Ocular surface microbiota in patients with aqueous tear-deficient dry eye/Experiment 3
Curated date: 2023/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, KateRasheed, WikiWorks
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
- ADDE
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Aqueous Deficient Dry Eye including those with and without Ocular Graft vs Host Disease as diagnosed using the criteria described by the International Chronic Ocular Graft-vs-Host-Disease (GVHD) Consensus. Group and the patients included were classified as either probable or definite chronic GVHD
- 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
- 39
- 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).
- 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
- 3
Signature 1
Source: Figure 5
Description: Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e. phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae. The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p <0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli for ADDE.
Abundance in Group 1: increased abundance in ADDE
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Bacillota | ||
| Brevibacterium | ||
| Enhydrobacter | ||
| Moraxellaceae | ||
| Brevibacteriaceae |
Revision editor(s): Mary Bearkland, WikiWorks
Signature 2
Source: Figure 5
Description: Fig. 5. Bacterial biomarkers identified with the LEfSe algorithm. A. Circular cladogram displaying the relation between taxa at different taxonomic levels (i.e. phylum to genus level). Among the enriched bacteria (biomarkers) in aqueous tear-deficient dry eye (ADDE) (red) was Bacilli and for controls (green) was Pseudomonadaceae. The size of the nodes represents the taxa abundance. B. Scores for linear discriminant analysis (LDA) with LEfSe tool for taxa with LDA score >3 and p <0.05 are shown in the histogram. Similarly, as the cladogram demonstrated, among the bacterial biomarkers, Pseudomonas was identified for controls and Bacilli for ADDE.
Abundance in Group 1: decreased abundance in ADDE
| NCBI | Quality Control | Links |
|---|---|---|
| Carnobacteriaceae | ||
| Carnobacterium | ||
| Flavobacteriaceae | ||
| Pseudomonadaceae | ||
| Pseudomonadota | ||
| Pseudomonas | ||
| Mycobacteriales | ||
| Corynebacteriaceae | ||
| Micrococcaceae |
Revision editor(s): Mary Bearkland, WikiWorks
