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

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-29
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z, Zhao L
Journal
mBio
Year
2023
Keywords:
COVID-19, guild, gut microbiome
Coronavirus disease 2019 (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 from 300 in-hospital COVID-19 patients, collected at the 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 determined 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 AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on 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 able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. 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. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.

Experiment 1


Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/07

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Mild severity
Group 1 name Corresponds to the case (exposed) group for case-control studies
Moderate severity
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 Patients with moderate severity symptoms.
Group 0 sample size Number of subjects in the control (unexposed) group
88
Group 1 sample size Number of subjects in the case (exposed) group
196

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Dunn's test
Kruskall-Wallis
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/09

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: increased abundance in Moderate severity

NCBI Quality ControlLinks
Akkermansia muciniphila
Anaerotignum
Barnesiella intestinihominis
Dorea
Enterocloster bolteae
Enterococcus avium
Enterococcus faecium
Intestinibacter bartlettii
Lachnospiraceae
Ligilactobacillus salivarius
Limosilactobacillus fermentum
Phascolarctobacterium faecium
Ruthenibacterium lactatiformans
Acutalibacteraceae

Revision editor(s): Zheeburg, Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/10

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: decreased abundance in Moderate severity

NCBI Quality ControlLinks
Faecalibacterium prausnitzii
Allisonella histaminiformans
Acutalibacteraceae
Negativibacillus
Clostridium
Romboutsia timonensis
Coprococcus
Ruminococcus
Ruminococcus bromii
Lachnospiraceae

Revision editor(s): Zheeburg, Aleru Divine

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/08

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Severe/Critical severity
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
COVID-19 Patients with severe/critical severity symptoms.
Group 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/09

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: increased abundance in Severe/Critical severity

NCBI Quality ControlLinks
Akkermansia muciniphila
Anaerotignum
Barnesiella intestinihominis
Dorea
Enterocloster bolteae
Enterococcus avium
Enterococcus faecium
Intestinibacter bartlettii
Lachnospiraceae
Ligilactobacillus salivarius
Limosilactobacillus fermentum
Phascolarctobacterium faecium
Ruthenibacterium lactatiformans
Acutalibacteraceae

Revision editor(s): Zheeburg, Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/10

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: decreased abundance in Severe/Critical severity

NCBI Quality ControlLinks
Faecalibacterium prausnitzii
Allisonella histaminiformans
Acutalibacteraceae
Negativibacillus
Clostridium
Romboutsia timonensis
Coprococcus
Ruminococcus
Ruminococcus bromii
Lachnospiraceae

Revision editor(s): Zheeburg, Aleru Divine

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/08

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Moderate severity
Group 0 sample size Number of subjects in the control (unexposed) group
196

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/10

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: increased abundance in Severe/Critical severity

NCBI Quality ControlLinks
Akkermansia muciniphila
Anaerotignum
Barnesiella intestinihominis
Candidatus Dorea massiliensis
Enterocloster bolteae
Enterococcus avium
Enterococcus faecium
Intestinibacter bartlettii
Lachnospiraceae
Ligilactobacillus salivarius
Limosilactobacillus fermentum
Phascolarctobacterium faecium
Ruthenibacterium lactatiformans
Acutalibacteraceae

Revision editor(s): Zheeburg, Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-29

Curated date: 2024/03/10

Curator: Zheeburg

Revision editor(s): Zheeburg, Aleru Divine

Source: Fig. 2A

Description: Heatmap of 33 high-quality metagenome-assembled genomes (HQMAGs) identified by redundancy analysis (RDA) and showing differential abundance between the 3 severity groups.

Abundance in Group 1: decreased abundance in Severe/Critical severity

NCBI Quality ControlLinks
Faecalibacterium prausnitzii
Allisonella histaminiformans
Acutalibacteraceae
Negativibacillus
Clostridium
Romboutsia timonensis
Coprococcus
Ruminococcus
Ruminococcus bromii
Lachnospiraceae

Revision editor(s): Zheeburg, Aleru Divine