Gut Microbiome Associated With Graves Disease and Graves Orbitopathy: The INDIGO Multicenter European Study
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Belgium
- Germany
- Italy
- United Kingdom
- 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
- Graves disease Basedow disease,Basedow's disease,exophthalmic goiter,Flajani-Basedow-Graves disease,grave's disease,Graves disease,Graves' disease,Graves' hyperthyroidism,parry disease,toxic diffuse goiter,graves disease
- 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
- Graves’ disease (GD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Graves’ disease (GD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Three months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- T-Test
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, smoking behavior, geographic area, sex
Signature 1
Source: Figure 1A and 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: increased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacterium sp. | ||
| Fusicatenibacter sp. |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 1A and 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: decreased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Bacteroides sp. |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Graves ophthalmopathy Congestive Ophthalmopathy,Dysthyroid Ophthalmopathy,dysthyroid/thyroid-associated orbitopathy (TAO),Edematous Ophthalmopathy,Graves' ophthalmopathy,Graves' orbitopathy,Myopathic Ophthalmopathy,thyroid eye disease (TED),Thyroid-Associated Ophthalmopathies,Thyroid-Associated Ophthalmopathy,Graves ophthalmopathy,graves ophthalmopathy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Graves’ ophthalmopathy (GO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Graves’ ophthalmopathy (GD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1A
Description: Distributions of the main phyla Bacteroidetes, Firmicutes, and Actinobacteria in controls (HCs), GD, and Graves orbitopathy (GO) patients.
Abundance in Group 1: increased abundance in Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 1A
Description: Distributions of the main phyla Bacteroidetes, Firmicutes, and Actinobacteria in controls (HCs), GD, and Graves orbitopathy (GO) patients.
Abundance in Group 1: decreased abundance in Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Graves’ ophthalmopathy (GO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with mild Graves’ ophthalmopathy (GD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: increased abundance in Mild Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium sp. | ||
| Fusicatenibacter sp. |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: decreased abundance in Mild Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe Graves’ ophthalmopathy (GO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with severe Graves’ ophthalmopathy (GD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: increased abundance in Severe Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Graves’ disease (GD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: increased abundance in Severe Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mild Graves’ ophthalmopathy (GO)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: increased abundance in Severe Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2
Description: Significantly different genera across eye-disease severity (distributed as control, no sign/Graves disease [GD] only, mild, moderate-severe according to the EUGOGO guidelines).
Abundance in Group 1: decreased abundance in Severe Graves’ ophthalmopathy (GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium sp. |
Revision editor(s): Aleru Divine
