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. 2024 May 8;32(5):651-660.e4.
doi: 10.1016/j.chom.2024.04.005. Epub 2024 Apr 23.

The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome

Qi Su  1 , Raphaela I Lau  1 , Qin Liu  2 , Moses K T Li  2 , Joyce Wing Yan Mak  3 , Wenqi Lu  1 , Ivan S F Lau  3 , Louis H S Lau  3 , Giann T Y Yeung  3 , Chun Pan Cheung  1 , Whitney Tang  1 , Chengyu Liu  1 , Jessica Y L Ching  1 , Pui Kuan Cheong  1 , Francis K L Chan  4 , Siew C Ng  5
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Free article

The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome

Qi Su et al. Cell Host Microbe. .
Free article

Abstract

The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.

Keywords: gut microbiome; long COVID; machine learning; metagenomics; post-acute COVID-19 syndrome.

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Conflict of interest statement

Declaration of interests F.K.L.C. is a board member of CUHK Medical Centre. He is a co-founder, non-executive board chairman, and shareholder of GenieBiome Ltd. He receives patent royalties through his affiliated institutions. He has received fees as an advisor and honoraria as a speaker for EISAI Co. Ltd, AstraZeneca, Pfizer Inc., Takeda Pharmaceutical Co., and Takeda (China) Holdings Co. Ltd. S.C.N. has served as an advisory board member for Pfizer, Ferring, Janssen, and AbbVie and received honoraria as a speaker for Ferring, Tillotts, Menarini, Janssen, AbbVie, and Takeda. S.C.N. has received research grants through her affiliated institutions from Olympus, Ferring, and AbbVie. S.C.N. is a scientific co-founder and shareholder of GenieBiome Ltd. S.C.N. receives patent royalties through her affiliated institutions. Q.S., W.T., F.K.L.C., and S.C.N. are named inventors of patent applications held by the CUHK and MagIC that cover the therapeutic and diagnostic use of the microbiome.

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