Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome
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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
- United States of America
- 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 , Conjunctiva Free margin of eyelid,Margin of eyelid,margin of eyelid,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
- Control subject samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients samples with eyedrops
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from glaucoma patients that were treated with eyedrops
- 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
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 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).
- relative abundances
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- 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
- increased
Signature 1
Source: Figure 4A, B
Description: Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls
Abundance in Group 1: increased abundance in Patients samples with eyedrops
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 4A, B
Description: Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls
Abundance in Group 1: decreased abundance in Patients samples with eyedrops
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients samples with no eyedrops
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from glaucoma patients that were not treated with eyedrops
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4C, D
Description: Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls
Abundance in Group 1: increased abundance in Patients samples with no eyedrops
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 4C, D
Description: Linear discriminant analysis (LDA) effect size (LEfSe) plot of taxonomic biomarkers identified in the ocular surface microbiome of patients and controls
Abundance in Group 1: decreased abundance in Patients samples with no eyedrops
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients samples with eyedrops
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from glaucoma patients that were treated with eyedrops
Lab analysis
Statistical Analysis
- Statistical test
- Wald Test
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Table 4, Supplemental Table 1
Description: Significant differentially abundant taxa between patient samples with eyedrops and control subject samples
Abundance in Group 1: increased abundance in Patients samples with eyedrops
Revision editor(s): Anne-mariesharp
Signature 2
Source: Table 4, Supplemental Table 1
Description: Significant differentially abundant taxa between patient samples with eyedrops and control subject samples
Abundance in Group 1: decreased abundance in Patients samples with eyedrops
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients samples without eyedrops
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from glaucoma patients that were not treated with eyedrops
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Table 4, Supplemental Table 2
Description: Significant differentially abundant taxa between patient samples without eyedrops and control subject samples
Abundance in Group 1: increased abundance in Patients samples without eyedrops
Revision editor(s): Anne-mariesharp
Signature 2
Source: Table 4, Supplemental Table 2
Description: Significant differentially abundant taxa between patient samples without eyedrops and control subject samples
Abundance in Group 1: decreased abundance in Patients samples without eyedrops
Revision editor(s): Anne-mariesharp
