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.
Authors
- Yong Xue (ORCID: https://orcid.org/0000-0002-6376-5006)
- Tao Yuan (ORCID: https://orcid.org/0000-0002-6026-9584)
- Na Lv (ORCID: https://orcid.org/0000-0001-8522-0560)
- Qian Xiong (ORCID: https://orcid.org/0000-0002-9079-5956)
- Yuanlong Pan (ORCID: https://orcid.org/0000-0001-9074-713X)
- Shulei Jia (ORCID: https://orcid.org/0000-0003-2483-0300)
- Yaqiong Guo (ORCID: https://orcid.org/0000-0002-3901-2549)
- Wanting Dong (ORCID: https://orcid.org/0000-0003-0237-1297)
- Weigang Zhao (ORCID: https://orcid.org/0000-0002-1472-7118)
- Ruifu Yang (ORCID: https://orcid.org/0000-0003-3219-7269)
- X. Fan (ORCID: https://orcid.org/0000-0003-0524-5237)
- Siyi Wang (ORCID: https://orcid.org/0000-0003-1146-2473)
- Baoli Zhu (ORCID: https://orcid.org/0000-0001-5326-9503)
- Xi Chen (ORCID: https://orcid.org/0009-0003-4589-3025)
Institutions
- Nanjing Agricultural University (CN)
- Chinese Academy of Sciences (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Peking Union Medical College Hospital (CN)
- Southwest Medical University (CN)
- State Key Laboratory of Plant Genomics (CN)
- Institute of Microbiology (CN)
- Jinan University (LB)
- Beijing Academy of Science and Technology (CN)
- University of Chinese Academy of Sciences (CN)
- China Agricultural University (CN)
- Tianjin Medical University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-15
- DOI
- https://doi.org/10.1038/s41467-024-51864-y
- Citations
- 28
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 6.55
Funders
- National Natural Science Foundation of China