Human gut microbiota changes reveal the progression of glucose intolerance
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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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Glucose Tolerance (NGT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes mellitus (T2DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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)?
- No
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: Table 2, Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the NGT and T2DM groups.
Abundance in Group 1: increased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia | ||
| Eubacteriales | ||
| Eubacterium | ||
| Lachnospiraceae | ||
| Peptostreptococcus | ||
| Oscillospiraceae | ||
| Ruminococcus | ||
| Sporobacter | ||
| Subdoligranulum | ||
| Abiotrophia | ||
| Betaproteobacteria |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Table 2, Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the NGT and T2DM groups.
Abundance in Group 1: decreased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia | ||
| Eubacteriales | ||
| Haemophilus | ||
| Lachnospiraceae | ||
| Megamonas | ||
| Roseburia | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Prediabetes syndrome borderline diabetes,Prediabetes,prediabetes,prediabetes syndrome,Prediabetic State,prediabetic state,Prediabetes syndrome
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (Pre-DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
Lab analysis
Statistical Analysis
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: Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the NGT and PreDM groups.
Abundance in Group 1: increased abundance in Prediabetes (Pre-DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the NGT and PreDM groups.
Abundance in Group 1: decreased abundance in Prediabetes (Pre-DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Prediabetes (Pre-DM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes mellitus (T2DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
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: Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the T2DM and PreDM groups.
Abundance in Group 1: increased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiia | ||
| Verrucomicrobiota |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Table S3 and Table S4
Description: The relative abundance of OTUs enriched in the T2DM and PreDM groups.
Abundance in Group 1: decreased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Glucose Tolerance (NGT)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
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 S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: increased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lachnospiraceae | ||
| Eubacterium | ||
| Peptostreptococcus | ||
| Sporobacter | ||
| Subdoligranulum | ||
| Ruminococcus | ||
| Abiotrophia |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: decreased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Prediabetes syndrome borderline diabetes,Prediabetes,prediabetes,prediabetes syndrome,Prediabetic State,prediabetic state,Prediabetes syndrome
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (Pre-DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
Lab analysis
Statistical Analysis
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 S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: increased abundance in Prediabetes (Pre-DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lachnospiraceae | ||
| Ruminococcus | ||
| Abiotrophia |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: decreased abundance in Prediabetes (Pre-DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Prediabetes (Pre-DM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes mellitus (T2DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
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 S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: increased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium | ||
| Lachnospiraceae | ||
| Peptostreptococcus | ||
| Sporobacter | ||
| Subdoligranulum | ||
| Ruminococcus | ||
| Abiotrophia |
Revision editor(s): Aleru Divine, WikiWorks
Signature 2
Source: Figure S4
Description: Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.
Abundance in Group 1: decreased abundance in Type 2 diabetes mellitus (T2DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia |
Revision editor(s): Aleru Divine, WikiWorks
