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An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases.
- Source :
-
Nature communications [Nat Commun] 2024 Sep 15; Vol. 15 (1), pp. 8084. Date of Electronic Publication: 2024 Sep 15. - Publication Year :
- 2024
-
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&#95;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.<br /> (© 2024. The Author(s).)
- Subjects :
- Humans
Chronic Disease
Klebsiella pneumoniae genetics
Klebsiella pneumoniae pathogenicity
Klebsiella pneumoniae isolation & purification
Diabetes Mellitus, Type 2 microbiology
Diabetes Mellitus, Type 2 genetics
Escherichia coli genetics
Escherichia coli pathogenicity
Escherichia coli isolation & purification
Bacteria genetics
Bacteria classification
Bacteria isolation & purification
Bacteria pathogenicity
Databases, Genetic
Bacterial Infections microbiology
Virulence Factors genetics
Gastrointestinal Microbiome genetics
Subjects
Details
- Language :
- English
- ISSN :
- 2041-1723
- Volume :
- 15
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Nature communications
- Publication Type :
- Academic Journal
- Accession number :
- 39278950
- Full Text :
- https://doi.org/10.1038/s41467-024-51864-y