ArticleNature communications2024
An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Antimicrobial Peptides Improved Growth Performance by Intervening Ileac Microorganisms and Metabolites in Holstein Steers.Probiotics and antimicrobial proteins · 2026Article
- Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026Article
- Combining genotoxic gut bacterial strains increases tumor burden and accelerates onset in a germ-free mouse model of colon carcinogenesis.Cell reports · 2026Article
- New isolates from the 1970s to early 2000s provide insights into the evolution ofMicrobial genomics · 2026Article
- A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Reprogramming of bacterial virulence by lysine acetylation.Nature communications · 2026Article
- Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway.Nature communications · 2026Article
- Draft genomes of twoMicrobiology resource announcements · 2026Article
- Draft genome sequence of soil isolateMicrobiology resource announcements · 2026Article
- Isolation and characterization of a novel phage AbT1 and evaluating its anti-biofilm activity and antibiotic synergy.Molecular biology reports · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Reactive oxygen species in the rhizosphere orchestrate the recruitment of beneficial bacteria.The EMBO journal · 2026Article
- Article
- Leveraging whole-genome sequencing for microbial contamination tracking and risk assessment in pharmaceutical manufacturing.Frontiers in microbiology · 2026Article
- Comparative genomic analyses provide new insights into phylogenetic and functional diversification in genusFrontiers in microbiology · 2026Article
- Microbial inoculants for soil restoration: a risk-proportional stewardship framework integrating strain-resolved genomics and adaptive governance.Sustainable microbiology · 2026Review
- Adaptation without Dominance in Pseudomonas syringae Pathovars.Microbial ecology · 2025Article
- Virulence factor genes analysis of extended spectrum β-Lactamase producing Escherichia coli isolated from broiler chickens in Indonesia.The Journal of veterinary medical science · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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