Comparative portrayal of ocular surface microbe with and without dry eye
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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
Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M, Yi G
Journal
Journal of microbiology (Seoul, Korea)
Year
2019
Keywords:
16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria
rRNA gene high-throughput sequencing was performed in the conjunctival swab samples to investigate the composition of the OS bacterial community in DE (n=35) and NDE (n=54) and compared the composition of MGD (n=25) and NMGD (n=10) among DE subjects. Deep sequencing of OS 16S rDNA from DE (n=35) and NDE (n=54) demonstrated great a difference in alpha and beta diversity between the OS bacterial flora (P < 0.05). The similar OS microbial structures were shown at the phylum and genus levels by bioinformatics analysis between them, and in LEfSe (linear discriminant analysis effect size) analysis, Bacteroidia and Bacteroidetes were enriched in DE, while Pseudomonas was plentiful in NDE (linear discriminant analysis [LDA] > 4.0). Among the DE group, there was no significant difference in α and β diversity between MGD and NMGD (P > 0.05). Surprisingly, Bacilli was the dominant microbe in MGD, and Bacteroidetes was the superior bacteria in NMGD among DE subjects (LDA > 4.0). Different diversity of OS bacteria composition between DE and NDE and the altered diversity of OS bacteria may play an important role in DE. Moreover, the lower dominance of OS bacteria in DE may be associated with the occurrence and development of DE. Although there was no significant difference in alpha and beta analysis, the OS dominant microbe between MGD and NMGD among DE was different.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Curated date: 2023/09/09
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, Folakunmi
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
- Conjunctiva Conjunctiva,conjunctiva,Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of 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,Dry eye syndrome
- 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
- 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
- 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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Curated date: 2023/09/09
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Peace Sandy, Folakunmi
Source: Figure 4
Description: 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 |
Revision editor(s): Mary Bearkland, Peace Sandy, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Source: Figure 4
Description: 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 |
|---|---|---|
| Gammaproteobacteria | ||
| Pseudomonadaceae | ||
| Pseudomonadota | ||
| Pseudomonas | ||
| Pseudomonas plecoglossicida |
Revision editor(s): Mary Bearkland, Folakunmi
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Source: Figure 6
Description: 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 |
|---|---|---|
| Bacillaceae | ||
| Bacillales | ||
| Bacilli | ||
| Bacillus pumilus |
Revision editor(s): Mary Bearkland, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
Curated date: 2023/09/09
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Aleru002, Folakunmi
Source: Figure 6
Description: 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 LEfSe algorithm.
Abundance in Group 1: decreased abundance in MGD
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Bacteroidales | ||
| Eubacterium coprostanoligenes | ||
| Oscillospiraceae | ||
| Thermomonas |
Revision editor(s): Mary Bearkland, Aleru002, Folakunmi
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