Project name: Guild-level microbiome signature associated with COVID-19 severity and prognosis

Description: COVID-19 severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples collected from 300 in-hospital COVID-19 patients at time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), Redundancy Analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis found that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the Guild-level microbiome index (GMI) classified patients from different severity groups (average AUCROC = 0.83). Moreover, age adjusted partial spearman correlation showed that GMI at admission were related with 8 clinical parameters, which are predictors for COVID-19 prognosis, at Day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was be able to classify patients with different COVID-19 symptom severity in different geographies and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent datasets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission.

Data type: Metagenome

Sample scope: Other

Relevance: Medical

Release date: 2023-01-20

Last updated: 2022-12-15

Data size: 1.61TB