Oral Fungal Alterations in Patients with COVID-19 and Recovered 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
- Surface of tongue Tongue surface,Surface of tongue,surface of tongue
- 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 and Post Covid-19 Groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy Controls Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were 132 age- and sex-matched healthy individuals (controls)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 93
- Group 1 sample size Number of subjects in the case (exposed) group
- 132
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 8 weeks
Lab analysis
- Sequencing type
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Source: Figure 4g
Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.
Abundance in Group 1: increased abundance in Healthy Controls Group
Revision editor(s): Victoria, Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls and Post-Covid-19 Groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19 Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were COVID-19 patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 154
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.
Abundance in Group 1: increased abundance in Covid-19 Group
Revision editor(s): Victoria, Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls and Covid-19 Groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Covid-19 Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 22 patients who have recovered from Covid-19.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 203
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.
Abundance in Group 1: increased abundance in Post-Covid-19 Group
Revision editor(s): Victoria
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19-N group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 56 Covid-19 patients without comorbidities.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 132
- Group 1 sample size Number of subjects in the case (exposed) group
- 56
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Supplemental Figure S4
Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels.
Abundance in Group 1: increased abundance in Covid-19-N group
| NCBI | Quality Control | Links |
|---|---|---|
| Acrodictys | ||
| Candida | ||
| Hydnobolites | ||
| Raffaelea | ||
| Harringtonia lauricola | ||
| Acrodictys fluminicola | ||
| Hydnobolites roseus | ||
| Candida albicans |
Revision editor(s): Victoria
Signature 2
Source: Supplemental Figure S4
Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels
Abundance in Group 1: decreased abundance in Covid-19-N group
Revision editor(s): Victoria
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19-C group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 15 Covid-19 patients with comorbidities.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Supplemental Figure S4
Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels.
Abundance in Group 1: increased abundance in Covid-19-C group
| NCBI | Quality Control | Links |
|---|---|---|
| Candida albicans | ||
| Candida | ||
| Raffaelea | ||
| Hydnobolites | ||
| Hydnobolites roseus |
Revision editor(s): Victoria
Signature 2
Source: Supplemental Figure S4
Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels.
Abundance in Group 1: decreased abundance in Covid-19-C group
| NCBI | Quality Control | Links |
|---|---|---|
| Zanclospora | ||
| Cryptococcus | ||
| Diversispora | ||
| Zanclospora jonesii | ||
| Diversispora spurca | ||
| Vanrija longa |
Revision editor(s): Victoria
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Covid-19-N group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 56
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Figure S4
Description: The 10 most abundant fungi among the differential fungi among the three groups at the genus and species levels.
Abundance in Group 1: increased abundance in Covid-19-C group
| NCBI | Quality Control | Links |
|---|---|---|
| Blumeria | ||
| Blumeria spe Incertae sedisBlumeria spe Incertae sedis |
Revision editor(s): Victoria
Experiment 7
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 Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were Covid-19 patients from the test phase.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 1E, F and Figure S3B
Description: The ten most abundant fungi among the differential fungi between COVID-19 and controls at the phylum, genus and species levels.
Abundance in Group 1: increased abundance in Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Acrodictys | ||
| Acrodictys fluminicola | ||
| Candida | ||
| Candida albicans | ||
| Hydnobolites | ||
| Simplicillium | ||
| Simplicillium sympodiophorum | ||
| Zoopagomycota | ||
| Ascomycota |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 1E, F and Figure S3B
Description: The ten most abundant fungi among the differential fungi between COVID-19 and controls at the phylum, genus and species levels.
Abundance in Group 1: decreased abundance in Covid-19 Group
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were COVID-19 patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 132
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: increased abundance in Covid-19 Group
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: decreased abundance in Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Diaporthe | ||
| Talaromyces | ||
| Milospium | ||
| Zanclospora | ||
| Diaporthe kochmanii | ||
| Milospium graphideorum | ||
| Malassezia restricta | ||
| Zanclospora jonesii | ||
| Basidiomycota | ||
| Mucoromycota | ||
| Cryptomycota |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post Covid-19 Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were recovered COVID-19 patients.
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: increased abundance in Post Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Fusarium | ||
| Nigrospora | ||
| Peroneutypa | ||
| Mucoromycota | ||
| Fusarium fujikuroi | ||
| Nigrospora oryzae | ||
| Penicillium hirsutum | ||
| Aspergillus tennesseensis |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: decreased abundance in Post Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Ascomycota | ||
| Diaporthe | ||
| Diaporthe kochmanii | ||
| Harringtonia lauricola | ||
| Milospium | ||
| Raffaelea | ||
| Talaromyces | ||
| Fungi phy Incertae sedisFungi phy Incertae sedis | ||
| Milospium graphideorum |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Covid-19 Group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 71
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: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: increased abundance in Post Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Ascomycota | ||
| Fungi phy Incertae sedisFungi phy Incertae sedis | ||
| Milospium | ||
| Milospium graphideorum | ||
| Talaromyces | ||
| Harringtonia lauricola | ||
| Raffaelea |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4E, S6b and S6c
Description: The differential fungi among Healthy controls, Covid-19 and Post-Covid-19 groups at the phyla, genus and species levels.
Abundance in Group 1: decreased abundance in Post Covid-19 Group
| NCBI | Quality Control | Links |
|---|---|---|
| Mucoromycota | ||
| Diaporthe kochmanii | ||
| Malassezia restricta |
Revision editor(s): Aleru Divine
