Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients/Experiment 1
Curated date: 2021/06/05
Curator: Claregrieve1
Revision editor(s): Claregrieve1, WikiWorks, Atrayees
Subjects
- Location of subjects
- United States of America
- 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
- COVID-19 cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Positive for SaRS-CoV-2 by diagnostic RT-PCR
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
Lab analysis
- Sequencing type
- WMS
- 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
- Nanopore
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Curated date: 2021/06/05
Curator: Claregrieve1
Revision editor(s): Claregrieve1, Aiyshaaaa, Atrayees
Source: Figure 3
Description: Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples
Abundance in Group 1: decreased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium accolens |
Revision editor(s): Claregrieve1, Aiyshaaaa, Atrayees
Signature 2
Curated date: 2021/06/05
Curator: Claregrieve1
Revision editor(s): Claregrieve1, Aiyshaaaa, Atrayees
Source: Figure 3
Description: Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples
Abundance in Group 1: increased abundance in COVID-19 cases
| NCBI | Quality Control | Links |
|---|---|---|
| Propionibacteriaceae |
Revision editor(s): Claregrieve1, Aiyshaaaa, Atrayees
