Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
Curated date: 2021/09/28
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Victoria
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
- Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx
- 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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed COVID-19 cases by RT-PCR
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 94
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
Source: Figure 3b, 3d
Description: Differential microbial abundance between COVID-19 cases and healthy controls
Abundance in Group 1: increased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Halomonas | ||
| Granulicatella | ||
| Leptotrichia | ||
| Streptococcus | ||
| unclassified Bacteria | ||
| Bacillota |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
Source: Figure 3b, 3d
Description: Differential microbial abundance between COVID-19 cases and healthy controls
Abundance in Group 1: decreased abundance in COVID-19 cases
Revision editor(s): Claregrieve1
