Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls/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
