The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome, 2024, Su et al.

The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome
Qi Su; Raphaela I. Lau; Qin Liu; Moses K.T. Li; Joyce Wing Yan Mak; Wenqi Lu; Ivan S.F. Lau; Louis H.S. Lau; Giann T.Y. Yeung; Chun Pan Cheung; Whitney Tang; Chengyu Liu; Jessica Y.L. Ching; Pui Kuan Cheong; Francis K.L. Chan; Siew C. Ng

SUMMARY
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.

HIGHLIGHTS

• The gut microbiome in subjects with post-acute COVID-19 syndrome (PACS) was analyzed

• Gut microbiome composition associates with the heterogeneity of PACS

• Gut enterotypes associate with distinct phenotypic manifestations of PACS

• Microbiome-based multi-label machine learning model accurately predicts PACS symptoms

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