The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study/Experiment 3
From BugSigDB
Needs review
Subjects
- Location of subjects
- United Kingdom
- 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 Expectoration,Sputum,sputum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bronchiectasis Polynesian bronchiectasis,Bronchiectasis,bronchiectasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Stable samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Exacerbation samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sputum samples at onset of exacerbation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- PERMANOVA
- Random Forest Analysis
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, smoking status, Confounders controlled for: "macrolide use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.macrolide use, Confounders controlled for: "inhaled antibiotic use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.inhaled antibiotic use, Confounders controlled for: "previous exacerbations" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.previous exacerbations, Confounders controlled for: "FEV1" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.FEV1
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Figure 4C
Description: Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.
Abundance in Group 1: increased abundance in Exacerbation samples
| NCBI | Quality Control | Links |
|---|---|---|
| Eikenella | ||
| Granulicatella |
Revision editor(s): Scholastica
Signature 2
Needs review
Source: Figure 4C
Description: Random forest plot showing the bacterial taxa associated with exacerbation samples, and those associated with stable samples from 64 pairs of one stable and one exacerbation sample per patient.
Abundance in Group 1: decreased abundance in Exacerbation samples
| NCBI | Quality Control | Links |
|---|---|---|
| Agrobacterium | ||
| Campylobacter | ||
| Chryseobacterium | ||
| Fusobacterium | ||
| Gemellaceae | ||
| Haemophilus | ||
| Leptotrichia | ||
| Megasphaera | ||
| Neisseria | ||
| Prevotella | ||
| Pseudomonas | ||
| Streptococcus | ||
| Veillonella | ||
| Rothia |
Revision editor(s): Scholastica
