LDMD: A database of microbes in human lung disease

Background Lungs were initially thought to be sterile. However, with the development of sequencing technologies, various commensal microorganisms, especially bacteria, have been observed in the lungs of healthy humans. Several studies have also linked lung microbes to infectious lung diseases. However, few databases have focused on the metagenomics of lungs to provide microbial compositions and corresponding metadata information. Such a database would be handy for researching and treating lung diseases. Methods To provide researchers with a preliminary understanding of lung microbes and their research methods, the LDMD collated nearly 10,000 studies in the literature covering over 30 diseases, gathered basic information such as the sources of lung microbe samples, sequencing methods, and processing software, as well as analyzed the metagenomic sequencing characteristics of lung microbes. Besides, the LDMD also contained data collected in our laboratory. Results In this study, we established the Lung Disease Microorganisms Database (LDMD), a comprehensive database of microbes involved in lung disease. The LDMD offered sequence analysis capabilities, allowing users to upload their sequencing results, align them with the data collated in the database, and visually analyze the results. Conclusion In conclusion, the LDMD possesses various functionalities that provide a convenient and comprehensive resource to study the lung metagenome and treat lung diseases.

[1]  Xingming Zhao,et al.  mBodyMap: a curated database for microbes across human body and their associations with health and diseases , 2021, Nucleic Acids Res..

[2]  A. Marques,et al.  Saliva as a non-invasive specimen for COPD assessment , 2021, Respiratory Research.

[3]  Mushal Allam,et al.  Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa , 2021, Scientific Reports.

[4]  G. Huffnagle,et al.  The Lung Microbiome during Health and Disease , 2021, International journal of molecular sciences.

[5]  M. Contoli,et al.  Inhaled Corticosteroids and the Lung Microbiome in COPD , 2021, Biomedicines.

[6]  R. Collman,et al.  The lung microbiome: progress and promise. , 2021, The Journal of clinical investigation.

[7]  S. Heath,et al.  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. , 2021, The Lancet. Microbe.

[8]  A. Dalpke,et al.  Changes in the Cystic Fibrosis Airway Microbiome in Response to CFTR Modulator Therapy , 2021, Frontiers in Cellular and Infection Microbiology.

[9]  J. Clemente,et al.  Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism , 2021, European Respiratory Journal.

[10]  Zhiyong Lu,et al.  Database resources of the National Center for Biotechnology Information , 2020, Nucleic Acids Res..

[11]  James R. Brown,et al.  The sputum microbiome is distinct between COPD and health, independent of smoking history , 2020, Respiratory Research.

[12]  Xiaoxing Li,et al.  gutMEGA: a database of the human gut MEtaGenome Atlas , 2020, Briefings Bioinform..

[13]  Rikky W. Purbojati,et al.  Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease , 2020, American journal of respiratory and critical care medicine.

[14]  J. Clemente,et al.  Methods in Lung Microbiome Research. , 2020, American journal of respiratory cell and molecular biology.

[15]  Rongchang Chen,et al.  A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-Levels , 2020, bioRxiv.

[16]  Tomasz P. Wypych,et al.  The influence of the microbiome on respiratory health , 2019, Nature Immunology.

[17]  C. Jenkins,et al.  Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma. , 2019, American journal of respiratory and critical care medicine.

[18]  Florian P Breitwieser,et al.  A review of methods and databases for metagenomic classification and assembly , 2019, Briefings Bioinform..

[19]  N. Segata,et al.  Multiple levels of the unknown in microbiome research , 2019, BMC Biology.

[20]  James R. Brown,et al.  Airway host-microbiome interactions in chronic obstructive pulmonary disease , 2019, Respiratory Research.

[21]  M. ROTH-KLEINER,et al.  Early-Life Formation of the Microbial and Immunological Environment of the Human Airways. , 2018, Cell host & microbe.

[22]  Thomas M. Keane,et al.  The European Nucleotide Archive in 2018 , 2018, Nucleic Acids Res..

[23]  J. Erb-Downward,et al.  Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study , 2018, BMJ Open Respiratory Research.

[24]  D. Descamps,et al.  Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma , 2018, Front. Physiol..

[25]  J. Nielandt,et al.  Disbiome database: linking the microbiome to disease , 2018, BMC Microbiology.

[26]  I. Pavord,et al.  Biological exacerbation clusters demonstrate asthma and chronic obstructive pulmonary disease overlap with distinct mediator and microbiome profiles , 2018, Journal of Allergy and Clinical Immunology.

[27]  R. Knight,et al.  Improving saliva shotgun metagenomics by chemical host DNA depletion , 2018, Microbiome.

[28]  James R. Brown,et al.  Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations , 2018, Thorax.

[29]  B. Finlay,et al.  Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting , 2017, The Journal of allergy and clinical immunology.

[30]  Zhiyong Lu,et al.  Towards PubMed 2.0 , 2017, eLife.

[31]  Maureen A. O’Malley,et al.  Dysbiosis and Its Discontents , 2017, mBio.

[32]  Cristina Aurrecoechea,et al.  MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments , 2017, bioRxiv.

[33]  Mario Castro,et al.  Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment , 2017, Journal of Allergy and Clinical Immunology.

[34]  Luis A. J. Mur,et al.  A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer , 2017, PloS one.

[35]  S. Wootton,et al.  A prospective, observational cohort study of the seasonal dynamics of airway pathogens in the aetiology of exacerbations in COPD , 2017, Thorax.

[36]  Aleksandra A. Kolodziejczyk,et al.  Dysbiosis and the immune system , 2017, Nature Reviews Immunology.

[37]  G. Huffnagle,et al.  The respiratory tract microbiome and lung inflammation: a two-way street , 2016, Mucosal Immunology.

[38]  Toshihisa Takagi,et al.  DNA Data Bank of Japan , 2016, Nucleic Acids Res..

[39]  J. Goedert,et al.  Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features , 2016, Genome Biology.

[40]  S. Sethi,et al.  The lung microbiome and exacerbations of COPD , 2016, Current opinion in pulmonary medicine.

[41]  W. R. Wikoff,et al.  Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype , 2016, Nature Microbiology.

[42]  F. Martinez,et al.  The Microbiome and the Respiratory Tract. , 2016, Annual review of physiology.

[43]  R. Milo,et al.  Revised Estimates for the Number of Human and Bacteria Cells in the Body , 2016, bioRxiv.

[44]  V. Pérez-Brocal,et al.  Functional Metagenomics of the Bronchial Microbiome in COPD , 2015, PloS one.

[45]  Jodie L Simpson,et al.  Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma , 2015, European Respiratory Journal.

[46]  N. Kaakoush.  Insights into the Role of Erysipelotrichaceae in the Human Host , 2015, Front. Cell. Infect. Microbiol..

[47]  Joseph R Arron,et al.  The airway microbiome in patients with severe asthma: Associations with disease features and severity. , 2015, The Journal of allergy and clinical immunology.

[48]  Jeffrey L. Curtis,et al.  Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals , 2015, mBio.

[49]  Sarah K. Hilton,et al.  Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia , 2014, Journal of Clinical Microbiology.

[50]  Patrick D Schloss,et al.  Comparison of the respiratory microbiome in healthy nonsmokers and smokers. , 2013, American journal of respiratory and critical care medicine.

[51]  Richard E. Isaacson,et al.  The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease , 2012, PloS one.

[52]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[53]  J. Curtis,et al.  Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD , 2011, PloS one.

[54]  Lior Pachter,et al.  Disordered Microbial Communities in Asthmatic Airways , 2010, PloS one.