• 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).

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.

• Systematically extracted and curated relevant metadata of the groups from public databases (NCBI, ENA, PubMed) and related research articles.
• Re-analyses of the raw data using state-of-the-art methods.
• Implemented rigorous quality control (QC) methods and stringent criteria to ensure only high-quality data was included.

• BIOM files (.rds) stored in the database.
• Curated metadata stored in the database.
• Users can also further analyze the data, e.g., according to country, gender, age, smoking status, and many other available metadata.

• A summary of BioProjects is available here.
• The source code of MDPD is available in a GitHub repository - https://github.com/PulmonomicsLab/mdpd

Name	Tool/Package/Library	Version	Usage
Trim galore	Perl wrapper	0.6.7	Quality trimming of the raw FastQ reads.
dada2	R package	1.26	Taxonomic inference from Amplicon-16S and Amplicon-ITS sequencing data.
Kraken2	Tool	2.1.3	Taxonomic inference from Whole Metagenome Sequencing data.
Bracken	Tool	3.1	Re-estimating species' relative abundance at the level using kmer information from the Kraken2 report file.
Pavian	Web application	1.0	To explore the classified taxonomic reads (%) from Whole Metagenome Sequencing data.
phyloseq	R package	1.42.0	Manipulation of the .biom files.
psadd	R package	0.1.3	Generate interactive Krona plots using the Kronatools.
file2meco	R package	0.7.1	Conversion of the Phyloseq object to a microtable object
microeco	R package	1.8.0	Detecting taxonomic abundance at the genus/species level. Microbial marker identification using LEfSe (Kruskal-Wallis’ test and Wilcoxon rank-sum tests) and edgeR (generalized linear models) with Benjamini-Hochberg (BH) method for FDR correction.
Maaslin2	R package	1.12.0	Finding the association of the microbes with the covariates, such as age groups and gender, using linear mixed models.
bugphyzz	R package	1.0	Functional annotation of the identified microbes.
taxonomizr	R package	0.11.1	Fetch the NCBI taxonomy information, such as taxonomy IDs.
mboost	R package	2.9.11	Model-based gradient boosting for generating co-occurrence networks.
boot	R package	1.3.30	Bootstrap Resampling for making the co-occurrence networks.
Plotly.js	JavaScript library	3.0.1	Creating interactive plots.
Cytoscape.js	JavaScript library	3.31.2	Building microbial co-occurrence networks.
SVG 3D Tag Cloud jQuery plugin	JavaScript library	-	Drawing the 3D interactive plot on the home page

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© 2025 Bose Institute. All rights reserved. For queries, please contact Dr. Sudipto Saha (ssaha4@jcbose.ac.in, ssaha4@gmail.com).