Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients
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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
- Nasopharynx , Throat Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx,Gula,Throat,throat
- 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
- local controls
- 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
- Hospitalized COVID-19 patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Fig 2A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.
Abundance in Group 1: increased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Alloprevotella | ||
| Atopobium | ||
| Megasphaera | ||
| Prevotella | ||
| Solobacterium | ||
| Sphingomonas | ||
| Veillonella | ||
| Prevotella_7Prevotella_7 |
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Fig 2A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients versus local controls.
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Abiola-Salako, Scholastica
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Abnormality of the respiratory system Respiratory abnormality,Abnormality of the respiratory system,abnormality of the respiratory system
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Covid-19 Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses.
- Group 1 sample size Number of subjects in the case (exposed) group
- 69
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig 2B
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.
Abundance in Group 1: increased abundance in Non-Covid-19 Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Dolosigranulum | ||
| Lacticaseibacillus | ||
| Lactobacillus | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Megasphaera | ||
| Prevotella | ||
| Rothia | ||
| Veillonella | ||
| Prevotella_7Prevotella_7 |
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Fig 2B
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized non-COVID-19 patients versus local controls.
Abundance in Group 1: decreased abundance in Non-Covid-19 Patients
Revision editor(s): Abiola-Salako, Scholastica
Experiment 3
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
- non-Covid-19 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
- Hospitalised Covid-19 patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
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: Fig 2C
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.
Abundance in Group 1: increased abundance in Covid-19 patients
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Fig 2C
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 versus non-COVID-19 patients.
Abundance in Group 1: decreased abundance in Covid-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroglobus | ||
| Lacticaseibacillus | ||
| Lactobacillus | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Mogibacterium | ||
| Rothia |
Revision editor(s): Abiola-Salako, Scholastica
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Pneumonia acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Covid-19 with no Pneumonia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19 with Pneumonia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized COVID-19 patients with Pneumonia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.
Abundance in Group 1: increased abundance in Covid-19 with Pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. |
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Figure 6A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with pneumonia compared to those with no pneumonia.
Abundance in Group 1: decreased abundance in Covid-19 with Pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella | ||
| Peptoniphilus |
Revision editor(s): Abiola-Salako, Scholastica
Experiment 5
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
- viral load (≤7.5)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- viral load (>7.5)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with viral load greater than 7.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6B
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.
Abundance in Group 1: increased abundance in viral load (>7.5)
| NCBI | Quality Control | Links |
|---|---|---|
| Acholeplasma | ||
| Bacteroides | ||
| Porphyromonas | ||
| [Eubacterium] nodatum | ||
| Family XIII UCG-001Family XIII UCG-001 |
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Figure 6B
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized COVID-19 patients with viral load ≤7.5 versus viral load >7.5.
Abundance in Group 1: decreased abundance in viral load (>7.5)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Gemella | ||
| Paraburkholderia caballeronis | ||
| Pseudomonas |
Revision editor(s): Abiola-Salako, Scholastica
Experiment 6
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
- local controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hospitalized patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized COVID and non-COVID patients,
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 145
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 4A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.
Abundance in Group 1: increased abundance in Hospitalized patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Alloprevotella | ||
| Atopobium | ||
| Centipeda | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Megasphaera | ||
| Prevotella | ||
| Solobacterium | ||
| Veillonella | ||
| Prevotella_7Prevotella_7 |
Revision editor(s): Abiola-Salako, Scholastica
Signature 2
Source: Figure 4A
Description: Discriminative bacterial genera identified by Linear discriminant analysis (LDA) effect size (LEfSe) in hospitalized (COVID-19 and non-COVID-19) patients versus local controls.
Abundance in Group 1: decreased abundance in Hospitalized patients
Revision editor(s): Abiola-Salako, Scholastica
