Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa/Experiment 7
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
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
- Viral load viral burden,viral titer,viral titre,Viral load,viral load
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low and mid Ct CoV+ patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high Ct CoV+ patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SARS-CoV-2 positive patients with high cycle threshold value (>34.6)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Low and Mid Ct
Abundance in Group 1: increased abundance in high Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-26
Source: figure 3A
Description: Differentially abundant genera in the nasal microbiome between CoV+ individuals stratified by viral RNA load into High, Mid and Low Ct
Abundance in Group 1: decreased abundance in high Ct CoV+ patients
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Cutibacterium | ||
| Neisseria | ||
| Pseudomonas |
Revision editor(s): Folakunmi
