Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19
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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 (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
- 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
- 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 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed COVID-19 cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Source: Figure 4c
Description: Differential microbial abundance between COVID-19 patients and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 patients
NCBI | Links |
---|---|
Arachnia | |
Mobiluncus | |
Oribacterium | |
Oribacterium sp. oral taxon 108 | |
Rothia | |
Rothia sp. HSID18069 | |
Slackia | |
Arachnia propionica |
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 4c
Description: Differential microbial abundance between COVID-19 patients and healthy controls
Abundance in Group 1: increased abundance in COVID-19 patients
NCBI | Links |
---|---|
Veillonella | |
Liquorilactobacillus nagelii |
Revision editor(s): Claregrieve1
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Flu 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
- Confirmed COVID-19 cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Source: Figure 4c
Description: Differential microbial abundance between COVID-19 patients and other flu patients
Abundance in Group 1: decreased abundance in COVID-19 patients
NCBI | Links |
---|---|
Arachnia | |
Limosilactobacillus fermentum | |
Oribacterium | |
Oribacterium sp. oral taxon 108 | |
Prevotella amnii | |
Rothia | |
Rothia sp. HSID18069 | |
Slackia | |
Arachnia propionica |
Revision editor(s): Claregrieve1
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
- 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
- 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
- Flu patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with influenza B
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4c
Description: Differential microbial abundance between flu patients and healthy controls
Abundance in Group 1: increased abundance in Flu patients
NCBI | Links |
---|---|
Veillonella | |
Liquorilactobacillus nagelii | |
Limosilactobacillus fermentum | |
Prevotella amnii |
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 4c
Description: Differential microbial abundance between flu patients and healthy controls
Abundance in Group 1: decreased abundance in Flu patients
NCBI | Links |
---|---|
Oribacterium | |
Arachnia | |
Rothia | |
Mobiluncus | |
Rothia sp. HSID18069 | |
Oribacterium sp. oral taxon 108 | |
Arachnia propionica |
Revision editor(s): Claregrieve1
Experiment 4
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
- 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
- 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 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed COVID-19 cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- 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
Signature 1
Source: Figure 2a-b
Description: Differential microbial abundance between COVID-19 patients and healthy controls by LefSe
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 2a-b
Description: Differential microbial abundance between COVID-19 patients and healthy controls by LefSe
Abundance in Group 1: increased abundance in COVID-19 patients
NCBI | Links |
---|---|
Megasphaera | |
Veillonella | |
Abiotrophia |
Revision editor(s): Claregrieve1
Experiment 5
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
- 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
- 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
- Flu patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with influenza B
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- 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
Signature 1
Source: Figure 2a
Description: Differential microbial abundance between flu patients and healthy controls by LefSe
Abundance in Group 1: decreased abundance in Flu patients
NCBI | Links |
---|---|
Streptococcus | |
Actinomyces | |
Rothia | |
Oribacterium | |
Xylanimonas ⚠ | |
Arachnia | |
Cardiobacterium | |
Varibaculum ⚠ |
Revision editor(s): Claregrieve1
Signature 2
Source: Figure 2a
Description: Differential microbial abundance between flu patients and healthy controls by LefSe
Abundance in Group 1: increased abundance in Flu patients
NCBI | Links |
---|---|
Megasphaera | |
Veillonella |
Revision editor(s): Claregrieve1