Microbiome Database of Pulmonary Diseases (MDPD)

MDPD unveils diverse microbial patterns across wide range of human body sites highlighting variations in different subtypes of pulmonary diseases. It contains a total of 59,362 runs compiled from 430 BioProjects. It is a manually curated microbiome database of 19 lung diseases and healthy categorized broadly into six groups namely Obstructive, Restrictive, Vascular, Infectious, Malignancy and Healthy.

Accessing the database

MDPD is available at: http://bicresources.jcbose.ac.in/ssaha4/mdpd. The data statistics of MDPD is available in the Statistics page. Please refer to the Help page for understanding how to use the database.

Groups

• Obstructive diseases - Asthma, COPD, Bronchiectasis, Bronchitis, Asthma-COPD Overlap (ACO), and COPD-Bronchiectasis Association (CBA)
• Restrictive diseases - ARDS, Cystic Fibrosis, ILD, IPF, Sarcoidosis, and Pneumonitis
• Vascular diseases - Pulmonary Hypertension
• Infectious diseases - Bronchiolitis, COVID-19, Pneumonia, Tuberculosis, and Other Pulmonary Infections (OPI)
• Malignancy diseases - Lung Cancer
• Healthy

Microbiome sites

It is developed to provide insights about the microbiome profiles of 10 microbiome sites in human body, namely Nasal, Oral, Upper Repiratory Tract, Lower Respiratory Tract, Lung, Stomach, Large Instestine, Gut, Rectum and Anus.

Data Summary

• Amplicon-16S, Amplicon-ITS, and whole metagenome sequencing.
• 430 BioProjects and 59,362 runs/samples.
• 19 different pulmonary diseases and a healthy group.
• 278 subgroups different diseases and healthy.
• 10 human microbiome body sites.
• Microbial information of Bacteria (n = 2296), Eukaryota (n = 219), Virus (n = 193), and Archaea (n = 13).

Features of MDPD

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.

R scripts

All the R scripts used in developing the database are given in the R/ folder.

Team

Paramita Roy^{^}, Dibakar Roy^{^}, Sudipto Bhattacharjee^{^}, Abhirupa Ghosh, and Sudipto Saha.

Please contact Dr. Sudipto Saha ([email protected]) regarding any further queries.