Ocular microbiome changes in dry eye disease and meibomian gland dysfunction
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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
Curated date: 2023/08/22
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- Location of subjects
- Australia
- 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
- Margin of eyelid Free margin of eyelid,Margin of eyelid,margin of eyelid
- 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
- Meibomian Gland Dysfunction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian Gland Dysfunction + Lacrimal Dysfunction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No use of antibiotics in the prior 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
- Linear Regression
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas putida |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium accolens | ||
| Corynebacterium macginleyi | ||
| Corynebacterium simulans |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 2
Curated date: 2023/08/22
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
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
Signature 1
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas putida |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus nagyae |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 3
Curated date: 2023/08/23
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- 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
- Meibomian Gland Dysfunction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with MGD corresponding to evaporative dry eye disease (moderate).
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
Signature 1
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium accolens | ||
| Corynebacterium macginleyi | ||
| Corynebacterium simulans |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Source: Figure 4
Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus nagyae |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 4
Curated date: 2023/08/23
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Meibomian Gland Dysfunction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian Gland Dysfunction + Lacrimal Dysfunction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
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
Signature 1
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Caballeronia zhejiangensis | ||
| Pseudomonas azotoformans | ||
| Ectopseudomonas oleovorans |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium kroppenstedtii | ||
| Corynebacterium macginleyi |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 5
Curated date: 2023/08/23
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
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
Signature 1
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups- MGD+LD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Caballeronia zhejiangensis | ||
| Pseudomonas azotoformans | ||
| Ectopseudomonas oleovorans |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 6
Curated date: 2023/08/23
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Folakunmi, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian Gland Dysfunction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with MGD to evaporative dry eye disease (moderate DED).
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
Signature 1
Source: Figure 3
Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium kroppenstedtii | ||
| Corynebacterium macginleyi |
Revision editor(s): Mary Bearkland, Folakunmi
