Comparative portrayal of ocular surface microbe with and without 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
- China
- 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
- Conjunctiva Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac,Conjunctiva
- 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
- healthy controls
- 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 Dry Eye (with or without Meibomian Gland Disease).
Subjects were considered to have DE if a positive dry eye survey OSDI ≥ 13 was recorded in addition to a positive score in one or more tests (tear break-up time ≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8 mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival spots, or lid margin ≥ 2 mm length, and 25% width).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics for 6 months prior to study entry
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4
Description: Fig. 4. Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the DE patients and NDE subjects as computed by the use of the LEfSe algorithm.
Abundance in Group 1: increased abundance in Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidia | ||
| bacteroidetesbacteroidetes |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 4
Description: Fig. 4. Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the DE patients and NDE subjects as computed by the use of the LEfSe algorithm.
Abundance in Group 1: increased abundance in Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas plecoglossicida | ||
| Pseudomonadaceae | ||
| Pseudomonas | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-MGD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MGD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Dry Eye with Meibomian Gland Disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6
Description: Fig. 6. Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of the LEfSe algorithm.
Abundance in Group 1: increased abundance in MGD
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus pumilus | ||
| Bacillaceae | ||
| Bacillales | ||
| Bacilli |
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 6
Description: Fig. 6. Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use ofthe LEfSe algorithm.
Abundance in Group 1: decreased abundance in MGD
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| ruminococcaceaeruminococcaceae | ||
| Eubacterium coprostanoligenes | ||
| Alloprevotella | ||
| Thermomonas |
Revision editor(s): Mary Bearkland
