Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-29
Subjects
- Location of subjects
- India
- 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
- Upper respiratory tract Upper respiratory tract,upper respiratory tract
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- SARS-CoV-2-related disease COVID-19-related disease,SARS-CoV-2-related disease,sARS-CoV-2-related disease
- 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 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients infected with COVID-19 virus (Delta and Omicron)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 2
Description: LEfSe analysis of core species of COVID-19 patients and healthy controls.
Abundance in Group 1: increased abundance in COVID-19 patients
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Source: FIG 2
Description: Relative abundances of bacteria in upper respiratory tract (URT) of Covid-19 patients and healthy group
Abundance in Group 1: decreased abundance in COVID-19 patients
