Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- South Africa
- 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
- Chronic obstructive pulmonary disease Airflow Obstruction, Chronic,Airflow Obstructions, Chronic,CAFL - Chronic airflow limitation,CAL - Chronic airflow limitation,CAO - Chronic airflow obstruction,Chronic airflow limitation,Chronic Airflow Obstruction,Chronic Airflow Obstructions,Chronic airway disease,Chronic airway obstruction,chronic airway obstruction, NEC in ICD9CM_2006,chronic airway obstruction, not elsewhere classified,Chronic irreversible airway obstruction,CHRONIC OBSTRUCTIVE AIRWAY DIS,chronic obstructive airway disease,Chronic Obstructive Airways Disease,chronic obstructive airways disease,chronic obstructive airways disease NOS,chronic obstructive airways disease NOS (disorder),CHRONIC OBSTRUCTIVE LUNG DIS,Chronic Obstructive Lung Disease,chronic obstructive lung disease,chronic obstructive lung disease (disorder),chronic obstructive lung disease [Ambiguous],Chronic obstructive lung disease, NEC,Chronic obstructive lung disease, NOS,CHRONIC OBSTRUCTIVE PULM DIS,chronic obstructive pulmonary disease,Chronic Obstructive Pulmonary Disease (COPD),chronic obstructive pulmonary disease (COPD),chronic obstructive pulmonary disease and allied conditions,Chronic obstructive pulmonary disease finding,Chronic obstructive pulmonary disease finding (finding),Chronic obstructive pulmonary disease NOS,CHRONIC OBSTRUCTIVE PULMONARY DISEASE, (COPD),chronic obstructive pulmonary disease, (COPD),COAD,COAD - Chronic obstructive airways disease,COLD,cold,COLD (chronic obstructive lung disease),cold (chronic obstructive lung disease),COLD - Chronic obstructive lung disease,COPD,COPD - Chronic obstructive pulmonary disease,COPD NOS,COPD, CHRONIC OBSTRUCTIVE PULMONARY DISEASE,COPD, chronic obstructive pulmonary disease,DISEASE (COPD), CHRONIC OBSTRUCTIVE,disease (COPD), chronic obstructive,Dops,obstructive lung disease, chronic,OBSTRUCTIVE PULMONARY DISEASE (COPD), CHRONIC,obstructive pulmonary disease (COPD), chronic,PULM DIS CHRONIC OBSTRUCTIVE,PULMONARY DISEASE (COPD), CHRONIC OBSTRUCTIVE,pulmonary disease (COPD), chronic obstructive,Pulmonary Disease, Chronic Obstructive,Chronic obstructive pulmonary disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Stable state COPD patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Exacerbated state COPD patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the exacerbated state of chronic obstructive pulmonary disease (COPD).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Group 0: past month Group 1: past 24 hours
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Needs review
Source: Figure 2
Description: Graph of the DESeq2 analysis showing the log2fold differential abundance of the different genera between the exacerbated state and stable state of disease (n=24) in the sputum microbiome of chronic obstructive pulmonary disease (COPD) participants.
Abundance in Group 1: increased abundance in Exacerbated state COPD patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Neisseria | ||
| Streptococcus | ||
| Prevotella | ||
| Lactobacillus | ||
| Veillonella | ||
| Haemophilus | ||
| Granulicatella |
Revision editor(s): Aleru Divine
