Metagenomic Profiling of Ocular Surface Microbiome Changes in 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
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
- Meibum Tarsal gland secretion,Meibum,meibum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Meibomian cyst chalazia,Chalazion,chalazion,cyst, Meibomian,Meibomian cyst,meibomian gland lipogranuloma,meibomian cyst
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control (HCs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Meibomian gland dysfunction (MGD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Meibomian gland dysfunction (MGD)
- 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
- 61
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months.
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
- Welch's T-Test
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table 1 and Supplementary Figure S2D
Description: Pathogens with differential incidences in meibum between MGD patients and healthy controls (p<0.05)
Abundance in Group 1: increased abundance in Meibomian gland dysfunction (MGD)
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Table 1 and Supplementary Figure S2D
Description: Pathogens with differential incidences in meibum between MGD patients and healthy controls (p<0.05)
Abundance in Group 1: decreased abundance in Meibomian gland dysfunction (MGD)
Revision editor(s): Aleru Divine, WikiWorks
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplementary Table S4
Description: Comparison of significant changes at the different taxonomic levels in meibum microbiomes of patients with MGD.
Abundance in Group 1: increased abundance in Meibomian gland dysfunction (MGD)
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S4
Description: Comparison of significant changes at the different taxonomic levels in meibum microbiomes of patients with MGD.
Abundance in Group 1: decreased abundance in Meibomian gland dysfunction (MGD)
Revision editor(s): Aleru Divine, WikiWorks
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of eyelid Blepharon zone of skin,Eyelid skin,Eyelid zone of skin,Zone of skin of blepharon,Zone of skin of eyelid,Skin of eyelid,skin of eyelid
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplementary Table S4
Description: Comparison of significant changes at the different taxonomic levels in the eyelid skin microbiomes of patients with MGD.
Abundance in Group 1: increased abundance in Meibomian gland dysfunction (MGD)
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S4
Description: Comparison of significant changes at the different taxonomic levels in the eyelid skin microbiomes of patients with MGD.
Abundance in Group 1: decreased abundance in Meibomian gland dysfunction (MGD)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Cloacimonadota | ||
| Mycoplasmatota | ||
| Pseudomonadota | ||
| Rhodopseudomonas |
Revision editor(s): Aleru Divine, WikiWorks
