Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load 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
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- SARS coronavirus HCoV-SARS,Human coronavirus (strain SARS),SARS virus,Severe acute respiratory syndrome coronavirus,SARS coronavirus,sARS coronavirus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who tested positive for SARS-CoV-2 based on nasopharyngeal swabs and who did not require intensive care at admission.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "receipt of supplemental oxygen" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.receipt of supplemental oxygen
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Results text (Page 3)
Description: Differentially abundant taxa between COVID-19 positive patients versus controls
Abundance in Group 1: increased abundance in Covid-19
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella pallens |
Revision editor(s): MyleeeA, Scholastica
Signature 2
Source: Results text (Page 3)
Description: Differentially abundant taxa between COVID-19 positive patients versus controls
Abundance in Group 1: decreased abundance in Covid-19
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia mucilaginosa | ||
| Streptococcus sp. |
Revision editor(s): MyleeeA, Scholastica
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS Cov-2 Saliva Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS Cov-2 Saliva Positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with positive SARS-CoV-2 viral load in saliva
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva
Abundance in Group 1: increased abundance in SARS Cov-2 Saliva Positive
Revision editor(s): MyleeeA, Scholastica
Signature 2
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive (pink) versus -negative (blue) saliva
Abundance in Group 1: decreased abundance in SARS Cov-2 Saliva Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella denticola | ||
| Segatella oris | ||
| Streptococcus peroris | ||
| Streptococcus sp. | ||
| TM7 phylum sp. oral taxon 356 |
Revision editor(s): MyleeeA, Scholastica
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS Cov-2 Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS Cov-2 Low Viral Load
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who tested positive to SARS Cov-2 with low viral load (CT>30) in saliva
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva
Abundance in Group 1: increased abundance in SARS Cov-2 Low Viral Load
Revision editor(s): MyleeeA, Scholastica
Signature 2
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with low viral load (pink) versus negative (blue) saliva
Abundance in Group 1: decreased abundance in SARS Cov-2 Low Viral Load
Revision editor(s): MyleeeA, Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS-CoV-2 Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS-CoV-2 High Viral load
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who tested positive to SARS-CoV-2 with high (CT<30) viral load in saliva
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva
Abundance in Group 1: increased abundance in SARS-CoV-2 High Viral load
Revision editor(s): MyleeeA, Scholastica
Signature 2
Source: Figure 3
Description: Differentially abundant taxa based on SARS-CoV-2 viral load in SARS-CoV-2-positive with high viral load (pink) versus negative (blue) saliva
Abundance in Group 1: decreased abundance in SARS-CoV-2 High Viral load
Revision editor(s): MyleeeA, Scholastica
