Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study
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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
Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E, Al-Haroni M
Journal
Frontiers in cellular and infection microbiology
Year
2020
Keywords:
16S rRNA, juvenile idiopathic arthritis, next generation sequencing (NGS), oral health, salivary microbiome
Background: The oral microbiota has been connected to the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. The objective of this study was to characterize the salivary oral microbiome associated with juvenile idiopathic arthritis (JIA), and correlate it with the disease activity including gingival inflammation. Methods: Fifty-nine patients with JIA (mean age, 12.6 ± 2.7 years) and 34 healthy controls (HC; mean age 12.3 ± 3.0 years) were consecutively recruited in this Norwegian cross-sectional study. Information about demographics, disease activity, medication history, frequency of tooth brushing and a modified version of the gingival bleeding index (GBI) and the simplified oral hygiene index (OHI-S) was obtained. Microbiome profiling of saliva samples was performed by sequencing of the V1-V3 region of the 16S rRNA gene, coupled with a species-level taxonomy assignment algorithm; QIIME, LEfSe and R-package for Spearman correlation matrix were used for downstream analysis. Results: There were no significant differences between JIA and HC in alpha- and beta-diversity. However, differential abundance analysis revealed several taxa to be associated with JIA: TM7-G1, Solobacterium and Mogibacterium at the genus level; and Leptotrichia oral taxon 417, TM7-G1 oral taxon 352 and Capnocytophaga oral taxon 864 among others, at the species level. Haemophilus species, Leptotrichia oral taxon 223, and Bacillus subtilis, were associated with healthy controls. Gemella morbillorum, Leptotrichia sp. oral taxon 498 and Alloprevotella oral taxon 914 correlated positively with the composite juvenile arthritis 10-joint disease activity score (JADAS10), while Campylobacter oral taxon 44 among others, correlated with the number of active joints. Of all microbial markers identified, only Bacillus subtilis and Campylobacter oral taxon 44 maintained false discovery rate (FDR) < 0.1. Conclusions: In this exploratory study of salivary oral microbiome we found similar alpha- and beta-diversity among children with JIA and healthy. Several taxa associated with chronic inflammation were found to be associated with JIA and disease activity, which warrants further investigation.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Subjects
- Location of subjects
- Norway
- 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
- Juvenile idiopathic arthritis acute juvenile rheumatoid arthritis,Arthritis (juvenile idiopathic),arthritis, juvenile rheumatoid,breast myoepithelial carcinoma,chronic childhood arthritis,JIA,juvenile arthritis,juvenile chronic arthritis,Juvenile chronic arthritis (disorder),juvenile chronic polyarthritis,Juvenile idiopathic arthritis,juvenile idiopathic arthritis,Juvenile idiopathic arthritis (disorder),Juvenile rheumatoid a.,Juvenile Rheumatoid Arthritis,juvenile rheumatoid arthritis,Juvenile rheumatoid arthritis (disorder),Juvenile rheumatoid arthritis NOS (disorder),Juvenile rheumatoid arthritis, NOS,Juvenile seropositive polyarthritis,monarticular juvenile rheumatoid arthritis,pauciarticular juvenile arthritis,pauciarticular onset juvenile chronic arthritis,rheumatoid arthritis, systemic juvenile,systemic juvenile rheumatoid arthritis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JIA patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with juvenile idiopathic arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients on antibiotics prior to sampling were excluded.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Source: Figure 3
Description: Differentially abundant taxa
Abundance in Group 1: increased abundance in JIA patients
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Source: Figure 3C
Description: Differentially abundant taxa.
Abundance in Group 1: decreased abundance in JIA patients
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Temporomandibular joint disorder temporomandibular joint disorder,TMD,Temporomandibular joint disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- JIA patients without TMJ
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JIA patients with TMJ
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients on antibiotics on the day of sampling were excluded, but previous antibiotic use were not recorded.
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Source: Figure 6C,
Description: species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).
Abundance in Group 1: decreased abundance in JIA patients with TMJ
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-25
Source: Figure 6C, text
Description: species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).
Abundance in Group 1: increased abundance in JIA patients with TMJ
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