Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
Revision editor(s): Zheeburg, Aleru Divine
Signature 2
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
Revision editor(s): Zheeburg, Aleru Divine
Experiment 2
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
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
Revision editor(s): Zheeburg, Aleru Divine
Signature 2
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
Revision editor(s): Zheeburg, Aleru Divine
Experiment 3
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
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
Revision editor(s): Zheeburg, Aleru Divine
Signature 2
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
Revision editor(s): Zheeburg, Aleru Divine
