Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With 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: 2023/10/16
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Davvve, LGeistlinger
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
- Margin of eyelid , Conjunctival sac Free margin of eyelid,Margin of eyelid,Conjunctiva serous sac,Subbrillar sac,Conjunctival sac
- 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
- Meibomian Gland Dysfunction (MGD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with mild, moderate of severe diagnosis of MGD
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
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
Signature 1
Source: Fig 2a and 2b
Description: FIGURE 2. The relative abundances of dominant phyla and genera in the patients with MGD and the controls. (A) The relative abundances of top 5 most abundant phyla. Compared with the control group, the patients with MGD had significantly higher abundances of Firmicutes, Proteobacteria, and Deinococcus-Thermus, and a significantly lower abundance of Actinobacteria. (B) The relative abundances of top 6 most abundant genera. Compared with the control group, the patients with MGD had significantly higher abundances of Staphylococcus and Sphingomonas, and a significantly lower abundance of Corynebacterium (*P < 0.05, **P < 0.01, ***P < 0.001).
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction (MGD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Deinococcota | ||
| Pseudomonadota | ||
| Sphingomonas | ||
| Staphylococcus |
Revision editor(s): Mary Bearkland
Signature 2
Source: Fig 2a and 2b
Description: FIGURE 2. The relative abundances of dominant phyla and genera in the patients with MGD and the controls. (A) The relative abundances of top 5 most abundant phyla. Compared with the control group, the patients with MGD had significantly higher abundances of Firmicutes, Proteobacteria, and Deinococcus-Thermus, and a significantly lower abundance of Actinobacteria. (B) The relative abundances of top 6 most abundant genera. Compared with the control group, the patients with MGD had significantly higher abundances of Staphylococcus and Sphingomonas, and a significantly lower abundance of Corynebacterium (*P < 0.05, **P < 0.01, ***P < 0.001).
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction (MGD)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Corynebacterium |
Revision editor(s): Mary Bearkland
Experiment 2
Curated date: 2023/10/16
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Davvve, LGeistlinger
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig 3b
Description: Linear discriminant analysis scoring
< of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. ‘‘p’’, ‘‘c’’, ‘‘o’’, ‘‘f ’’, ‘‘g’’, and ‘‘s’’ referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.
Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction (MGD)
Revision editor(s): Mary Bearkland, Chikamso
Signature 2
Source: Figure 3
Description: Linear discriminant analysis scoring
< of biomarkers corresponding to (A), computed by the LEfSe tool. When the score of a taxon was >4.0 with P 0.01, it was listed in the histogram, which showed all the biomarkers found from the domain to species level. ‘‘p’’, ‘‘c’’, ‘‘o’’, ‘‘f ’’, ‘‘g’’, and ‘‘s’’ referred to phylum, class, order, family, genus, and species, respectively. At the genus level, the biomarkers were Staphylococcus and Sphingomonas in the patients with MGD, and Corynebacterium in the controls. The length of the histogram represented the linear discriminate analysis values of the different taxa.
Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction (MGD)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Actinomycetota | ||
| Corynebacteriaceae | ||
| Corynebacterium | ||
| Corynebacterium sp. | ||
| Actinomycetes |
Revision editor(s): Mary Bearkland, Chikamso
