Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism
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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
- 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
- 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 diagnosed with Graves’ disease (GD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- One month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: increased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lactobacillus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: decreased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| Blautia | ||
| Butyricicoccus | ||
| Clostridium | ||
| Collinsella | ||
| Dorea | ||
| [Ruminococcus] torques | ||
| unclassified Peptostreptococcaceae |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hypothyroidism hypothyroid,hypothyroidism,thyroid deficiency,thyroid insufficiency,underactive thyroid,Hypothyroidism
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hypothyroidism group (HT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Hypothyroidism group (HT)
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: increased abundance in Hypothyroidism group (HT)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: decreased abundance in Hypothyroidism group (HT)
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella | ||
| Anaerobutyricum hallii | ||
| [Ruminococcus] torques | ||
| Anaerostipes | ||
| Dorea | ||
| Blautia | ||
| Prevotella | ||
| Faecalibacterium | ||
| Subdoligranulum |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hypothyroidism , Graves disease hypothyroid,hypothyroidism,thyroid deficiency,thyroid insufficiency,underactive thyroid,Hypothyroidism,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
- Graves' disease (GD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
Lab analysis
Statistical Analysis
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: increased abundance in Hypothyroidism group (HT)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Eggerthella | ||
| unclassified Peptostreptococcaceae | ||
| Intestinibacter | ||
| Flavonifractor | ||
| unclassified Oscillospiraceae | ||
| Megasphaera |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3
Description: Mann-Whitney U test plots of the pairwise comparisons between the HT, GD, and control groups. This figure presents the top 10 genera that differed between groups in each pairwise comparison (HT versus Control, GD versus Control, and HT versus GD) according to the Mann-Whitney U test.
Abundance in Group 1: decreased abundance in Hypothyroidism group (HT)
| NCBI | Quality Control | Links |
|---|---|---|
| Hungatella | ||
| unclassified Lachnospiraceae | ||
| Faecalibacterium |
Revision editor(s): Aleru Divine
