Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome
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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
Song H, Xiao K, Chen Z, Long Q
Journal
Frontiers in medicine
Year
2022
Keywords:
Sjögren's syndrome, dry eyes, microbial composition, microbial diversity, ocular surface
PURPOSE: To analyze the conjunctival sac microbial communities in patients with Sjögren's syndrome-associated dry eyes (SSDE) and non-Sjögren's syndrome-associated dry eyes (NSSDE), compared with normal controls (NC). METHODS: Conjunctival sac swab samples from 23 eyes of SSDE, 36 eyes of NSSDE, and 39 eyes of NC were collected. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene high-throughput sequencing was performed on an Illumina MiSeq platform and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Alpha diversity was employed to analyze microbiome diversity through Chao1 and Shannon indexes. Beta diversity was demonstrated by the principal coordinates analysis (PCoA) and Partial Least Squares Discrimination Analysis (PLS-DA). The relative abundance was bioinformatically analyzed at the phylum and genus levels. RESULTS: The alpha diversity was lower in patients with dry eye disease (Shannon index: NC vs. SSDE: P = 0.020, NC vs. NSSDE: P = 0.029). The beta diversity showed divergent microbiome composition in different groups (NC vs. SSDE: P = 0.001, NC vs. NSSDE: P = 0.001, NSSDE vs. SSDE: P = 0.005). The top 5 abundant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria in all three groups. The top five abundant genera included Acinetobacter, Staphylococcus, Bacillus, Corynebacterium, and Clostridium_sensu_stricto_1. The relative microbiome abundance was different between groups. The Firmicutes/Bacteroidetes (F/B) ratio was 6.42, 7.31, and 9.71 in the NC, NSSDE, and SSDE groups, respectively (NC vs. SSDE: P = 0.038, NC vs. NSSDE: P = 0.991, SSDE vs. NSSDE: P = 0.048). CONCLUSION: The diversity of conjunctival sac microbiome in patients with NSSDE and SSDE was diminished compared with NC. The main microbiome at the phylum and genus level were similar between groups, but the relative abundance had variations. The Firmicutes/Bacteroidetes ratio was higher in the SSDE group.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
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
- Conjunctival sac Conjunctiva serous sac,Subbrillar sac,Conjunctival 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,Dry eye syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Control (NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sjogrens Syndrome Dry Eye (SSDE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Sjogrens Syndrome Dry Eye
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Application of antibiotic or immunomodulatory eyedrops in the previous 4 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
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: increased abundance in Sjogrens Syndrome Dry Eye (SSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Clostridium | ||
| Corynebacterium | ||
| Bacillota |
Revision editor(s): Mary Bearkland, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: decreased abundance in Sjogrens Syndrome Dry Eye (SSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Bacteroidota | ||
| Cyanobacteriota | ||
| Pseudomonadota |
Revision editor(s): Mary Bearkland, Peace Sandy
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non Sjogrens Syndrome Dry Eye (NSSDE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Non-Sjogrens Syndrome Dry Eye
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: increased abundance in Non Sjogrens Syndrome Dry Eye (NSSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Actinomycetota | ||
| Acinetobacter | ||
| Clostridium |
Revision editor(s): Mary Bearkland
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: decreased abundance in Non Sjogrens Syndrome Dry Eye (NSSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Cyanobacteriota |
Revision editor(s): Mary Bearkland
Experiment 3
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non Sjogrens Syndrome Dry Eye (NSSDE)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sjogrens Syndrome Dry Eye (SSDE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Sjogrens Syndrome Dry Eye
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: increased abundance in Sjogrens Syndrome Dry Eye (SSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Mary Bearkland
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-29
Source: Tables 3 and 4
Description: TABLE 3 Percentage of the top five phyla in each group. TABLE 4 Percentage of the top five genus in each group.
Abundance in Group 1: decreased abundance in Sjogrens Syndrome Dry Eye (SSDE)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Pseudomonadota |
Revision editor(s): Mary Bearkland
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