VFDB 2022: a general classification scheme for bacterial virulence factors

TLDR

VFDB is a comprehensive database of bacterial virulence factors, but existing classification schemes are fragmented, creating obstacles for pan‑bacterial metagenomic analyses amid growing sequencing data. The authors aimed to establish a unified category system for bacterial VFs and reorganize the VFDB accordingly. They reorganized the dataset through extensive literature mining and added a JavaScript‑independent web interface to enhance accessibility. The updated VFDB groups all known VFs from 32 common bacterial genera into 14 basal categories and over 100 subcategories, making it a coherent resource suitable for future pan‑bacterial virulence factor analyses.

Abstract

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.