Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19/Experiment 1
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Reviewed Marked as Reviewed by Fatima on 2022/04/20
Curated date: 2021/06/29
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Spain
- 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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- 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
- COVID-19 negative controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed COVID-19 infection and severe symptoms; required hospital admission
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
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).
- raw counts
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- 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
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/04/20
Source: Supplemental Table S5
Description: Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients
Abundance in Group 1: increased abundance in Severe COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Catonella | ||
| Lachnoanaerobaculum | ||
| Oribacterium | ||
| Prevotella | ||
| unclassified Erysipelotrichaceae |
Revision editor(s): Fatima, Claregrieve1
