Oral lesion and microbiome diversity in COVID-19 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
METHODS: Oral samples from SARS-CoV-2 positive patients were collected. After DNA extraction from the whole saliva samples, sequencing of the 16S rRNA gene using the Ion Torrent PGM platform was performed. Alpha and beta diversity analyses were conducted using the R program. Clinical data from electronic medical records were collected and multiple logistic regression model was constructed to assess the association between oral microbiome diversity and COVID-19 severity (oxygen therapy, mechanical ventilation). RESULTS: The study included a total of 115 samples from 125 patients, 14 had oral lesions, the majority were female (54.8%), with a mean age of 55.4 years old. Around 59.1% of patients were in intensive care units(ICUs), 87.2% were using antibiotics, and 18.3% died. The most frequently antibiotics used were third-generation cephalosporins(35.7%), piperacillin/tazobactam(27%), and glycopeptides(21.7%). In general, the most abundant phyla were Firmicutes, Proteobacteria, and Bacteroidetes, representing 86.3% of the oral microbiome. Oral microbiome diversity analysis revealed statistical differences in COVID-19 severity (Shannon p=0.05), presence of oral lesions Shannon p=0.05), antibiotic use(Shannon p=0.04), and oxygen therapy Observed p=0.04). Differential abundance analysis identified specific taxa related to each variable, such as Prevotella in severe patients and Staphylococcus in individuals with oral lesions. Multivariable logistic regression pointed out that the SARS-CoV-2 PCR positive on the oral cavity and the age (above 60 years) were risk factors for disease severity. CONCLUSION: Despite the small number of participants with oral cavity lesions, we found significant differences in the microbial communities, particularly in the genus Staphylococcus associated with oral lesions. Although the abundance of Prevotella was associated with severity of COVID-19 on the microbiome analysis, the multivariate model showed that only age and RT-PCR positive for SARS-CoV-2 on the oral cavity were independent risk factors for severity.
Experiment 1
Subjects
- Location of subjects
- Brazil
- 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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral ulcer Mouth sore,Mouth ulcer,Oral mucosal ulceration,Oral ulcer,oral ulcer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Covid-19 patients without oral lesions
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19 with oral lesions
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with the presence of oral lesions
- Group 0 sample size Number of subjects in the control (unexposed) group
- 101
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
- age, sex, Confounders controlled for: "immunosuppression" 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.immunosuppression, Confounders controlled for: "virus detection in saliva (Oral RT-PCR)" 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.virus detection in saliva (Oral RT-PCR)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fourth paragraph in section 3.3
Description: Significant difference found in Covid-10 patients who had oral lesions.
Abundance in Group 1: increased abundance in Covid-19 with oral lesions
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Nekembe, Aleru Divine
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Illness severity status Illness severity status,illness severity status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non severe COVID patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe COVID patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients with severe symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fourth paragraph in section 3.3
Description: Significant differences found in Covid-10 patients who had severe symptoms.
Abundance in Group 1: increased abundance in Severe COVID patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Nekembe, Aleru Divine
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No antibiotics use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotics use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients who had antibiotic therapy in the previous 3 months.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section
Description: Significant differences found in Covid-10 patients who were on antibiotic therapy in the previous 3 months.
Abundance in Group 1: increased abundance in Antibiotics use
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Neisseria | ||
| Prevotella | ||
| Staphylococcus |
Revision editor(s): Nekembe, Aleru Divine
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oxygen dioxygen,dioxygene,Disauerstoff,InChI=1/O2/c1-2,InChIKey=MYMOFIZGZYHOMD-UHFFFAOYAM,molecular oxygen,O(2),O2,O=O,OXYGEN MOLECULE,Oxygen,oxygen
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No oxygen therapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oxygen therapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients who had oxygen therapy.
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: Paragraph 4 in section 3.3 and Paragraph 5 in the discussion section
Description: Significant differences found in Covid-10 patients who were on oxygen therapy.
Abundance in Group 1: increased abundance in Oxygen therapy
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Veillonella |
Revision editor(s): Nekembe, Aleru Divine
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Illness severity status Illness severity status,illness severity status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non ICU patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICU patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients who were in intensive care units.
Lab analysis
Statistical Analysis
Signature 1
Source: Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section
Description: Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).
Abundance in Group 1: increased abundance in ICU patients
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Veillonella |
Revision editor(s): Aleru Divine
Signature 2
Source: Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section
Description: Significant differences found in Covid-10 patients who were in the Intensive Care Unit (ICU).
Abundance in Group 1: decreased abundance in ICU patients
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non enteral diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Covid-19 patients on enteral diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- COVID-19 patients who were on the enteral diet.
Lab analysis
Statistical Analysis
Signature 1
Source: Paragraph 4 in section 3.3 and Paragraph 6 in the discussion section
Description: Significant differences found in Covid-10 patients who were on enteral diet.
Abundance in Group 1: increased abundance in Covid-19 patients on enteral diet
| NCBI | Quality Control | Links |
|---|---|---|
| Cardiobacterium | ||
| Granulicatella | ||
| Haemophilus | ||
| Lactobacillus | ||
| Leptotrichia | ||
| Porphyromonas | ||
| Rothia | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Aleru Divine
