Ocular surface microbiota in patients with varying degrees of dry eye severity
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zou XR, Zhang P, Zhou Y, Yin Y
Journal
International journal of ophthalmology
Year
2023
Keywords:
dry eye, microbiota, ocular surface, tear film break up time
AIM: To elucidate the profiles of commensal bacteria on the ocular surfaces of patients with varying severity of dry eye (DE). METHODS: The single-center, prospective, case-control, observational study categorized all participants into three distinct groups: 1) control group (n=61), 2) mild DE group (n=56), and 3) moderate-to-severe DE group (n=82). Schirmer's tear secretion strips were used, and the bacterial microbiota was analyzed using 16S ribosomal ribonucleic acid gene sequencing. RESULTS: The three groups had significant differences in alpha diversity: the control group had the highest richness (Chao1, Faith's phylogenetic diversity), the mild DE group showed the highest diversity (Shannon, Simpson), and the moderate-to-severe DE group had the lowest of the above-mentioned indices. DE severity was positively correlated with a reduction in beta diversity of the microbial community, with the moderate-to-severe DE group exhibiting the lowest beta diversity. Linear discriminant analysis effect size presented distinct dominant taxa that significantly differed between each. Furthermore, the exacerbation of DE corresponded with the enrichment of certain pathogenic bacteria, as determined by random forest analysis. CONCLUSION: As DE severity worsens, microbial community diversity tends to decrease. DE development corresponds with changes in microbial constituents, primarily characterized by reduced microbial diversity and a more homogenous species composition.
Experiment 1
Needs review
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
- Tear film Precorneal film,Tear film,tear film
- 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
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild and Moderate to Severe Dry Eye
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2s<TFBUT<5s (Tear Film Breakup Time between 2 and 5 sec) and TFBUT<2s
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 138
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within 3 months excluded
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
- 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
- 2.92
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Needs review
Source: Figure 3a
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: decreased abundance in Mild and Moderate to Severe Dry Eye
Revision editor(s): Mary Bearkland
Signature 2
Needs review
Source: Figure 3
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: increased abundance in Mild and Moderate to Severe Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control and moderate-to-severe dry eye
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Dry Eye
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tear Film Breakup Time less than 2 sec and Tear Film Breakup Time >/=5 sec
- Group 0 sample size Number of subjects in the control (unexposed) group
- 143
- Group 1 sample size Number of subjects in the case (exposed) group
- 56
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 3a
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: increased abundance in Mild Dry Eye
Revision editor(s): Mary Bearkland
Signature 2
Needs review
Source: Figure 3a
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: decreased abundance in Mild Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control and mild dry eye
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate-to-severe dry eye
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tear Film Breakup Time less than 2 sec
- Group 0 sample size Number of subjects in the control (unexposed) group
- 117
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Needs review
Source: Figure 3a
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: increased abundance in Moderate-to-severe dry eye
Revision editor(s): Mary Bearkland
Signature 2
Needs review
Source: Figure 3a
Description: Linear Discriminant Analysis of the three groups
Abundance in Group 1: decreased abundance in Moderate-to-severe dry eye
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Mary Bearkland
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