Correlation between gut microbiota and the development of Graves' disease: A prospective 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
- 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
- Control group (Con)
- 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
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 65
- 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
- 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
- Welch's 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
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2A
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GD groups by STAMP analysis using Welch’s t test (p < 0.05, q < 0.05).
Abundance in Group 1: increased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Veillonella | ||
| Thomasclavelia |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2A
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GD groups by STAMP analysis using Welch’s t test (p < 0.05, q < 0.05).
Abundance in Group 1: decreased abundance in Graves’ disease (GD)
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Graves’ disease before treatment (GDT0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Graves’ disease after treatment (GDT3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Graves’ disease (GD) 3 months after treatment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 2B
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between GDT0and GDT3 groups by STAMP analysis using Welch’s t test.
Abundance in Group 1: increased abundance in Graves’ disease after treatment (GDT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Romboutsia | ||
| Lachnospira |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2B
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between GDT0 and GDT3 groups by STAMP analysis using Welch’s t test.
Abundance in Group 1: decreased abundance in Graves’ disease after treatment (GDT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Carnobacteriaceae | ||
| Streptococcaceae | ||
| Tyzzerella | ||
| Streptococcus | ||
| Granulicatella |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group (Con)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2C
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GDT3 groups by STAMP analysis using Welch’s t test.
Abundance in Group 1: increased abundance in Graves’ disease after treatment (GDT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Thomasclavelia |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2C
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between Con and GDT3 groups by STAMP analysis using Welch’s t test.
Abundance in Group 1: decreased abundance in Graves’ disease after treatment (GDT3)
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Graves’ disease before treatment (GDT0)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 5C
Description: LEfSe analysis shows bacterial taxa significantly enriched in the GDT0 (red) or GDT3(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDT0 and GDT3. Only taxa meeting a significant LDA threshold value of >3 are shown.
Abundance in Group 1: increased abundance in Graves’ disease after treatment (GDT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Intestinibacter | ||
| Terrisporobacter |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 5C
Description: LEfSe analysis shows bacterial taxa significantly enriched in the GDT0 (red) or GDT3(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDT0 and GDT3. Only taxa meeting a significant LDA threshold value of >3 are shown.
Abundance in Group 1: decreased abundance in Graves’ disease after treatment (GDT3)
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella | ||
| Carnobacteriaceae | ||
| Bacilli | ||
| Lactobacillales |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Graves’ disease without hepatic impairment (GDN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Graves’ disease with impaired liver function before treatment (GDH)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with confirmed Graves’ disease (GD) and impaired liver function before treatment (GDH)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Statistical test
- Welch's T-Test
- 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
- Not specified
Signature 1
Source: Figure 4A
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between GDH and GDN subgroups by STAMP analysis using Welch’s ttest (p < 0.05, q < 0.05).
Abundance in Group 1: increased abundance in Graves’ disease with impaired liver function before treatment (GDH)
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4A
Description: Differentially abundant taxa from the phylum to genus level were further analyzed between GDH and GDN subgroups by STAMP analysis using Welch’s ttest (p < 0.05, q < 0.05).
Abundance in Group 1: decreased abundance in Graves’ disease with impaired liver function before treatment (GDH)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Lactobacillaceae | ||
| Weissella |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 4B
Description: LEfSe analysis shows bacterial taxa significantly enriched in the GDH (red) or GDN(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDH and GDN. Only taxa meeting a significant LDA threshold value of >3 are shown.
Abundance in Group 1: increased abundance in Graves’ disease with impaired liver function before treatment (GDH)
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminiclostridium | ||
| Eubacterium ventriosum | ||
| Atopobiaceae | ||
| Olsenella | ||
| Candidatus Gastranaerophilales | ||
| Ruminococcaceae bacterium UCG-002Ruminococcaceae bacterium UCG-002 |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4B
Description: LEfSe analysis shows bacterial taxa significantly enriched in the GDH (red) or GDN(green) groups. Taxonomic cladogram and linear discriminant analysis (LDA) scores show differences among taxa between GDH and GDN. Only taxa meeting a significant LDA threshold value of >3 are shown.
Abundance in Group 1: decreased abundance in Graves’ disease with impaired liver function before treatment (GDH)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Enterobacterales | ||
| Gammaproteobacteria | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Pseudomonadota | ||
| Weissella |
Revision editor(s): Aleru Divine
