Alterations of ocular surface microbiome in glaucoma and its association with dry eye/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Subjects
- Location of subjects
- Tunisia
- 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
- Dry eye syndrome dry eye,Dry Eye Syndrome,dry eye syndrome,Dry Eye Syndromes,dry eye(s),eye(s), dry,KCS,Keraconjunctivitis sicca,Keratoconjunctivitis Sicca,Keratoconjunctivitis sicca,keratoconjunctivitis sicca,Keratoconjunctivitis sicca (disorder),sicca, keratoconjunctivitis,Tear film insufficiency,tear film insufficiency,Dry eye syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-only (Glaucomatous patients without dry eye syndrome)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-DED (Glaucomatous patients with dry eye syndrome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Glaucomatous patients with dry eye syndrome
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- 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)
- 0.05
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Source: Figure 2A, Supplementary table 2
Description: Most differentially abundant genera and phyla between groups, identified by DESeq2.
Abundance in Group 1: increased abundance in G-DED (Glaucomatous patients with dry eye syndrome)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Bacillota | ||
| Haemophilus | ||
| Kocuria | ||
| Micrococcus | ||
| Paracoccus | ||
| Pseudomonadota | ||
| Rhodobacter | ||
| Staphylococcus |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Source: Supplementary table 2
Description: Most differentially abundant genera between groups, identified by DESeq2.
Abundance in Group 1: decreased abundance in G-DED (Glaucomatous patients with dry eye syndrome)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Proteus |
Revision editor(s): Anne-mariesharp
