Ocular surface microbiota in patients with aqueous tear-deficient dry eye/Experiment 1
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Reviewed Marked as Reviewed by Folakunmi on 2024-1-5
Curated date: 2023/09/04
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, KateRasheed
Subjects
- Location of subjects
- Denmark
- 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
- Conjunctival fornix Conjunctiva fornix,Forniceal conjunctiva,Fornix conjunctiva,Conjunctival fornix,conjunctival fornix
- 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
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dry Eye
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Aqueous Deficient Dry Eye without Ocular Graft vs Host Disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 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
- DESeq2
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-5
Curated date: 2023/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks
Source: Figure 4a, within result text (Several genera were less abundant in ADDE, lines 8-15)
Description: Comparison of the relative abundances of genera with DESeq2 between patients with DryEye and Control
Abundance in Group 1: decreased abundance in Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Flavobacterium | ||
| Fusobacterium | ||
| Haemophilus | ||
| Massilia | ||
| Microbacterium | ||
| Ottowia | ||
| Rothia | ||
| Sphingomonas | ||
| Thermus | ||
| Veillonella |
Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks
