Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-11-8
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
- Samples sequenced by IS-pro method
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Samples sequenced by targeted metagenomics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Targeted metagenomics is a method that focuses on analyzing specific regions of the microbial genome, typically V1-V3 regions of the 16s rRNA gene, to study the composition and diversity of microbial communities. While the IS-Pro method targets the intergenic spacer (IS) region between the 16 S rRNA and 23 S rRNA.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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)
- 0.01
- 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
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-8
Source: Fig. 3
Description: Differential abundance in the sputum microbiota of Chronic obstructive pulmonary disease (COPD) patients between IS Pro and targeted metagenomics methods.
Abundance in Group 1: increased abundance in Samples sequenced by targeted metagenomics
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Granulicatella | ||
| Leptotrichia | ||
| Oleomonas | ||
| Veillonella |
Revision editor(s): KateRasheed, Svetlana up
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-8
Source: Figure 3
Description: Differential abundance in the sputum microbiota of COPD patients between IS Pro and targeted metagenomics methods.
Abundance in Group 1: decreased abundance in Samples sequenced by targeted metagenomics
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Parvimonas | ||
| Serratia | ||
| Pseudomonas | ||
| Lactobacillus | ||
| Fusobacterium | ||
| Peptostreptococcus | ||
| Eikenella | ||
| Escherichia | ||
| Micrococcus | ||
| Proteus | ||
| Neisseria | ||
| Burkholderia |
Revision editor(s): Aleru Divine
