Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z, Ren Z
Journal
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Year
2023
Keywords:
coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2
The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19). However, the oral fungal microbiota in COVID-19 remains unclear. This article aims to characterize the oral mycobiome in COVID-19 and recovered patients. Tongue coating specimens of 71 COVID-19 patients, 36 suspected cases (SCs), 22 recovered COVID-19 patients, 36 SCs who recovered, and 132 controls from Henan are collected and analyzed using internal transcribed spacer sequencing. The richness of oral fungi is increased in COVID-19 versus controls, and beta diversity analysis reveals separate fungal communities for COVID-19 and control. The ratio of Ascomycota and Basidiomycota is higher in COVID-19, and the opportunistic pathogens, including the genera Candida, Saccharomyces, and Simplicillium, are increased in COVID-19. The classifier based on two fungal biomarkers is constructed and can distinguish COVID-19 patients from controls in the training, testing, and independent cohorts. Importantly, the classifier successfully diagnoses SCs with positive specific severe acute respiratory syndrome coronavirus 2 immunoglobulin G antibodies as COVID-19 patients. The correlation between distinct fungi and bacteria in COVID-19 and control groups is depicted. These data suggest that the oral mycobiome may play a role in COVID-19.
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
- Control group
- 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
- This group consists of 71 patients with Covid-19.
- 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
- 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
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 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
Signature 2
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: decreased abundance in Covid-19 group
Revision editor(s): Victoria
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Covid-19 group
- 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 patients who have recovered from Covid-19.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 71
- 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 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
Signature 2
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: decreased abundance in Post-Covid-19 group
Revision editor(s): Victoria
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control 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
- 132
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 4g
Description: This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.
Abundance in Group 1: decreased abundance in Post-Covid-19 group
Revision editor(s): Victoria
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