Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease
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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
- 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
- Bulbar conjunctiva Ocular conjunctiva,Bulbar conjunctiva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- biological sex biological sex
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- female patients with dry eye disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- male patients with dry eye disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- male patients with dry eye disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- 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)
- 90 days prior to enrollment
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplemental 2c and 2d
Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.
Abundance in Group 1: increased abundance in male patients with dry eye disease
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
Signature 2
Source: Supp fig 2c and 2d
Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.
Abundance in Group 1: decreased abundance in male patients with dry eye disease
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas aeruginosa | ||
| Deinococcus sp. NW-56 |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- female
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- male
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- male
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supp fig 2c and 2d
Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.
Abundance in Group 1: increased abundance in male
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas aeruginosa |
Revision editor(s): Mary Bearkland
Signature 2
Source: Supp fig 2c and 2d
Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.
Abundance in Group 1: decreased abundance in male
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
Experiment 3
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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Aqueous tear deficient (ATD) DED
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian Gland Dysfunction (MGD) DED
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with MGD DED
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 90 days prior to study enrollment
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.15
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supp fig 5
Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction (MGD) DED
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus capitis | ||
| Staphylococcus aureus |
Revision editor(s): Mary Bearkland
Signature 2
Source: Supp fig 5
Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction (MGD) DED
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Revision editor(s): Mary Bearkland
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mixed DED
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with mixed type diagnosis of DED (more closely related to MGD than ATD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supp fig 5
Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.
Abundance in Group 1: increased abundance in Mixed DED
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus capitis | ||
| Staphylococcus aureus | ||
| Staphylococcus cohnii |
Revision editor(s): Mary Bearkland
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Meibomian Gland Dysfunction (MGD) DED
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
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
- unchanged
Signature 1
Source: Supp fig 5
Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.
Abundance in Group 1: increased abundance in Mixed DED
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
Signature 2
Source: Supp fig 5
Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.
Abundance in Group 1: decreased abundance in Mixed DED
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
