Comparative portrayal of ocular surface microbe with and without dry eye/Experiment 2
Subjects
- Location of subjects
- China
- 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
- Non-MGD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MGD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Dry Eye with Meibomian Gland Disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics for 6 months prior to study entry
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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6
Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of the LEfSe algorithm.
Abundance in Group 1: increased abundance in MGD
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Bacillales | ||
| Bacilli | ||
| Bacillus pumilus |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Curated date: 2023/09/09
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Aleru002, Folakunmi
Source: Figure 6
Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of LEfSe algorithm.
Abundance in Group 1: decreased abundance in MGD
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Bacteroidales | ||
| Eubacterium coprostanoligenes | ||
| Oscillospiraceae | ||
| Thermomonas |
Revision editor(s): Mary Bearkland, Aleru002, Folakunmi
