A metagenomic study of the gut microbiome in Behcet's disease
From BugSigDB
Jump to:navigation, search
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.
Authors
Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N, Yang P
Journal
Microbiome
Year
2018
Keywords:
Behcet’s disease, Fecal microbiota transplant, Gut microbiome, Metagenomic analysis
BACKGROUND: Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease. METHODS: Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD. RESULTS: Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ. CONCLUSIONS: Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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,behcet's syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Untreated active Behcet's disease (BD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Active BD was defined according to presence of active intraocular inflammation (case-control)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- WMS
- 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)
- 0.05
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Figure 2a
Description: Differentially abundant genera in Behcet's disease subjects compared to healthy controls.
Abundance in Group 1: increased abundance in Untreated active Behcet's disease (BD) patients
Revision editor(s): Fiddyhamma, Welile, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Figure 2a
Description: Differentially abundant genera in Behcet's disease subjects compared to healthy controls.
Abundance in Group 1: decreased abundance in Untreated active Behcet's disease (BD) patients
Revision editor(s): Fiddyhamma, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Differences from previous experiment shown
Subjects
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Behcet's disease (case-control)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Supplementary Figure S2, Supplementary Table S8
Description: Differences in altered oral microbial composition in Behcet's disease (BD) patients compared to healthy controls
Abundance in Group 1: increased abundance in Untreated active Behcet's disease (BD) patients
Revision editor(s): Fiddyhamma, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Curated date: 2024/03/12
Curator: Fiddyhamma
Revision editor(s): Fiddyhamma, Omojokunoluwatomisin, ChiomaBlessing
Source: Supplementary Figure S2, Supplementary Table S8
Description: Differences in altered oral microbial composition in Behcet's disease (BD) patients compared to healthy controls
Abundance in Group 1: decreased abundance in Untreated active Behcet's disease (BD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Neisseriaceae | ||
| Neisseriales | ||
| Pseudomonadota |
Revision editor(s): Fiddyhamma, Omojokunoluwatomisin, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control feces treated group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Behcet's disease (BD) feces treated group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- B10RIII mice (mice undergoing autoimmune uveitis) colonized with untreated BD patients stool samples (experimental)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
- Sequencing type
- Not specified
- 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
- Not specified
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Supplementary Figure S1c, Supplementary Table S9
Description: Abundance of altered genera in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice
Abundance in Group 1: increased abundance in Behcet's disease (BD) feces treated group
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Alloprevotella | ||
| Anaerofilum | ||
| Bilophila | ||
| Butyricimonas | ||
| Coprobacter | ||
| Mucispirillum | ||
| Paraprevotella | ||
| Clostridium IVClostridium IV |
Revision editor(s): Fiddyhamma, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Supplementary Figure S1c, Supplementary Table S9
Description: Abundance of altered genera in Behcet's disease (BD) patients’ feces treated group compared to healthy control feces treated mice
Abundance in Group 1: decreased abundance in Behcet's disease (BD) feces treated group
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella |
Revision editor(s): Fiddyhamma, ChiomaBlessing
Experiment 4
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Differences from previous experiment shown
Subjects
- 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,behcet's syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Untreated active Behcet's disease (BD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Active BD was defined according to presence of active intraocular inflammation (case-control)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Supplemental. Table S3
Description: Enriched/ depleted species in Behcet's disease subjects compared to healthy controls
Abundance in Group 1: increased abundance in Untreated active Behcet's disease (BD) patients
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-29
Source: Supplemental. Table S3
Description: Enriched/ depleted species in Behcet's disease subjects compared to healthy controls
Abundance in Group 1: decreased abundance in Untreated active Behcet's disease (BD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter sp. CAG:196 | ||
| Epichloe glyceriae |
Revision editor(s): ChiomaBlessing
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_927&oldid=123194"
Hidden category:
