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Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis.

Mingquan Guo1, Guojun Wu2,3, Yun Tan4

  • 1Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.

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|February 6, 2023
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Summary
This summary is machine-generated.

A novel gut microbiome signature, based on genome-resolved analysis of microbial guilds, can predict Coronavirus disease 2019 (COVID-19) severity and patient outcomes upon hospital admission. This guild-level microbiome index (GMI) aids in early risk stratification for severe COVID-19.

Keywords:
COVID-19guildgut microbiome

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Area of Science:

  • Microbiome research
  • Genomics
  • Infectious disease epidemiology

Background:

  • Gut microbiota alterations are linked to Coronavirus disease 2019 (COVID-19) severity, but the precise relationship with prognosis is unclear.
  • Previous studies often relied on taxonomic-level analysis, potentially overlooking intricate microbial interactions and genome-specific functions.

Purpose of the Study:

  • To investigate the genome-specific relationship between gut microbiome composition and COVID-19 prognosis using a genome-resolved metagenomic approach.
  • To develop a predictive microbiome-based index for stratifying COVID-19 patient severity and outcomes.

Main Methods:

  • Genome-resolved metagenomic analysis of fecal samples from 300 hospitalized COVID-19 patients.
  • Identification of differentially abundant high-quality metagenome-assembled genomes (HQMAGs) across severity groups.
  • Co-abundance network analysis to define microbial guilds and development of a guild-level microbiome index (GMI).

Main Results:

  • Thirty-three HQMAGs formed two competing guilds; Guild 1 (potentially beneficial) and Guild 2 (potentially detrimental) showed differential distribution based on COVID-19 severity.
  • The GMI effectively classified patients across mild, moderate, and severe/critical groups (AUROC = 0.83) and correlated with clinical prognosis predictors.
  • GMI at admission predicted outcomes in critical patients and consistently differentiated COVID-19 severity across independent datasets and populations.

Conclusions:

  • A genome-based, guild-level gut microbiome signature (GMI) can identify hospitalized COVID-19 patients at high risk for severe outcomes upon admission.
  • This approach moves beyond taxonomic limitations, highlighting genome-specific microbial interactions and their clinical relevance in COVID-19.
  • The GMI offers a promising tool for early risk stratification and personalized management of COVID-19 patients.