Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza
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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: 2021/06/03
Curator: Claregrieve1
Revision editor(s): Fatima, Claregrieve1, WikiWorks, Peace Sandy
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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Rothia | ||
Veillonella | ||
Thomasclavelia | ||
Actinomyces |
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 3a
Description: Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 cases
NCBI | Quality Control | Links |
---|---|---|
Agathobacter | ||
Anaerobutyricum hallii | ||
Anaerostipes | ||
Dorea | ||
Faecalibacterium | ||
Fusicatenibacter | ||
Intestinibacter | ||
Klebsiella | ||
Romboutsia | ||
Turicibacter | ||
[Ruminococcus] torques | ||
Clostridium |
Revision editor(s): Fatima, Claregrieve1
Experiment 2
Curated date: 2021/06/03
Curator: Claregrieve1
Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Victoria
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Influenza A (H1N1) Influenza A (H1N1),influenza A (H1N1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- H1N1 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary Figure 2
Description: Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls
Abundance in Group 1: decreased abundance in H1N1 cases
NCBI | Quality Control | Links |
---|---|---|
Blautia | ||
Romboutsia | ||
Collinsella | ||
Anaerobutyricum hallii | ||
Bifidobacterium | ||
Agathobacter | ||
Fusicatenibacter | ||
[Ruminococcus] torques | ||
Anaerostipes | ||
Dorea | ||
Ruminococcus sp. |
Revision editor(s): Claregrieve1
Signature 2
Source: Supplementary Figure 2
Description: Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls
Abundance in Group 1: increased abundance in H1N1 cases
NCBI | Quality Control | Links |
---|---|---|
Enterococcus | ||
Prevotella | ||
Finegoldia | ||
Peptoniphilus |
Revision editor(s): Claregrieve1
Experiment 3
Curated date: 2021/06/03
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Subjects
- 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
- H1N1 patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 4a
Description: Differences in microbiota composition between COVID-19 patients and H1N1 patients
Abundance in Group 1: increased abundance in COVID-19 patients
Revision editor(s): Fatima, Claregrieve1
Signature 2
Source: Figure 4a
Description: Differences in microbiota composition between COVID-19 patients and H1N1 patients
Abundance in Group 1: decreased abundance in COVID-19 patients
NCBI | Quality Control | Links |
---|---|---|
Prevotella | ||
Ezakiella | ||
Akkermansia | ||
Murdochiella | ||
Porphyromonas |
Revision editor(s): Claregrieve1
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2A, 2B, 2C, 2D
Description: Taxonomic differences in fecal microbiota between patients with covid-19 and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
NCBI | Quality Control | Links |
---|---|---|
Streptococcaceae | ||
Streptococcus | ||
Bacilli |
Revision editor(s): Fatima