Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study/Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2021/09/28

Curator: Tislam

Revision editor(s): Tislam, WikiWorks

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
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 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
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

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

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


Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2021/09/28

Curator: Tislam

Revision editor(s): Tislam, Atrayees

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

NCBI Quality ControlLinks
Rothia mucilaginosa
Lancefieldella parvula
Oribacterium sinus
Pseudoleptotrichia goodfellowii
Streptococcus sp. oral taxon 070
Bacillus subtilis
Haemophilus
Oribacterium
Atopobium
Bacillus
Actinomycetota
Rothia

Revision editor(s): Tislam, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-25

Curated date: 2021/09/28

Curator: Tislam

Revision editor(s): Tislam, Atrayees

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

NCBI Quality ControlLinks
Porphyromonas sp.
Prevotella sp. oral taxon 313
SR1 bacterium oral taxon 875
Oribacterium parvum
Eikenella corrodens
Hoylesella shahii
SR1 bacterium oral taxon 874
Alloprevotella sp.
Campylobacter sp. oral taxon 044
Kingella oralis
Hoylesella nanceiensis
Porphyromonas pasteri
Neisseria elongata
Prevotella pallens
Bergeyella sp.
Haemophilus parainfluenzae
Pseudomonadota
Eikenella
Haemophilus
Alloprevotella

Revision editor(s): Tislam, Atrayees