j.issn.1001-0939.2018.04.002","article-title":"Chinese guidelines for the dignosis and treatment of adults eith hospital-acquired and ventilator associated pneumonia","volume":"41","year":"2018","journal-title":"Chin. J. Tuberc Respir. Dis."},{"key":"B14","doi-asserted-by":"publisher","first-page":"190045","DOI":"10.1183\/16000617.0045-2019","article-title":"The contribution of infection and the respiratory microbiome in acute exacerbations of idiopathic pulmonary fibrosis","volume":"28","author":"Invernizzi","year":"2019","journal-title":"Eur. Respir. Rev."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0110240","article-title":"The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform","volume":"9","author":"Jeon","year":"2014","journal-title":"PLoS One"},{"key":"B16","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/s41563-020-00906-z","article-title":"Diagnostics for SARS-CoV-2 infections","volume":"20","author":"Kevadiya","year":"2021","journal-title":"Nat. Mater"},{"key":"B17","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00153-17","article-title":"Translating lung microbiome profiles into the next-generation diagnostic gold standard for pneumonia: a clinical investigator's perspective","volume":"3","author":"Kitsios","year":"2018","journal-title":"mSystems"},{"key":"B19","doi-asserted-by":"publisher","first-page":"e00245","DOI":"10.1128\/mBio.00245-10","article-title":"Microbial communities of the upper respiratory tract and otitis media in children","volume":"2","author":"Laufer","year":"2011","journal-title":"mBio"},{"key":"B20","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1007\/s10096-019-03734-5","article-title":"Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients","volume":"39","author":"Li","year":"2020","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B21","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1186\/s13054-022-04126-6","article-title":"Effect of invasive mechanical ventilation on the diversity of the pulmonary microbiota","volume":"26","author":"Liu","year":"2022","journal-title":"Crit. Care"},{"key":"B22","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1186\/s12931-022-02230-3","article-title":"Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing","volume":"23","author":"Miao","year":"2022","journal-title":"Respir. Res."},{"key":"B23","doi-asserted-by":"publisher","first-page":"S231","DOI":"10.1093\/cid\/ciy693","article-title":"Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice","volume":"67","author":"Miao","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1038\/srep40114","article-title":"Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections","volume":"7","author":"Mizrahi","year":"2017","journal-title":"Sci. Rep."},{"key":"B25","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/s41579-022-00821-x","article-title":"The dynamic lung microbiome in health and disease","volume":"21","author":"Natalini","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"3184","DOI":"10.1128\/JCM.01270-14","article-title":"Rothia bacteremia: a 10-year experience at Mayo Clinic, Rochester, Minnesota","volume":"52","author":"Ramanan","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(21)00035-5","article-title":"Lung microbiome composition and bronchial epithelial gene expression in patients with COPD versus healthy individuals: a bacterial 16S rRNA gene sequencing and host transcriptomic analysis","volume":"2","author":"Ramsheh","year":"2021","journal-title":"Lancet Microbe"},{"key":"B28","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13054-019-2701-5","article-title":"Impact of acyclovir use on survival of patients with ventilator-associated pneumonia and high load herpes simplex virus replication","volume":"24","author":"Schuierer","year":"2020","journal-title":"Crit. Care"},{"key":"B29","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/s41572-019-0131-y","article-title":"Diphtheria","volume":"5","author":"Sharma","year":"2019","journal-title":"Nat. Rev. Dis. Primers"},{"key":"B30","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s40981-017-0096-3","article-title":"Bacillus cereus pneumonia in an immunocompetent patient: a case report","volume":"3","author":"Shimoyama","year":"2017","journal-title":"JA Clin. Rep."},{"key":"B31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s40121-017-0180-z","article-title":"Who is the patient at risk of CMV recurrence: A review of the current scientific evidence with a focus on hematopoietic cell transplantation","volume":"7","author":"Styczynski","year":"2018","journal-title":"Infect. Dis. Ther."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics12010140","article-title":"The role of the respiratory microbiome in the pathogenesis of aspiration pneumonia: Implications for diagnosis and potential therapeutic choices","volume":"12","author":"Vallianou","year":"2023","journal-title":"Antibiotics (Basel)"},{"key":"B33","doi-asserted-by":"publisher","first-page":"638","DOI":"10.3390\/jcm9030638","article-title":"The dynamics of respiratory microbiota during mechanical ventilation in patients with pneumonia","volume":"9","author":"Woo","year":"2020","journal-title":"J. Clin. Med."},{"key":"B34","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01901-21","article-title":"Insights into the unique lung microbiota profile of pulmonary tuberculosis patients using metagenomic next-generation sequencing","volume":"10","author":"Xiao","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202203115","article-title":"Differential oral microbial input determines two microbiota pneumo-types associated with health status","volume":"9","author":"Zhang","year":"2022","journal-title":"Adv. Sci. (Weinh)"},{"key":"B37","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1016\/S0140-6736(15)60454-8","article-title":"Middle east respiratory syndrome","volume":"386","author":"Zumla","year":"2015","journal-title":"Lancet"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2023.1227581\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T17:29:55Z","timestamp":1697131795000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2023.1227581\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,12]]},"references-count":37,"alternative-id":["10.3389\/fcimb.2023.1227581"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2023.1227581","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,12]]},"article-number":"1227581"}}