ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome

Nucleic Acids Res. 2025 Dec 3:gkaf1194. doi: 10.1093/nar/gkaf1194. Online ahead of print.

ABSTRACT

The respiratory microbiome plays an important role in maintaining human health. Despite the rapid growth of literature and publicly accessible data on the respiratory microbiome, a large-scale, well-curated database is still lacking. Here, we introduced ResMicroDb, a comprehensive database and analysis platform for the human respiratory microbiome. ResMicroDb contains 106 464 samples from 514 projects, spanning 10 sample sites, 72 sample types, and 146 phenotypes. Notably, it includes ~7-fold more respiratory samples than existing multi-body-site resources. To improve the reusability and accessibility of data, a standardized bioinformatics pipeline was employed to generate taxonomic profiles, and 32 metadata fields were manually curated. ResMicroDb also provides 11 908 microbe-disease associations, identified from 132 case-control studies, to deepen the understanding of microbiome-disease relationships. Additionally, ResMicroDb offers three tools for in-depth analysis: "Microbiome Composition" for visualizing taxonomic profiles of user-selected samples; "Sample Similarity Search" for inferring the characteristics of new samples by comparing them to the database based on similarity; and "Cross-study Analysis" for identifying common and specific microbial characteristics across cohorts, phenotypes and sample sites. ResMicroDb serves as a versatile and valuable resource for advancing a broad spectrum of respiratory microbiome research and clinical relevance. ResMicroDb is freely accessed at https://resmicrodb.cncb.ac.cn.

PMID:41335096 | DOI:10.1093/nar/gkaf1194