The conjunctival microbiome in health and trachomatous disease: a case control study/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16
Subjects
- Location of subjects
- Gambia
- 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
- Conjunctiva Conjunctiva,conjunctiva,Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chlamydia trachomatis Chlamydozoon trachomatis,Rickettsia trachomae,Rickettsia trachomatis,Chlamydia trachomatis,chlamydia trachomatis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged < = 0 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Controls aged > 10 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 170
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- not mentioned
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
- Roche454
Statistical Analysis
- Statistical test
- Metastats
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16
Source: Table 2
Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years
Abundance in Group 1: increased abundance in Controls aged > 10 years
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Corynebacterium | ||
| Myceligenerans | ||
| Paracoccus | ||
| Promicromonosporaceae | ||
| Propionibacterium |
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16
Source: Table 2
Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years
Abundance in Group 1: decreased abundance in Controls aged > 10 years
| NCBI | Quality Control | Links |
|---|---|---|
| Brachybacterium | ||
| Kocuria | ||
| Micrococcus | ||
| Staphylococcus | ||
| Streptococcus |
