{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:18:41Z","timestamp":1789996721994,"version":"4.0.1"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,10,31]],"date-time":"2024-10-31T00:00:00Z","timestamp":1730332800000},"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>Introduction<\/jats:title><jats:p>The homeostasis of the microbiome in lower respiratory tract is crucial in sustaining normal physiological functions of the lung. Different pulmonary diseases display varying degrees of microbiome imbalance; however, the specific variability and clinical significance of their microbiomes remain largely unexplored.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>In this study, we delineated the pathogen spectrum and commensal microorganisms in the lower respiratory tract of various pulmonary diseases using metagenomic sequencing. We analyzed the disparities and commonalities of the microbial features and examined their correlation with disease characteristics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We observed distinct pathogen profiles and a diversity in lower airway microbiome in patients diagnosed with cancer, interstitial lung disease, bronchiectasis, common pneumonia, Nontuberculous mycobacteria (NTM) pneumonia, and severe pneumonia.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>This study illustrates the utility of Metagenomic Next-generation Sequencing (mNGS) in identifying pathogens and analyzing the lower respiratory microbiome, which is important for understanding the microbiological aspect of pulmonary diseases and essential for their early and precise diagnosis.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2024.1320831","type":"journal-article","created":{"date-parts":[[2024,10,31]],"date-time":"2024-10-31T06:11:13Z","timestamp":1730355073000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Pathogen spectrum and microbiome in lower respiratory tract of patients with different pulmonary diseases based on metagenomic next-generation sequencing"],"prefix":"10.3389","volume":"14","author":[{"given":"Rujun","family":"Hong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaxing","family":"Yi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lanfeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haitao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenshan","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuefang","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjie","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruotong","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiujuan","family":"Yao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baosong","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,10,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1006\/jmbi.1990.9999","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B2","first-page":"351","article-title":"Lung recruitment in unilateral lung disease","volume":"68","author":"Blanch","year":"2002","journal-title":"Minerva anestesiologica"},{"key":"B3","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.ijid.2021.05.028","article-title":"Rapid discrimination between tuberculosis and sarcoidosis using next-generation sequencing","volume":"108","author":"Chao","year":"2021","journal-title":"Int. J. Infect. diseases: IJID: Off. Publ. Int. Soc. Infect. Dis."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1016\/j.jaci.2017.02.004","article-title":"Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment","volume":"139","author":"Chung","year":"2017","journal-title":"J. Allergy Clin. Immunol."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0170622","article-title":"Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients","volume":"12","author":"Cox","year":"2017","journal-title":"PloS One"},{"key":"B6","doi-asserted-by":"publisher","first-page":"253","DOI":"10.2323\/jgam.2022.05.004","article-title":"16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin","volume":"68","author":"Deng","year":"2023","journal-title":"J. Gen. Appl. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1164\/rccm.201711-2180oc","article-title":"The lung microbiota of healthy mice are highly variable, cluster by environment, and reflect variation in baseline lung innate immunity","volume":"198","author":"Dickson","year":"2018","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B8","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":"B9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004923","article-title":"The lung microbiome: new principles for respiratory bacteriology in health and disease","volume":"11","author":"Dickson","year":"2015","journal-title":"PloS Pathog."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.650271","article-title":"Related factors to streptococcus pneumoniae invasive infection and clinical manifestations: the potential role of nasopharyngeal microbiome","volume":"8","author":"Dietl","year":"2021","journal-title":"Front. Med. (Lausanne)"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.708827","article-title":"Pathogen metagenomics reveals distinct lung microbiota signatures between bacteriologically confirmed and negative tuberculosis patients","volume":"11","author":"Ding","year":"2021","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1186\/s12931-024-02860-9","article-title":"Systemic antibiotics for Pseudomonas aeruginosa infection in outpatients with non-hospitalised exacerbations of pre-existing lung diseases: a randomised clinical trial","volume":"25","author":"Eklof","year":"2024","journal-title":"Respir. Res."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.7754\/clin.lab.2022.220139","article-title":"Clinical characteristics of chlamydia psittaci pneumonia confirmed by metagenomic next-generation sequencing","volume":"68","author":"Fang","year":"2022","journal-title":"Clin. Lab."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1176044","article-title":"Commensal bacteria of the lung microbiota synergistically inhibit inflammation in a three-dimensional epithelial cell model","volume":"14","author":"Goeteyn","year":"2023","journal-title":"Front. Immunol."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02491","article-title":"Dynamic changes in the microbiome and mucosal immune microenvironment of the lower respiratory tract by influenza virus infection","volume":"10","author":"Gu","year":"2019","journal-title":"Front. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1038\/s42003-019-0540-1","article-title":"Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing","volume":"2","author":"Gupta","year":"2019","journal-title":"Commun. Biol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1136\/thoraxjnl-2020-216179","article-title":"Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients","volume":"77","author":"H\u00e9rivaux","year":"2022","journal-title":"Thorax"},{"key":"B18","doi-asserted-by":"publisher","first-page":"21297","DOI":"10.1038\/s41598-021-00851-0","article-title":"Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes","volume":"11","author":"Hern\u00e1ndez-Ter\u00e1n","year":"2021","journal-title":"Sci. Rep."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008578","article-title":"Disordered microbial communities in asthmatic airways","volume":"5","author":"Hilty","year":"2010","journal-title":"PloS One"},{"key":"B20","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.tube.2018.02.006","article-title":"Meta-analysis of the lung microbiota in pulmonary tuberculosis","volume":"109","author":"Hong","year":"2018","journal-title":"Tuberculosis (Edinb)"},{"key":"B21","doi-asserted-by":"publisher","first-page":"1671","DOI":"10.1159\/000520126","article-title":"Drug-induced interstitial lung disease after anthracycline-combined chemotherapy for breast cancer: A case report and literature review","volume":"14","author":"Hoshina","year":"2021","journal-title":"Case Rep. Oncol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1753466619890538","DOI":"10.1177\/1753466619890538","article-title":"Autophagy and pulmonary disease","volume":"13","author":"Liao","year":"2019","journal-title":"Ther. Adv. Respir. Dis."},{"key":"B24","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 (London England)"},{"key":"B25","doi-asserted-by":"publisher","first-page":"6243","DOI":"10.1038\/s41467-021-26500-8","article-title":"Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host","volume":"12","author":"Llorens-Rico","year":"2021","journal-title":"Nat. Commun."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1111\/jam.15003","article-title":"A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing","volume":"131","author":"Luan","year":"2021","journal-title":"J.\u00a0Appl. Microbiol"},{"key":"B27","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","article-title":"The microbiota of the respiratory tract: gatekeeper to respiratory health","volume":"15","author":"Man","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"B28","first-page":"503","article-title":"Multifocal pneumonia: fever, cough, and dyspnea","volume":"103","author":"Mathew","year":"2021","journal-title":"Am. Family physician"},{"key":"B29","doi-asserted-by":"publisher","first-page":"151338","DOI":"10.1016\/j.ijmm.2019.151338","article-title":"Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study","volume":"309","author":"Moon","year":"2019","journal-title":"Int. J. Med. microbiology: IJMM"},{"key":"B30","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":"B31","doi-asserted-by":"publisher","first-page":"113041","DOI":"10.1016\/j.biopha.2022.113041","article-title":"Natural therapeutics and nutraceuticals for lung diseases: Traditional significance, phytochemistry, and pharmacology","volume":"150","author":"Rahman","year":"2022","journal-title":"Biomedicine pharmacotherapy = Biomedecine pharmacotherapie"},{"key":"B32","doi-asserted-by":"publisher","first-page":"e300","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":"B33","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1097\/CM9.0000000000000722","article-title":"Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study","volume":"133","author":"Ren","year":"2020","journal-title":"Chin. Med. J."},{"key":"B34","doi-asserted-by":"publisher","first-page":"2117","DOI":"10.1007\/s40265-021-01635-6","article-title":"The epidemiology and pathogenesis and treatment of pseudomonas aeruginosa infections: an update","volume":"81","author":"Reynolds","year":"2021","journal-title":"Drugs"},{"key":"B35","doi-asserted-by":"publisher","first-page":"776","DOI":"10.5858\/arpa.2016-0539-ra","article-title":"Validation of metagenomic next-generation sequencing tests for universal pathogen detection","volume":"141","author":"Schlaberg","year":"2017","journal-title":"Arch. Pathol. Lab. Med."},{"key":"B36","doi-asserted-by":"publisher","first-page":"528","DOI":"10.3967\/bes2022.070","article-title":"Using 16S rDNA Sequencing Technology to Preliminarily Analyze Intestinal Flora in Children with Mycoplasma pneumoniae Pneumonia","volume":"35","author":"Shi","year":"2022","journal-title":"Biomed. Environ. sciences: BES"},{"key":"B37","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s41479-020-00074-3","article-title":"Etiology of community-acquired pneumonia in adults: a systematic review","volume":"12","author":"Shoar","year":"2020","journal-title":"Pneumonia (Nathan)"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2022.888064","article-title":"Metagenomic next-generation sequencing reveals the profile of viral infections in kidney transplant recipients during the COVID-19 pandemic","volume":"10","author":"Tian","year":"2022","journal-title":"Front. Public Health"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1164\/rccm.201710-2118oc","article-title":"Airway microbiota is associated with upregulation of the PI3K pathway in lung cancer","volume":"198","author":"Tsay","year":"2018","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B40","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1158\/2159-8290.CD-20-0263","article-title":"Lower airway dysbiosis affects lung cancer progression","volume":"11","author":"Tsay","year":"2021","journal-title":"Cancer Discovery"},{"key":"B41","doi-asserted-by":"publisher","first-page":"2327","DOI":"10.1056\/NEJMoa1803396","article-title":"Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis","volume":"380","author":"Wilson","year":"2019","journal-title":"N Engl. J. Med."},{"key":"B42","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/s41590-019-0451-9","article-title":"The influence of the microbiome on respiratory health","volume":"20","author":"Wypych","year":"2019","journal-title":"Nat. Immunol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.cytogfr.2021.09.002","article-title":"FGF\/FGFR signaling: From lung development to respiratory diseases","volume":"62","author":"Yang","year":"2021","journal-title":"Cytokine Growth factor Rev."},{"key":"B45","doi-asserted-by":"publisher","first-page":"23","DOI":"10.5152\/TurkThoracJ.2017.16034","article-title":"Mycobacterium tuberculosis and nontuberculous mycobacteria coinfection of the lungs","volume":"18","author":"Y\u0131lmaz","year":"2017","journal-title":"Turkish Thorac. J."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.7754\/clin.lab.2022.220704","article-title":"T-SPOT.TB negative and diagnosed as interstitial pulmonary tuberculosis by NGS: a case report and literature review","volume":"69","author":"Zhang","year":"2023","journal-title":"Clin. Lab."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1320831\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,31]],"date-time":"2024-10-31T06:11:17Z","timestamp":1730355077000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1320831\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,31]]},"references-count":46,"alternative-id":["10.3389\/fcimb.2024.1320831"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2024.1320831","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,31]]},"article-number":"1320831"}}