Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment/Experiment 6
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
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
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Atopic asthma allergic asthma,Atopic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline (placebo group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post placebo treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- placebo treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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).
- raw counts
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects after placebo treatment
Abundance in Group 1: increased abundance in post placebo treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Eikenella | ||
| Spirochaetaceae | ||
| Mycoplasmataceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects after placebo treatment
Abundance in Group 1: decreased abundance in post placebo treatment
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Actinomycetaceae | ||
| Prevotellaceae | ||
| Peptostreptococcaceae |
Revision editor(s): WikiWorks
