Dysbiosis of saliva microbiome in patients with oral lichen planus

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-22
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

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
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

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 )

NCBI Quality ControlLinks
Abiotrophia
Acholeplasma
Aggregatibacter
Bacteroides
Eikenella
Ezakiella
Fluviicola
Leptotrichia
Neisseria
Sediminibacterium
Sulfuritalea
Tannerella
uncultured Oscillospiraceae bacterium
Prevotella 1Prevotella 1
Prevotella 2Prevotella 2
Prevotella 7Prevotella 7
Christensenellaceae R-7 groupChristensenellaceae R-7 group

Revision editor(s): Fiddyhamma, Scholastica

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Oribacterium
Spirochaetales
Spirochaetia

Revision editor(s): Fiddyhamma, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Abiotrophia
Aerococcaceae
Haemophilus
Neisseria

Revision editor(s): Fiddyhamma, Scholastica

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Haemophilus
Neisseria
Oribacterium

Revision editor(s): Fiddyhamma, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Abiotrophia
Aerococcaceae
Spirochaetales
Spirochaetia

Revision editor(s): Fiddyhamma, Scholastica

Experiment 6


Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/24

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Abiotrophia
Aerococcaceae
Spirochaetales
Spirochaetia

Revision editor(s): Fiddyhamma, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-22

Curated date: 2024/03/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Scholastica

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 ControlLinks
Haemophilus
Neisseria
Oribacterium

Revision editor(s): Fiddyhamma, Scholastica