Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
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-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
- 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
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
