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Machine learning aided construction of the quorum sensing communication network for human gut microbiota

Author

Listed:
  • Shengbo Wu

    (Tianjin University
    Tianjin University)

  • Jie Feng

    (Tianjin University)

  • Chunjiang Liu

    (Tianjin University
    Tianjin University)

  • Hao Wu

    (Zhejiang Shaoxing Research Institute of Tianjin University)

  • Zekai Qiu

    (Tianjin University)

  • Jianjun Ge

    (Tianjin University)

  • Shuyang Sun

    (Tianjin University)

  • Xia Hong

    (Tianjin University)

  • Yukun Li

    (Tianjin University)

  • Xiaona Wang

    (Tianjin University)

  • Aidong Yang

    (University of Oxford)

  • Fei Guo

    (Central South University)

  • Jianjun Qiao

    (Tianjin University
    Zhejiang Shaoxing Research Institute of Tianjin University
    Ministry of Education (Tianjin University))

Abstract

Quorum sensing (QS) is a cell-cell communication mechanism that connects members in various microbial systems. Conventionally, a small number of QS entries are collected for specific microbes, which is far from being able to fully depict communication-based complex microbial interactions in human gut microbiota. In this study, we propose a systematic workflow including three modules and the use of machine learning-based classifiers to collect, expand, and mine the QS-related entries. Furthermore, we develop the Quorum Sensing of Human Gut Microbes (QSHGM) database ( http://www.qshgm.lbci.net/ ) including 28,567 redundancy removal entries, to bridge the gap between QS repositories and human gut microbiota. With the help of QSHGM, various communication-based microbial interactions can be searched and a QS communication network (QSCN) is further constructed and analysed for 818 human gut microbes. This work contributes to the establishment of the QSCN which may form one of the key knowledge maps of the human gut microbiota, supporting future applications such as new manipulations to synthetic microbiota and potential therapies to gut diseases.

Suggested Citation

  • Shengbo Wu & Jie Feng & Chunjiang Liu & Hao Wu & Zekai Qiu & Jianjun Ge & Shuyang Sun & Xia Hong & Yukun Li & Xiaona Wang & Aidong Yang & Fei Guo & Jianjun Qiao, 2022. "Machine learning aided construction of the quorum sensing communication network for human gut microbiota," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30741-6
    DOI: 10.1038/s41467-022-30741-6
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    1. Jiandui Mi & Xiaoping Jing & Chouxian Ma & Fuyu Shi & Ze Cao & Xin Yang & Yiwen Yang & Apurva Kakade & Weiwei Wang & Ruijun Long, 2024. "A metagenomic catalogue of the ruminant gut archaeome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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