Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

27283393

DOI Digital object identifier for electronic documents.

10.1016/j.clim.2016.06.002

URI Uniform resource identifier for web resources.

Authors

Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H, Sawalha AH

Journal

Clinical immunology (Orlando, Fla.)

Year

2016

Behçet's disease (BD) is characterized by recurrent oro-genital ulcers, mucocutaneous lesions, and serious organ involvement. We investigated the salivary microbiome in BD using high-throughput sequencing of the 16S rRNA V4 region. Stimulated saliva samples were collected from 31 BD patients and 15 healthy controls, and in 9 BD patients, a second saliva sample was collected following dental and periodontal treatment. Sequence analysis identified a total of 908 operational taxonomic units (OTUs) present across all samples. Patients had a microbial community structure that is significantly less diverse than healthy controls. The most overabundant species in BD was Haemophilus parainfluenzae, while the most depleted included Alloprevotella rava and species in the genus Leptotrichia. Periodontal treatment improved oral health indices in BD but had no short-term effect on bacterial community structure. Neither the BD-associated genetic risk locus within the HLA-B/MICA region nor being on immunosuppressive medications explained the differences between patients and controls.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, LGeistlinger

Subjects

Location of subjects: Turkey

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Behcet's syndrome Adamantiades-Behcet disease,BD,Bechet syndrome,BEHCET DIS,Behcet Disease,Behcet disease,Behcet syndrome,Behcet's disease,Behcet's syndrome,Behcets Syndrome,Behet's syndrome,Behet's syndrome (disorder),Behçet disease,Behçet syndrome,Behçet's disease,Behçet's syndrome,Behçet-Adamantiades syndrome,Behçet’s disease,Morbus Behçet's syndrome,silk road disease,triple symptom complex,Triple-Symptom Complex

Group 0 name Corresponds to the control (unexposed) group for case-control studies: controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: behcet's disease
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: 31
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

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

Statistical test: LEfSe

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Signature 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2018-12-13

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Table 4

Description: The LEfSe analysis revealed 22 OTUs with a consistent and significant overabundance in either patients or controls

Abundance in Group 1: increased abundance in behcet's disease

NCBI	Links
Haemophilus parainfluenzae
Alloprevotella

Revision editor(s): WikiWorks743

Signature 2

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2018-12-13

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Table 4

Description: The LEfSe analysis revealed 22 OTUs with a consistent and significant overabundance in either patients or controls

Abundance in Group 1: decreased abundance in behcet's disease

NCBI	Links
Alloprevotella rava
Campylobacter concisus
Leptotrichia sp.
Selenomonas sp.
Eubacteriales
Actinomyces graevenitzii
Prevotella pallens
Lancefieldella parvula
Lachnospiraceae
Bacteroidota
Lachnoanaerobaculum orale
Solobacterium moorei
Veillonella sp.
Hoylesella enoeca

Revision editor(s): WikiWorks743

Experiment 2

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Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, LGeistlinger

Subjects

Location of subjects: Turkey

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Behcet's syndrome Adamantiades-Behcet disease,BD,Bechet syndrome,BEHCET DIS,Behcet Disease,Behcet disease,Behcet syndrome,Behcet's disease,Behcet's syndrome,Behcets Syndrome,Behet's syndrome,Behet's syndrome (disorder),Behçet disease,Behçet syndrome,Behçet's disease,Behçet's syndrome,Behçet-Adamantiades syndrome,Behçet’s disease,Morbus Behçet's syndrome,silk road disease,triple symptom complex,Triple-Symptom Complex

Group 0 name Corresponds to the control (unexposed) group for case-control studies: non-immunosuppressent users among behcet's patients
Group 1 name Corresponds to the case (exposed) group for case-control studies: immunosuppressant users
Group 0 sample size Number of subjects in the control (unexposed) group: 19
Group 1 sample size Number of subjects in the case (exposed) group: 12
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

Lab analysis

Sequencing type: 16S

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): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No