VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

By Lihong Chen, Zhaohui Xiong, Lilian Sun, Jian Yang, Qi Jin. Nucleic Acids Res., 2011

526 citations recorded by the source corpus.

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has served as a comprehensive repository of bacterial virulence factors (VFs) for >7 years. Bacterial virulence is an exciting and dynamic field, due to the availability of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes. The intricacy of virulence mechanisms offers a challenge, and there exists a clear need to decipher the ‘language’ used by VFs more effectively. In this article, we present the recent major updates of VFDB in an attempt to summarize some of the most important virulence mechanisms by comparing different compositions and organizations of VFs from various bacterial pathogens, identifying core components and phylogenetic clades and shedding new light on the forces that shape the evolutionary history of bacterial pathogenesis. In addition, the 2012 release of VFDB provides an improved user interface.

Subfields: Food Science, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1cd33675d04880718955cbb3fd23df94148b84c8

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Citations in the corpus

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED (2015, methodology): “We created six Illumina-like synthetic metagenomes with material spiked in from the ARDB and VFDB sequence datasets.”
VFDB 2019: a comparative pathogenomic platform with an interactive web interface (2018, methodology): “To date, 32 genera of pathogens with medical importance are formally included in VFDB (with full information available), and 42 additional genera are also partially included in the database for the intergenus comparison of VFs, as previously described (12) (a full list of pathogens is available from”
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data (2013, background): “There are many databases available containing genes encoding toxins and virulence factors along with other genes traditionally associated with pathogenicity [13,14].”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, methodology): “…gene sets related to pathogenicity and antibiotic resistance will be carried out using information derived from external sources such as VFDB (36), MvirDB (37), ARDB (38), TBDReaMDB (39) and periodic targeted literature-based curation efforts that will be used to identify gene sets of…”
VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on (2015, methodology): “In an attempt to maximize the power of the comparative genomics platform in VFDB, the third release (R3) in 2012 included inter-genera comparative analysis of VFs involved in four major categories: (i) host cell attachment and invasion; (ii) bacterial secretion systems and effectors; (iii) toxins an”
VFDB 2022: a general classification scheme for bacterial virulence factors (2021, background): “However, unlike the previous scheme proposed in the 2012 release (12), which contains only four major bacterial VF categories (i.”
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, methodology): “Another focus of the database has been on integrating high-quality data on virulence factors from sources including the Virulence Factor Database (9), Victors Virulence Factors from the PHIDIAS database (10) and our own curation.”