An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases

Virulence factor genes (VFGs) play pivotal roles in bacterial infections and have been identified within the human gut microbiota. However, their involvement in chronic diseases remains poorly understood. Here, we establish an expanded VFG database (VFDB 2.0) consisting of 62,332 nonredundant orthologues and alleles of VFGs using species-specific average nucleotide identity ( https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases ). We further develop the MetaVF toolkit, facilitating the precise identification of pathobiont-carried VFGs at the species level. A thorough characterization of VFGs for 5452 commensal isolates from healthy individuals reveals that only 11 of 301 species harbour these factors. Further analyses of VFGs within the gut microbiomes of nine chronic diseases reveal both common and disease-specific VFG features. Notably, in type 2 diabetes patients, long HiFi sequencing confirms that shared VF features are carried by pathobiont strains of Escherichia coli and Klebsiella pneumoniae . These findings underscore the critical importance of identifying and understanding VFGs in microbiome-associated diseases. Here, by mining 18,521 complete bacterial genomes, the authors construct VFDB 2.0, an expanded database of virulence factor genes, consisting of 62,332 nonredundant orthologues and alleles with annotated host taxa using species-specific average nucleotide identity, and present MetaVF, a toolkit that facilitates precise identification and quantification of virulence factor genes carried by specific pathobionts in human gut metagenomes.