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An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases

Author

Listed:
  • Wanting Dong

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Xinyue Fan

    (Chinese Academy of Sciences)

  • Yaqiong Guo

    (Beijing Academy of Science and Technology)

  • Siyi Wang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Shulei Jia

    (Tianjin Medical University)

  • Na Lv

    (Chinese Academy of Sciences)

  • Tao Yuan

    (Chinese Academy of Medical Science and Peking Union Medical College)

  • Yuanlong Pan

    (Chinese Academy of Sciences)

  • Yong Xue

    (China Agricultural University)

  • Xi Chen

    (Nanjing Agricultural University)

  • Qian Xiong

    (Chinese Academy of Sciences)

  • Ruifu Yang

    (Beijing Institute of Microbiology and Epidemiology)

  • Weigang Zhao

    (Chinese Academy of Medical Science and Peking Union Medical College)

  • Baoli Zhu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Southwest Medical University
    Jinan Microecological Biomedicine Shandong Laboratory)

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.

Suggested Citation

  • Wanting Dong & Xinyue Fan & Yaqiong Guo & Siyi Wang & Shulei Jia & Na Lv & Tao Yuan & Yuanlong Pan & Yong Xue & Xi Chen & Qian Xiong & Ruifu Yang & Weigang Zhao & Baoli Zhu, 2024. "An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51864-y
    DOI: 10.1038/s41467-024-51864-y
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    as
    1. Qiang Feng & Suisha Liang & Huijue Jia & Andreas Stadlmayr & Longqing Tang & Zhou Lan & Dongya Zhang & Huihua Xia & Xiaoying Xu & Zhuye Jie & Lili Su & Xiaoping Li & Xin Li & Junhua Li & Liang Xiao & , 2015. "Gut microbiome development along the colorectal adenoma–carcinoma sequence," Nature Communications, Nature, vol. 6(1), pages 1-13, May.
    2. Nan Qin & Fengling Yang & Ang Li & Edi Prifti & Yanfei Chen & Li Shao & Jing Guo & Emmanuelle Le Chatelier & Jian Yao & Lingjiao Wu & Jiawei Zhou & Shujun Ni & Lin Liu & Nicolas Pons & Jean Michel Bat, 2014. "Alterations of the human gut microbiome in liver cirrhosis," Nature, Nature, vol. 513(7516), pages 59-64, September.
    3. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    4. R. Gacesa & A. Kurilshikov & A. Vich Vila & T. Sinha & M. A. Y. Klaassen & L. A. Bolte & S. Andreu-Sánchez & L. Chen & V. Collij & S. Hu & J. A. M. Dekens & V. C. Lenters & J. R. Björk & J. C. Swarte , 2022. "Environmental factors shaping the gut microbiome in a Dutch population," Nature, Nature, vol. 604(7907), pages 732-739, April.
    5. Sarkis K. Mazmanian & June L. Round & Dennis L. Kasper, 2008. "A microbial symbiosis factor prevents intestinal inflammatory disease," Nature, Nature, vol. 453(7195), pages 620-625, May.
    6. Zhuye Jie & Huihua Xia & Shi-Long Zhong & Qiang Feng & Shenghui Li & Suisha Liang & Huanzi Zhong & Zhipeng Liu & Yuan Gao & Hui Zhao & Dongya Zhang & Zheng Su & Zhiwei Fang & Zhou Lan & Junhua Li & Li, 2017. "The gut microbiome in atherosclerotic cardiovascular disease," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    7. Vinod K. Gupta & Minsuk Kim & Utpal Bakshi & Kevin Y. Cunningham & John M. Davis & Konstantinos N. Lazaridis & Heidi Nelson & Nicholas Chia & Jaeyun Sung, 2020. "A predictive index for health status using species-level gut microbiome profiling," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    8. Kristoffer Forslund & Falk Hildebrand & Trine Nielsen & Gwen Falony & Emmanuelle Le Chatelier & Shinichi Sunagawa & Edi Prifti & Sara Vieira-Silva & Valborg Gudmundsdottir & Helle Krogh Pedersen & Man, 2015. "Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota," Nature, Nature, vol. 528(7581), pages 262-266, December.
    9. Cayetano Pleguezuelos-Manzano & Jens Puschhof & Axel Rosendahl Huber & Arne van Hoeck & Henry M. Wood & Jason Nomburg & Carino Gurjao & Freek Manders & Guillaume Dalmasso & Paul B. Stege & Fernanda L., 2020. "Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli," Nature, Nature, vol. 580(7802), pages 269-273, April.
    10. Junjie Qin & Yingrui Li & Zhiming Cai & Shenghui Li & Jianfeng Zhu & Fan Zhang & Suisha Liang & Wenwei Zhang & Yuanlin Guan & Dongqian Shen & Yangqing Peng & Dongya Zhang & Zhuye Jie & Wenxian Wu & Yo, 2012. "A metagenome-wide association study of gut microbiota in type 2 diabetes," Nature, Nature, vol. 490(7418), pages 55-60, October.
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