Dysbiosis of saliva microbiome in patients with oral lichen planus
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- 10
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
Source: Table 5, Supplemental figure (Excel sheet) and Text
Description: The Differential Taxa of Bacteria Between OLP (combined E and NE) and Control Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: increased abundance in Oral lichen planus ( Both erosive and non-erosive )
| NCBI | Quality Control | Links |
|---|---|---|
| Oribacterium | ||
| Megasphaera | ||
| Butyrivibrio 2Butyrivibrio 2 | ||
| Altererythrobacter | ||
| Mobiluncus | ||
| Arthrobacter |
Revision editor(s): Fiddyhamma
Signature 2
Source: Table 5, Supplemental figure (Excel sheet) and Text
Description: Description: The Differential Taxa of Bacteria Between OLP (combined E and NE) and Control Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: decreased abundance in Oral lichen planus ( Both erosive and non-erosive )
Revision editor(s): Fiddyhamma
Experiment 2
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
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
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
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
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: increased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Spirochaetia | ||
| Oribacterium | ||
| Spirochaetales |
Revision editor(s): Fiddyhamma
Signature 2
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: decreased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Abiotrophia | ||
| Haemophilus | ||
| Aerococcaceae |
Revision editor(s): Fiddyhamma
Experiment 5
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
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: increased abundance in OLP patients without erosive lesions (NE)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Haemophilus | ||
| Oribacterium |
Revision editor(s): Fiddyhamma
Signature 2
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: decreased abundance in OLP patients without erosive lesions (NE)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Spirochaetia | ||
| Aerococcaceae | ||
| Spirochaetales |
Revision editor(s): Fiddyhamma
Experiment 6
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
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
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: increased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Spirochaetia | ||
| Aerococcaceae | ||
| Spirochaetales |
Revision editor(s): Fiddyhamma
Signature 2
Source: Table 4 and Text
Description: The differential Taxa of Bacteria Among Three Study Groups. Data was presented as mean ± SD, which was the log value from the Mean Decrease Gini index of each group, developed from the operational taxonomic unit (OTU)-level abundances (read abundance %) analyzed by Random Forest classification. The higher the value, the less read abundance the bacteria
Abundance in Group 1: decreased abundance in OLP patients with erosive lesions (E)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Haemophilus | ||
| Oribacterium |
Revision editor(s): Fiddyhamma
