gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms

Nucleic Acids Res. 2025 Dec 8:gkaf1205. doi: 10.1093/nar/gkaf1205. Online ahead of print.

ABSTRACT

gutMSNP (https://bio-computing.hrbmu.edu.cn/gutMSNP/home) is a user-friendly database designed to provide a systematic and comprehensive resource for single-nucleotide polymorphisms (SNPs) in the human gut microbiome. Given that even a single SNP in gut microbial genomes can profoundly modulate microbial pathogenicity and thereby impact host health, a large-scale, standardized SNP repository is indispensable for elucidating microbial functions and the molecular mechanisms underpinning microbiota-driven disorders. The current release of gutMSNP includes: (i) 164 015 783 SNPs identified across human gut microbial genomes and categorized into three coverage confidence levels; (ii) 364 species-level and 8251 gene-level microbial records, each exhibiting phenotype-specific SNP distribution patterns; (iii) 8146 representative reference genomes of human gut microbes; and (iv) an online tool for capturing SNPs. The database enables users to search for SNPs in microbial species of interest along with detailed functional and positional annotations, explore phenotype-specific SNP distribution patterns in selected species and their associated genes, download reference genomes for downstream analyses, and detect as well as annotate SNPs in user-uploaded microbial genome files. With its massive SNP dataset, versatile query capabilities, and integrated analytical tools, gutMSNP will serve as a fundamental resource for SNP-based investigations in the human gut microbiome.

PMID:41359024 | DOI:10.1093/nar/gkaf1205