Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Botswana
- 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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Pneumonia acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- S.pneumoniae positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- clinical pneumonnia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 74
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
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
- Illumina
Statistical Analysis
- Statistical test
- Logistic Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- primary care clinic, date
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 3
Description: Relative abundance of highly abundant genera by S. pneumoniae colonization
Abundance in Group 1: increased abundance in S.pneumoniae positive
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella | ||
| Streptococcus |
Revision editor(s): WikiWorks
Signature 2
Needs review
Source: Figure 3
Description: Relative abundance of highly abundant genera by S. pneumoniae colonization
Abundance in Group 1: decreased abundance in S.pneumoniae positive
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Staphylococcus |
Revision editor(s): WikiWorks
