Alterations of ocular surface microbiome in glaucoma and its association with dry eye
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Kamdougha H, Taminiau B, Fall PA, Ben Amor S, Trigui A, Daube G, Mnif B
Journal
Journal of medical microbiology
Year
2025
Keywords:
conjunctiva, dry eye disease, dysbiosis, glaucoma, microbiome, preservatives
Introduction. Alterations in ocular surface microbiota (OSM) have been noted in both dry eye disease (DED) and glaucoma. However, the combined effects of these conditions on OSM have not been explored.Hypothesis. We hypothesized that patients with both glaucoma and dry eye would exhibit distinct changes in OSM composition and diversity compared to those with only glaucoma, only dry eye or healthy individuals.Aim. We employed amplicon sequencing to investigate OSM profiles in patients with glaucoma and/or dry eye disease.Methods. Swab samples from the conjunctiva of both eyes were collected from 28 glaucomatous patients [13 without dry eye syndrome (G-only) and 15 with dry eye syndrome (G-DED)], 13 DED patients without glaucoma (DED-only) and 31 age-matched healthy controls (HCs). After V3-V4 16S rRNA sequencing, MOTHUR tools and R language were used to elucidate and compare OSM composition and diversity between groups.Results. Our data revealed very diverse bacterial communities with 28 phyla and 785 genera. All the groups shared the three most abundant phyla, Actinobacteria (67.47%), Firmicutes (17.14%) and Proteobacteria (13.73%). Corynebacterium (54.75%), Staphylococcus (10.71%), Cutibacterium (8.77%) and Streptococcus (3.20%) were the most abundant genera. Only the G-DED group showed higher alpha diversity than the HC group (P<0.05). However, significant differences in beta diversity were observed between all three patient groups and the HC group. The Differential Expression for Sequencing 2 (DESeq2) analysis unveiled an increased presence of opportunistic bacteria across all pathological groups, with the G-DED group demonstrating the most pronounced alterations.Conclusions. Our findings confirm the predominance of Gram-positive bacteria in normal OSM and the rise of opportunistic Gram-negative bacteria in glaucoma and dry eye disease. This is the first study to characterize OSM in glaucoma patients with DED.
Experiment 1
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
- Glaucoma glaucoma,glaucoma (disease),Glaucoma (disorder),Glaucoma associated with other ocular disorders,Glaucoma associated with other ocular disorders (disorder),Glaucoma associated with other ocular disorders NOS,Glaucoma associated with other ocular disorders NOS (disorder),GLAUCOMA NEC,Glaucoma NOS,Glaucoma NOS (disorder),Glaucoma, NOS,Glaucomas,Other specified forms of glaucoma,Other specified forms of glaucoma (disorder),Other specified glaucoma,Other specified glaucoma NOS,Other specified glaucoma NOS (disorder),Unspecified glaucoma,Glaucoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HC (Healthy Controls)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-only (Glaucomatous patients without dry eye syndrome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Glaucomatous patients without dry eye syndrome
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
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-only (Glaucomatous patients without dry eye syndrome)
Revision editor(s): Anne-mariesharp
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
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
- increased
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)
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 |
Revision editor(s): Anne-mariesharp
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- DED-only (Dry eye syndrome patients without glaucoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dry eye syndrome (DED) patients without glaucoma
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
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: Supplementary table 2
Description: Most differentially abundant genera between groups, identified by DESeq2.
Abundance in Group 1: increased abundance in DED-only (Dry eye syndrome patients without glaucoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Bradyrhizobium | ||
| Corynebacterium | ||
| Cutibacterium | ||
| Enterobacter | ||
| Haemophilus | ||
| Pseudomonas | ||
| Staphylococcus | ||
| Streptococcus | ||
| Veillonella | ||
| Escherichia/Shigella sp. |
Revision editor(s): Anne-mariesharp
Experiment 4
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
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
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Glaucoma glaucoma,glaucoma (disease),Glaucoma (disorder),Glaucoma associated with other ocular disorders,Glaucoma associated with other ocular disorders (disorder),Glaucoma associated with other ocular disorders NOS,Glaucoma associated with other ocular disorders NOS (disorder),GLAUCOMA NEC,Glaucoma NOS,Glaucoma NOS (disorder),Glaucoma, NOS,Glaucomas,Other specified forms of glaucoma,Other specified forms of glaucoma (disorder),Other specified glaucoma,Other specified glaucoma NOS,Other specified glaucoma NOS (disorder),Unspecified glaucoma,Glaucoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- DED-only (Dry eye syndrome patients without glaucoma)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-only (Glaucomatous patients without dry eye syndrome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Glaucomatous patients without dry eye syndrome
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
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-only (Glaucomatous patients without dry eye syndrome)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Pseudomonadota |
Revision editor(s): Anne-mariesharp
Experiment 6
Reviewed Marked as Reviewed by KateRasheed on 2025-8-28
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
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
Description: Most differentially abundant 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 |
|---|---|---|
| Bacillota | ||
| Pseudomonadota | ||
| Bacteroidota |
Revision editor(s): Anne-mariesharp
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