Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients
-
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: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (A) between hospitalized COVID patients and 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 sp. 1-8 |
Revision editor(s): Abiola-Salako
Signature 2
Source: Fig 2A
Description: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (A) between hospitalized COVID patients and local controls.
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Abiola-Salako
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: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (B) between hospitalized non-COVID patients and 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 sp. 1-8 |
Revision editor(s): Abiola-Salako
Signature 2
Source: Fig 2B
Description: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera(B) between hospitalized non-COVID patients and local controls.
Abundance in Group 1: decreased abundance in Non-Covid-19 Patients
Revision editor(s): Abiola-Salako
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: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (C) between hospitalized COVID and non-COVID patients.
Abundance in Group 1: increased abundance in Covid-19 patients
Revision editor(s): Abiola-Salako
Signature 2
Source: Fig 2C
Description: Linear discriminant analysis (LDA) effect size (LEfSe) identifying discriminative bacterial genera (C) between hospitalized COVID and non-COVID patients.
Abundance in Group 1: decreased abundance in Covid-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Mogibacterium | ||
| Lactobacillus | ||
| Lacticaseibacillus | ||
| Anaeroglobus | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Rothia |
Revision editor(s): Abiola-Salako
Experiment 4
Subjects
- 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
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 6A
Description: Associations between clinical parameters and the relative abundance of the naso-oropharyngeal microbiota in COVID patients. Discriminative bacterial genera between COVID patients with different (A) pneumonia status identified by LEfSe.
Abundance in Group 1: increased abundance in Covid-19 with Pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. |
Revision editor(s): Abiola-Salako
Signature 2
Source: Figure 6A
Description: Associations between clinical parameters and the relative abundance of the naso-oropharyngeal microbiota in COVID patients. Discriminative bacterial genera between COVID patients with different (A) pneumonia status Identified by LEfSe.
Abundance in Group 1: decreased abundance in Covid-19 with Pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella | ||
| Peptoniphilus |
Revision editor(s): Abiola-Salako
Experiment 5
Subjects
- 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
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 6B
Description: Associations between clinical parameters and the relative abundance of the naso-oropharyngeal microbiota in COVID patients. The Discriminative bacterial genera between COVID patients with different (B) viral load Identified by Lefse.
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
Signature 2
Source: Figure 6B
Description: Associations between clinical parameters and the relative abundance of the naso-oropharyngeal microbiota in COVID patients. Discriminative bacterial genera between COVID patients with different (B) viral load identified by LEfSe.
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
Experiment 6
Subjects
- 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: Dysbiosis of the oropharyngeal microbiota in hospitalized patients (COVID and non-COVID) compared to local controls. (A) Discriminative bacterial genera distinguishing hospitalized patients from local controls by LEfSe.
Abundance in Group 1: increased abundance in Hospitalized patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Alloprevotella | ||
| Atopobium | ||
| Centipeda | ||
| Ligilactobacillus | ||
| Limosilactobacillus | ||
| Megasphaera | ||
| Prevotella | ||
| Prevotella sp. 1-8 | ||
| Solobacterium | ||
| Veillonella |
Revision editor(s): Abiola-Salako
Signature 2
Source: Figure 4A
Description: Dysbiosis of the oropharyngeal microbiota in hospitalized patients (COVID and non-COVID) compared to local controls. (A) Discriminative bacterial genera distinguishing hospitalized patients from local controls by LEfSe.
Abundance in Group 1: decreased abundance in Hospitalized patients
Revision editor(s): Abiola-Salako
