Dysbiosis of saliva microbiome in patients with oral lichen planus
From BugSigDB
Jump to:navigation, search
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.
Authors
Yu FY, Wang QQ, Li M, Cheng YH, Cheng YL, Zhou Y, Yang X, Zhang F, Ge X, Zhao B, Ren XY
Journal
BMC microbiology
Year
2020
Keywords:
16S rDNA, High-throughput sequencing, Oral lichen planus, Salivary microbiome
BACKGROUND: Oral microbiota is not only important for maintaining oral health but also plays a role in various oral diseases. However, studies regarding microbiome changes in oral lichen planus (OLP) are very limited. To the best of our knowledge, there has been only two studies investigating salivary microbiome changes in OLP. Therefore, the purpose of this study was to identify the characteristic microbial profile in the saliva of OLP patients, with or without erosive lesions, and compare that with recurrent aphthous ulcer (RAU), a common oral immunological disorder that also shows multiple erosive/ulcerative lesions. Whole saliva samples were collected from 20 patients with OLP (erosive E, n = 10 and non-erosive NE, n = 10), 10 patients with RAU (U) and 10 healthy controls (C). DNA was extracted from the saliva samples, and the 16S rDNA gene V4 hypervariable region was analyzed using Illumina sequencing. RESULTS: We obtained 4949 operational taxonomic units (OTUs) from the V4 region in all saliva samples. Community composition analysis showed a clear decreased relative abundance of genera Streptococcus and Sphingomonas in saliva from RAU patients when compared to the other three groups. Relative abundance of Lautropia and Gemella were higher in E group, whereas relative abundance of Haemophilus and Neisseria were higher in NE group when compared to C group. Abiotrophia and Oribacterium were higher in OLP (combining E and NE groups), while Eikenella and Aggregatibacter were lower when compared to C group. There was statistically significance in α-diversity between E and RAU groups(p < 0.05). Significant differences in β-diversity were detected in bacteria between E and C; NE and C; as well as E and NE groups. The LDA effect size algorithm identified the g_Haemophilus might be the potential biomarker in NE group. CONCLUSIONS: We found that salivary microbiome in erosive OLP was significantly different from that found in RAU; and these changes may be related to the underlying disease process rather than presence of ulcerative/erosive lesions clinically. In addition, our findings in bacterial relative abundance in OLP were significantly different from the previously reported findings, which points to the need for further research in salivary microbiome of OLP.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral lichen planus Oral lichen planus,oral lichen planus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral lichen planus (both erosive and non-erosive )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oral lichen planus (OLP) is a common oral mucosal disease with or without accompanying lesions in skin, nails, eyes, or urogenital tissue
- 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
- 20
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Random Forest Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 5, Supplemental figure (Excel sheet) and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group
Abundance in Group 1: increased abundance in Oral lichen planus (both erosive and non-erosive )
| NCBI | Quality Control | Links |
|---|---|---|
| Altererythrobacter | ||
| Arthrobacter | ||
| Megasphaera | ||
| Mobiluncus | ||
| Oribacterium | ||
| Butyrivibrio 2Butyrivibrio 2 |
Revision editor(s): Fiddyhamma, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 5, Supplemental figure (Excel sheet) and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with and without erosive lesions (E and NE) versus control group
Abundance in Group 1: decreased abundance in Oral lichen planus (both erosive and non-erosive )
Revision editor(s): Fiddyhamma, Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- OLP patients without erosive lesions (NE)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with oral aphthous ulcer (RAU/U)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Recurrent aphthous ulceration (RAU) is a common oral mucosal disease also characterized by multiple oral ulcers, a feature similar to erosive OLP but different from OLP in the pattern of the clinical lesions and the pathogenesis mechanism
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Statistical test
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with oral aphthous ulcer (U/RAU)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- OLP patients with erosive lesions (E)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces
Lab analysis
Statistical Analysis
- Statistical test
- Random Forest Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group
Abundance in Group 1: increased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Oribacterium | ||
| Spirochaetales | ||
| Spirochaetia |
Revision editor(s): Fiddyhamma, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with erosive lesions (E) versus control group
Abundance in Group 1: decreased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Aerococcaceae | ||
| Haemophilus | ||
| Neisseria |
Revision editor(s): Fiddyhamma, Scholastica
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- OLP patients without erosive lesions (NE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Non-erosive OLP is a common oral mucosal disease without accompanying lesions in skin, nails, eyes, or urogenital tissue
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group
Abundance in Group 1: increased abundance in OLP patients without erosive lesions (NE)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Neisseria | ||
| Oribacterium |
Revision editor(s): Fiddyhamma, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients without erosive lesions (NE) versus control group
Abundance in Group 1: decreased abundance in OLP patients without erosive lesions (NE)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Aerococcaceae | ||
| Spirochaetales | ||
| Spirochaetia |
Revision editor(s): Fiddyhamma, Scholastica
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with oral aphthous ulcer (U/RAU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- OLP patients with erosive lesions (E)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Erosive OLP is a common oral mucosal disease characterized by multiple oral ulcers in its clinical presentation with chronic and painful ulceration of the skin and mucosal surfaces
Lab analysis
Statistical Analysis
- Statistical test
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 7
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- OLP patients without erosive lesions (NE)
Lab analysis
Statistical Analysis
- Statistical test
- Random Forest Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions
Abundance in Group 1: increased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Aerococcaceae | ||
| Spirochaetales | ||
| Spirochaetia |
Revision editor(s): Fiddyhamma, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
Source: Table 4 and Text
Description: The differential taxa of bacteria in oral lichen planus (OLP) patients with (E) compared to patients without (NE) erosive lesions
Abundance in Group 1: decreased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Neisseria | ||
| Oribacterium |
Revision editor(s): Fiddyhamma, Scholastica
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_1063&oldid=126260"
