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

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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
Keywords:
16s rRNA, Behçet's disease, Genetics, Microbiome, Oral microbial diversity, Sequencing
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


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): LGeistlinger, WikiWorks

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

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 Quality ControlLinks
Haemophilus parainfluenzae
Alloprevotella

Revision editor(s): WikiWorks

Signature 2

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 Quality ControlLinks
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): WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): LGeistlinger, WikiWorks

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

Signature 1

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: text

Description: the association between the use of immunosuppressants in BD patients with gut microbiota

Abundance in Group 1: increased abundance in immunosuppressant users

NCBI Quality ControlLinks
Bergeyella
Prevotella
Porphyromonas catoniae

Revision editor(s): WikiWorks

Signature 2

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: text

Description: the association between the use of immunosuppressants in BD patients with gut microbiota

Abundance in Group 1: decreased abundance in immunosuppressant users

NCBI Quality ControlLinks
Prevotella baroniae
Oribacterium sp.

Revision editor(s): WikiWorks