Microbiome datasets of MDPD (Microbiome Database of Pulmonary Diseases)

The microbiome database for Pulmonary Diseases (MDPD) is an open-access resource featuring microbiome data from 19 pulmonary diseases and healthy individuals. It contains microbiome data from 10 human body sites, including the nasal, oral, upper respiratory tract, lower respiratory tract, lung, stomach, gut, large intestine, rectum, and anus. The 19 pulmonary diseases are broadly categorised into five major groups; 1. Obstructive diseases - Asthma, Chronic Obstructive Pulmonary Disease (COPD), Bronchiectasis, Bronchitis, Asthma-COPD Overlap (ACO), and COPD-Bronchiectasis Association (CBA). 2. Restrictive diseases - Acute Respiratory Distress Syndrome (ARDS), Cystic Fibrosis, Interstitial Lung Disease (ILD), Idiopathic Pulmonary Fibrosis (IPF), Sarcoidosis, and Pneumonitis. 3. Vascular diseases - Pulmonary Hypertension. 4. Infectious diseases - Bronchiolitis, COVID-19, Pneumonia, Tuberculosis, and Other Pulmonary Infections (OPI). 5. Malignancy - Lung Cancer. 6. Healthy. BioProject IDs are manually curated from public databases, such as PubMed (Data availability section) and NCBI BioProject. The raw data (.fastq) for all the BioProjects were downloaded and re-analysed using an in-house pipeline (DADA2, Kraken2, and Bracken). It includes Amplicon-16S, Amplicon-ITS, and whole metagenome sequencing data from 430 BioProjects and 59,362 runs/samples. MDPD collects data on approximately 278 subgroups of diseases and healthy, including COPD stable, Eosinophilic asthma, healthy nonsmokers and others. It provides comprehensive microbial information of Bacteria (n = 2296), Eukaryotes (n = 219), Viruses (n = 193), and Archaea (n = 13), such as Biofilm formation, Pulmonary disease association, and pathogenicity. MDPD captures the dynamics of the microbes in different human body sites, including their composition and abundance, association of the microbes with various covariates (age, gender, smoking status), microbial markers for different groups (diseases/healthy) and their subgroups, cross-disease or healthy subgroup comparisons, and microbial community structure. This repository contains the metadata information of all the BioProjects (430) along with the .biom files for reproducibility and downstream applications (machine learning, meta-analysis).