Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2023-12-18
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
- Nasal cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- Asthma Samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants ranged between the ages of 6 and 20 years, with physician-diagnosed asthma for at least one year prior to the time of recruitment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- 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)
- N/A
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Needs review
Source: Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)
Description: Differential relative abundance between asthma and control communities
Abundance in Group 1: increased abundance in Asthma Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Moraxella catarrhalis | ||
| Psychrobacter sp. PRwf-1 |
Signature 2
Needs review
Source: Figure 3b, and within result text (Microbial identification and relative abundance in asthma and control communities, paragraphs 2 and 3)
Description: Differential relative abundance between asthma and control communities
Abundance in Group 1: decreased abundance in Asthma Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus prevotii |
