Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study
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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
Curated date: 2021/07/04
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Subjects
- Location of subjects
- South Korea
- 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
- Infected COVID-19 samples (respiratory positive)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recovered COVID-19 samples (respiratory negative)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No history of antibiotics or probiotics
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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).
- raw counts
- Statistical test
- Linear Regression
- 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
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table S1
Description: Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples
Abundance in Group 1: increased abundance in Recovered COVID-19 samples (respiratory negative)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Bacteroidia | ||
| Bacteroidales |
Revision editor(s): Claregrieve1
Signature 2
Source: Supplementary Table S1
Description: Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples
Abundance in Group 1: decreased abundance in Recovered COVID-19 samples (respiratory negative)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales |
Revision editor(s): Claregrieve1
Experiment 2
Curated date: 2021/07/04
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Supplementary Table S2
Description: Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls
Abundance in Group 1: decreased abundance in Recovered COVID-19 samples (respiratory negative)
Revision editor(s): Claregrieve1, Merit
Signature 2
Source: Supplementary Table S2
Description: Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls
Abundance in Group 1: increased abundance in Recovered COVID-19 samples (respiratory negative)
Revision editor(s): Claregrieve1
Experiment 3
Curated date: 2021/07/04
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infected COVID-19 samples (respiratory positive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table S2
Description: Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls
Abundance in Group 1: decreased abundance in Infected COVID-19 samples (respiratory positive)
Revision editor(s): Claregrieve1, Merit
Signature 2
Source: Supplementary Table S2
Description: Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls
Abundance in Group 1: increased abundance in Infected COVID-19 samples (respiratory positive)
Revision editor(s): Claregrieve1
