Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa
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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: 2021/08/06
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
Subjects
- Location of subjects
- United States of America
- 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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- 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
- COVID-19 negative controls and healthcare workers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 positive patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients positive for SARS-CoV-2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 66
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 2a
Description: Differential microbial abundance between COVID-19 patients and non-COVID patients (COVID negative patients and healthcare workers)
Abundance in Group 1: increased abundance in COVID-19 positive patients
NCBI | Quality Control | Links |
---|---|---|
Acinetobacter | ||
Micrococcus | ||
Moraxella | ||
Pseudomonas | ||
Rothia |
Revision editor(s): Claregrieve1, Iram jamshed
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 negative controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative patients
Abundance in Group 1: increased abundance in COVID-19 positive patients
NCBI | Quality Control | Links |
---|---|---|
Anoxybacillus | ||
Acinetobacter | ||
Pseudomonas | ||
Pseudomonas aeruginosa |
Revision editor(s): Claregrieve1
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- COVID-19 negative healthcare workers (controls)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers
Abundance in Group 1: increased abundance in COVID-19 positive patients
NCBI | Quality Control | Links |
---|---|---|
Anoxybacillus | ||
Pseudomonas aeruginosa |
Revision editor(s): Claregrieve1
Signature 2
Source: Figures 2b-h
Description: Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers
Abundance in Group 1: decreased abundance in COVID-19 positive patients
NCBI | Quality Control | Links |
---|---|---|
Burkholderia cepacia |
Revision editor(s): Claregrieve1
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Viral load viral burden,viral titer,viral titre,Viral load,viral load
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- high Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with low cycle threshold value (>23.5)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Low Ct
Abundance in Group 1: increased abundance in low Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Neisseria | ||
Pseudomonas | ||
Pseudomonas aeruginosa |
Revision editor(s): Folakunmi
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mid Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with mid cycle threshold value (32.9-25.0)
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct
Abundance in Group 1: increased abundance in mid Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Neisseria |
Revision editor(s): Folakunmi
Signature 2
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High and Mid Ct
Abundance in Group 1: decreased abundance in mid Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Streptococcus |
Revision editor(s): Folakunmi
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mid Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with low cycle threshold value (>23.5)
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into Mid and Low Ct
Abundance in Group 1: increased abundance in low Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Pseudomonas aeruginosa |
Revision editor(s): Folakunmi
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low and mid Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with high cycle threshold value (>34.6)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Low and Mid Ct
Abundance in Group 1: increased abundance in high Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Streptococcus |
Revision editor(s): Folakunmi
Signature 2
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Mid and Low Ct
Abundance in Group 1: decreased abundance in high Ct CoV+ patients
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Cutibacterium | ||
Neisseria | ||
Pseudomonas |
Revision editor(s): Folakunmi