Bacterial biogeography of adult airways in atopic asthma/Experiment 7
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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Chloe, Claregrieve1, 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
- Nose Nasal sac,Nasus,Nose,Olfactory apparatus,Peripheral olfactory organ,Proboscis,nose
- 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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- atopic asthma subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with atopic asthma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- 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
- Zero-Inflated 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
Alpha Diversity
- 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 S6B
Description: Asthmatic subjects showed significant enrichment in a number of specific Staphylococcus taxa in NB samples compared to HCs.
Abundance in Group 1: increased abundance in atopic asthma subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus | ||
| Neisseriaceae | ||
| Corynebacterium | ||
| Hydrogenophaga | ||
| Staphylococcus epidermidis | ||
| Planococcaceae |
Revision editor(s): Claregrieve1, WikiWorks, Chloe
