The lung microbiome in moderate and severe chronic obstructive pulmonary disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- Lung
- 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
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic obstructive pulmonary disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have Chronic obstructive pulmonary disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- 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)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/07/16
Source: Table 2
Description: Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls
Abundance in Group 1: increased abundance in Chronic obstructive pulmonary disease
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 2
Description: Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls
Abundance in Group 1: decreased abundance in Chronic obstructive pulmonary disease
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Candidatus Blastococcus massiliensis | ||
| Modestobacter | ||
| Nakamurellaceae | ||
| Thermoactinomyces | ||
| Thermoactinomycetaceae | ||
| Citrobacter | ||
| Arthrobacter |
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