Analysis of oral microbiome in glaucoma patients using machine learning prediction models
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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 Uniform resource identifier for web resources.
Authors
Yoon BW, Lim SH, Shin JH, Lee JW, Lee Y, Seo JH
Journal
Journal of oral microbiology
Year
2021
Keywords:
Neurodegenerative, biomarker, dysbiosis, glaucoma, oral microbiome
Purpose: The microbiome is considered an environmental factor that contributes to the progression of several neurodegenerative diseases. However, the association between microbiome and glaucoma remains unclear. This study investigated the features of the oral microbiome in patients with glaucoma and analyzed the microbiome biomarker candidates using a machine learning approach to predict the severity of glaucoma. Methods: The taxonomic composition of the oral microbiome was obtained using 16S rRNA gene sequencing, operational taxonomic unit analysis, and diversity analysis. The differentially expressed gene (DEG) analysis was performed to determine the taxonomic differences between the microbiomes of patients with glaucoma and the control participants. Multinomial logistic regression and association rule mining analysis using machine learning were performed to identify the microbiome biomarker related to glaucoma severity. Results: DEG analysis of the oral microbiome of patients with glaucoma revealed significant depletion of Lactococcus (P = 3.71e-31), whereas Faecalibacterium was enriched (P = 9.19e-14). The candidate rules generated from the oral microbiome, including Lactococcus, showed 96% accuracy for association with glaucoma. Conclusions: Our findings indicate microbiome biomarkers for glaucoma severity with high accuracy. The relatively low oral Lactococcus in the glaucoma population suggests that microbial dysbiosis could play an important role in the pathophysiology of glaucoma.
Experiment 1
Needs review
Subjects
- Location of subjects
- Republic of Korea
- 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
- Buccal mucosa Buccal mucosa,buccal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Glaucoma glaucoma,glaucoma (disease),Glaucoma (disorder),Glaucoma associated with other ocular disorders,Glaucoma associated with other ocular disorders (disorder),Glaucoma associated with other ocular disorders NOS,Glaucoma associated with other ocular disorders NOS (disorder),GLAUCOMA NEC,Glaucoma NOS,Glaucoma NOS (disorder),Glaucoma, NOS,Glaucomas,Other specified forms of glaucoma,Other specified forms of glaucoma (disorder),Other specified glaucoma,Other specified glaucoma NOS,Other specified glaucoma NOS (disorder),Unspecified glaucoma,Glaucoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Glaucoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with glaucoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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).
- raw counts
- Statistical test
- edgeR
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.00001
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Figure 5b, Supplementary Table S1
Description: Differentially abundant taxa between glaucoma patients and control subjects
Abundance in Group 1: increased abundance in Glaucoma
Revision editor(s): Anne-mariesharp
Signature 2
Needs review
Source: Figure 5b, Supplementary Table S1
Description: Differentially abundant taxa between glaucoma patients and control subjects
Abundance in Group 1: decreased abundance in Glaucoma
Revision editor(s): Anne-mariesharp
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Open-angle glaucoma glaucoma (primary open-angle),glaucoma simplex,glaucoma, open-angle,open angle glaucoma,open-angle glaucoma,pigmentary glaucoma,wide-angle glaucoma,Open-angle glaucoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- POAG (Primary open-angle glaucoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with primary open-angle glaucoma
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Figure 6b, Supplementary Table S2
Description: Differentially abundant taxa between primary open-angle glaucoma patients and control subjects
Abundance in Group 1: increased abundance in POAG (Primary open-angle glaucoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospiraceae incertae sedis | ||
| Blautia | ||
| Parabacteroides | ||
| Sulfophobococcus |
Revision editor(s): Anne-mariesharp
Signature 2
Needs review
Source: Figure 6b, Supplementary Table S2
Description: Differentially abundant taxa between primary open-angle glaucoma patients and control subjects
Abundance in Group 1: decreased abundance in POAG (Primary open-angle glaucoma)
Revision editor(s): Anne-mariesharp
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