Ocular surface microbiota in patients with aqueous tear-deficient dry eye
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Denmark
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- 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)
- For controls- those with hx of recent (within 3 mos) use of antibiotics (local or systemic) were excluded. ADDE patients were allowed and 7/21 had received local or systemic antibiotics within the previous 3 mos.
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
- 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
Source: Figure 4a
Description: Comparison of the relative abundances of genera with DESeq2 between patients with aqueous tear-deficient dry eye and controls. The relative abundances for the identified genera were analyzed in groups (in pairs of two), where patients with dry eye disease with ocular graft-versus-host disease (OGVHD) and dry eye disease (DryEye) were compared separately to healthy controls (Control). A genus was defined as significant if the log2FoldChange was >2 (relative abundance) and padj < 0.05. The 10 genera with the lowest p-values and the significant genera from the most common 29 genera in the study population are shown the figure. Color scheme for genera: Brown triangles = significant padj-values; however, without log2FoldChange >2, blue triangles = log2FoldChange >2 but no significant padjvalues, grey triangles no log2FoldChange >2 and no significant padj-values. A) DryEye compared with Control, 52 genera were significantly less abundant (red dots) in the DryEye group.
Abundance in Group 1: decreased abundance in Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Ottowia | ||
| Veillonella | ||
| Microbacterium | ||
| Flavobacterium | ||
| Massilia | ||
| Fusobacterium | ||
| Thermus | ||
| Haemophilus | ||
| Sphingomonas | ||
| Rothia |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- OGVHD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Aqueous Deficient Dry Eye and 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 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 4b
Description: Fig. 4. Comparison of the relative abundances of genera with DESeq2 between patients with aqueous tear-deficient dry eye and controls. The relative abundances for the identified genera were analyzed in groups (in pairs of two), where patients with dry eye disease with ocular graft-versus-host disease (OGVHD) and dry eye disease (DryEye) were compared separately to healthy controls (Control). A genus was defined as significant if the log2FoldChange was >2 (relative abundance) and padj < 0.05. The 10 genera with the lowest p-values and the significant genera from the most common 29 genera in the study population are shown the figure. Color scheme for genera: Brown triangles = significant padj-values; however, without log2FoldChange >2, blue triangles = log2FoldChange >2 but no significant padjvalues, grey triangles no log2FoldChange >2 and no significant padj-values. B) For OGVHD compared with Control, there were 28 significantly less abundant genera (orange dots) in the OGVHD group.
Abundance in Group 1: decreased abundance in OGVHD
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Carnobacterium | ||
| Cloacibacterium | ||
| Listeria | ||
| Microbacterium |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 4b
Description: Fig. 4. Comparison of the relative abundances of genera with DESeq2 between patients with aqueous tear-deficient dry eye and controls. The relative abundances for the identified genera were analyzed in groups (in pairs of two), where patients with dry eye disease with ocular graft-versus-host disease (OGVHD) and dry eye disease (DryEye) were compared separately to healthy controls (Control). A genus was defined as significant if the log2FoldChange was >2 (relative abundance) and padj < 0.05. The 10 genera with the lowest p-values and the significant genera from the most common 29 genera in the study population are shown the figure. Color scheme for genera: Brown triangles = significant padj-values; however, without log2FoldChange >2, blue triangles = log2FoldChange >2 but no significant padjvalues, grey triangles no log2FoldChange >2 and no significant padj-values. B) For OGVHD compared with Control, there were 28 significantly less abundant genera (orange dots) in the OGVHD group.
Abundance in Group 1: increased abundance in OGVHD
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus |
Revision editor(s): Mary Bearkland
Experiment 3
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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 |
|---|---|---|
| Brevibacterium | ||
| Streptomyces violaceusniger | ||
| Bacilli | ||
| Bacillota | ||
| Moraxellaceae | ||
| Enhydrobacter |
Revision editor(s): Mary Bearkland
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 |
|---|---|---|
| Pseudomonas | ||
| Pseudomonadaceae | ||
| Pseudomonadota | ||
| Flavobacteriaceae | ||
| Carnobacterium | ||
| Streptomyces rubiginosus | ||
| Mycobacteriales bacterium | ||
| Carnobacteriaceae |
Revision editor(s): Mary Bearkland
