Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
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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.
URI
Authors
Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS, Makharia GK
Journal
Frontiers in microbiology
Year
2019
Keywords:
H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
Experiment 1
Subjects
- Location of subjects
- India
- 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
- Duodenum , Feces Proximal intestine,Upper intestine,Duodenum,duodenum,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
- Celiac disease CD - Celiac disease,CD - Coeliac disease,CELIAC DIS,celiac disease,Celiac disease (disorder),Celiac disease NOS,Celiac disease NOS (disorder),Celiac rickets,Celiac rickets (disorder),Celiac Sprue,celiac sprue,Celiac syndrome,Coeliac disease,coeliac disease,Coeliac disease [Ambiguous],Coeliac disease NOS,Coeliac rickets,Coeliac sprue,Coeliac syndrome,CS - Celiac sprue,CS - Coeliac sprue,Disease, Celiac,Enteropathies, Gluten,Enteropathies, Gluten-Sensitive,Enteropathy, Gluten,Enteropathy, Gluten-Sensitive,Gluten Enteropathies,Gluten enteropathy,Gluten Sensitive Enteropathy,Gluten-Induced Enteropathy,gluten-induced enteropathy,Gluten-induced enteropathy syndrome,Gluten-responsive sprue,Gluten-Sensitive Enteropathies,Gluten-Sensitive Enteropathy,GSE - Gluten-sensitive enteropathy,Idiopathic steatorrhea,idiopathic steatorrhea,Idiopathic steatorrhoea,Non Tropical Sprue,non tropical sprue,Non-tropical sprue,Nontropical Sprue,Sprue,Sprue, Celiac,Sprue, Nontropical,Steatorrhoea - idiopathic,Wheat-sensitive enteropathy,Celiac disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FDRs of patient with CeD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- First degree relatives of patients with Celiac Disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- 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
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex design
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1
Description: Site Specific Comparison of Duodenal and Fecal Microbiota of FDRs, CeD and Control Group
Abundance in Group 1: decreased abundance in FDRs of patient with CeD
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Temi
Signature 2
Source: Figure 2
Description: Phylum level distribution of ASVs in duodenal microbiota. Pairwise comparisons were done using Wilcoxon tests.
Abundance in Group 1: increased abundance in FDRs of patient with CeD
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Bacteroidia | ||
| Eubacteriales | ||
| Euryarchaeota | ||
| Pseudomonadota | ||
| Verrucomicrobiota |
Revision editor(s): Temi
Signature 3
Source: Figure 3
Description: Comparison of differential abundance of microbial ASVs between the diagnosis groups in duodenal microbiota.
Abundance in Group 1: decreased abundance in FDRs of patient with CeD
Revision editor(s): Temi
Signature 4
Source: Figure 4
Description: Phylum level distribution of ASVs in fecal microbiota. Pairwise comparisons were done using Wilcoxon tests.
Abundance in Group 1: decreased abundance in FDRs of patient with CeD
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Eubacteriales | ||
| Euryarchaeota | ||
| Pseudomonadota | ||
| Verrucomicrobiota | ||
| Bacteroidia | ||
| Bacteroidales |
Revision editor(s): Temi
Signature 5
Source: Figure 5
Description: Comparison of differential abundance of microbial ASVs between the diagnosis groups in fecal microbiota
Abundance in Group 1: decreased abundance in FDRs of patient with CeD
| NCBI | Quality Control | Links |
|---|---|---|
| Pediococcus | ||
| Methanomassiliicoccus | ||
| Lactobacillus | ||
| Intestinibacter | ||
| Dorea | ||
| Blautia | ||
| Prevotella | ||
| Akkermansia | ||
| Haemophilus |
Revision editor(s): Temi
Signature 6
Source: Figure 6
Description: KO abundance for Xaa-pro dipeptidase enzyme in feces inferred from predicted metagenome for fecal samples. Comparison was done using ANOVA.
Abundance in Group 1: decreased abundance in FDRs of patient with CeD
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella phage No. 11 |
Revision editor(s): Temi
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