Ocular microbiome changes in dry eye disease and meibomian gland dysfunction/Experiment 4
Curated date: 2023/08/23
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- Location of subjects
- Australia
- 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
- Meibomian Gland Dysfunction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian Gland Dysfunction + Lacrimal Dysfunction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No use of antibiotics in the prior 3 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Caballeronia zhejiangensis | ||
| Pseudomonas azotoformans | ||
| Ectopseudomonas oleovorans |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium kroppenstedtii | ||
| Corynebacterium macginleyi |
Revision editor(s): Mary Bearkland, Folakunmi
