Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening

From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2022/03/22
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L, Zhang
Journal
Scientific reports
Year
2018
The key to arthritis management is early diagnosis and treatment to prevent further joint destruction and maximize functional ability. Osteoarthritis (OA) and rheumatoid arthritis (RA) are two common types of arthritis that the primary care provider must differentiate, in terms of diagnosis and treatment. Effective and non-invasive strategies for early detection and disease identification are sorely needed. Growing evidence suggests that RA has a correlation with oral microbiome and may be affected by its dynamic variations. There is already a study comparing oral microbiome in patients with RA and OA, however, it did not screen for potential biomarkers for arthritis. In this study, we assessed the oral microbiome in saliva samples from 110 RA patients, 67 OA patients and 155 healthy subjects, using 16S rRNA gene amplicon sequencing. The structure and differences in oral microbiome between RA, OA and healthy subjects were analyzed. Eight oral bacterial biomarkers were identified to differentiate RA from OA. This report provides proof of oral microbiota as an informative source for discovering non-invasive biomarkers for arthritis screening.

Experiment 1


Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/16

Curator: Tislam

Revision editor(s): WikiWorks, Lwaldron, Chloe, Tislam, Peace Sandy

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
Rheumatoid arthritis , Osteoarthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid disease,Rheumatoid arthritis,Arthritides, Degenerative,Arthritis, Degenerative,arthrosis,Degenerative Arthritides,Degenerative Arthritis,degenerative arthritis,degenerative joint disease,hypertrophic arthritis,OA,Osteoarthritides,osteoarthritis,Osteoarthroses,Osteoarthrosis,osteoarthrosis,osteoarthrosis and allied disorder,Osteoarthrosis Deformans,Osteoarthritis
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
arthritis patient
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
arthritis
Group 0 sample size Number of subjects in the control (unexposed) group
155
Group 1 sample size Number of subjects in the case (exposed) group
177

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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)
.05
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/16

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 2, text

Description: (c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).

Abundance in Group 1: increased abundance in arthritis patient

NCBI Quality ControlLinks
Fusobacterium
Lautropia
Leptotrichia
Granulicatella
Actinomyces
Streptococcus
Rothia
Haemophilus
Veillonella dispar
Veillonella
Porphyromonas
Prevotella melaninogenica
Neisseria
Prevotella

Revision editor(s): Tislam

Signature 2

Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/16

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 2, text

Description: (c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).

Abundance in Group 1: decreased abundance in arthritis patient

NCBI Quality ControlLinks
Acinetobacter
Chryseobacterium
Pseudomonas
Enhydrobacter
Stenotrophomonas
Sphingomonas
Wautersiella
Brevundimonas diminuta
Bacteroides
Comamonas
Sphingomonas yabuuchiae
Mycoplana

Revision editor(s): Tislam

Experiment 2


Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/17

Curator: Tislam

Revision editor(s): WikiWorks, LGeistlinger, Chloe, Tislam

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Rheumatoid arthritis , Osteoarthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid disease,Rheumatoid arthritis,Arthritides, Degenerative,Arthritis, Degenerative,arthrosis,Degenerative Arthritides,Degenerative Arthritis,degenerative arthritis,degenerative joint disease,hypertrophic arthritis,OA,Osteoarthritides,osteoarthritis,Osteoarthroses,Osteoarthrosis,osteoarthrosis,osteoarthrosis and allied disorder,Osteoarthrosis Deformans,Osteoarthritis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Osteoarthritis
Group 1 name Corresponds to the case (exposed) group for case-control studies
rheumatoid arthritis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patient with rheumatoid arthritis
Group 0 sample size Number of subjects in the control (unexposed) group
67
Group 1 sample size Number of subjects in the case (exposed) group
110

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/17

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 2, text

Description: c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).

Abundance in Group 1: increased abundance in rheumatoid arthritis

NCBI Quality ControlLinks
Haemophilus parahaemolyticus
Actinobacillus
Aggregatibacter
Alloprevotella tannerae
Fusobacterium
Veillonella
Prevotella
Veillonella dispar
Haemophilus
Haemophilus parainfluenzae
Neisseria subflava
Neisseria

Revision editor(s): Tislam

Signature 2

Reviewed Marked as Reviewed by Chloe on 2022/03/22

Curated date: 2021/08/17

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 2

Description: (c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).

Abundance in Group 1: decreased abundance in rheumatoid arthritis

NCBI Quality ControlLinks
Streptococcus
Actinomyces
Lautropia
Rothia
Granulicatella
Rothia dentocariosa
Ruminococcus
Oribacterium
Mediterraneibacter gnavus
Abiotrophia

Revision editor(s): Tislam