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Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome

Author

Listed:
  • Qin Liu

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Qi Su

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Fen Zhang

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Hein M. Tun

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Joyce Wing Yan Mak

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Grace Chung-Yan Lui

    (The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong)

  • Susanna So Shan Ng

    (The Chinese University of Hong Kong, Hong Kong)

  • Jessica Y. L. Ching

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Amy Li

    (The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Wenqi Lu

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Chenyu Liu

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Chun Pan Cheung

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • David S. C. Hui

    (The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong)

  • Paul K. S. Chan

    (The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Francis Ka Leung Chan

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Siew C. Ng

    (Microbiota I-Center (MagIC)
    The Chinese University of Hong Kong, Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

Abstract

Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months. Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.

Suggested Citation

  • Qin Liu & Qi Su & Fen Zhang & Hein M. Tun & Joyce Wing Yan Mak & Grace Chung-Yan Lui & Susanna So Shan Ng & Jessica Y. L. Ching & Amy Li & Wenqi Lu & Chenyu Liu & Chun Pan Cheung & David S. C. Hui & P, 2022. "Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34535-8
    DOI: 10.1038/s41467-022-34535-8
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    1. Bo Diao & Chenhui Wang & Rongshuai Wang & Zeqing Feng & Ji Zhang & Han Yang & Yingjun Tan & Huiming Wang & Changsong Wang & Liang Liu & Ying Liu & Yueping Liu & Gang Wang & Zilin Yuan & Xiaotao Hou & , 2021. "Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 infection," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    2. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
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