Bacterial biogeography of adult airways in atopic asthma/Experiment 5
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, Victoria
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
- Sputum , Mouth Expectoration,Sputum,sputum,Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- induced sputum specimens
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oral wash specimens
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- oral wash specimen type
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- 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).
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21
Source: Figure 3
Description: Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types
Abundance in Group 1: increased abundance in oral wash specimens
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21
Source: Figure 3
Description: Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types
Abundance in Group 1: decreased abundance in oral wash specimens
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Prevotella | ||
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
