Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark
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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
- Denmark
- 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
- Type II diabetes mellitus adult onset diabetes,Adult-Onset Diabetes,adult-onset diabetes,Adult-Onset Diabetes Mellitus,diabetes mellitis type 2,diabetes mellitis type II,DIABETES MELLITUS TYPE 02,diabetes mellitus type 2,Diabetes Mellitus, Adult Onset,Diabetes Mellitus, Adult-Onset,Diabetes Mellitus, Ketosis Resistant,Diabetes Mellitus, Ketosis-Resistant,Diabetes Mellitus, Maturity Onset,Diabetes Mellitus, Maturity-Onset,Diabetes Mellitus, Non Insulin Dependent,Diabetes Mellitus, Non-Insulin-Dependent,Diabetes Mellitus, Noninsulin Dependent,diabetes mellitus, noninsulin-dependent,Diabetes Mellitus, Slow Onset,Diabetes Mellitus, Slow-Onset,Diabetes Mellitus, Stable,Diabetes Mellitus, Type 2,diabetes mellitus, type 2,diabetes mellitus, type 2, protection against,Diabetes Mellitus, Type II,Diabetes, Type 2,diabetes, type 2,insulin resistance, susceptibility to,Ketosis-Resistant Diabetes Mellitus,Maturity Onset Diabetes Mellitus,maturity-onset diabetes,Maturity-Onset Diabetes Mellitus,MODY,NIDDM,Non-Insulin Dependent Diabetes,non-insulin dependent diabetes,Non-Insulin Dependent Diabetes Mellitus,non-insulin dependent diabetes mellitus,non-insulin-dependent diabetes mellitus,noninsulin dependent diabetes,noninsulin-dependent diabetes mellitus,Slow-Onset Diabetes Mellitus,Stable Diabetes Mellitus,T2DM - Type 2 Diabetes mellitus,T2DM - type 2 diabetes mellitus,Type 2 Diabetes,type 2 diabetes,Type 2 Diabetes Mellitus,type 2 diabetes mellitus,Type 2 Diabetes Mellitus Non-Insulin Dependent,type 2 diabetes mellitus non-insulin dependent,Type II Diabetes,type II diabetes,type II diabetes mellitus,Type II diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (NG) controls - Danish Cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (PD) - Danish Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes (PD) - Danish Cohort refers to patients in their early stage of prediabetes.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 138
- Group 1 sample size Number of subjects in the case (exposed) group
- 121
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-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).
- raw counts
- Statistical test
- DESeq2
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 11: Table S9A
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified using a negative binomial Wald test.
Abundance in Group 1: increased abundance in Prediabetes (PD) - Danish Cohort
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 11: Table S9A
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified using a negative binomial Wald test.
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Danish Cohort
Revision editor(s): KateRasheed
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "waist-to-hip ratio" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.waist-to-hip ratio, Confounders controlled for: "Systolic BP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Systolic BP, Confounders controlled for: "IL6" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.IL6, Confounders controlled for: "TNFα" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.TNFα, Confounders controlled for: "LBP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.LBP, Confounders controlled for: "IAP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.IAP
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 11: Table S9B
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP) using a negative binomial Wald test.
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Danish Cohort
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 11: Table S9B
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Danish cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP) using a negative binomial Wald test.
Abundance in Group 1: increased abundance in Prediabetes (PD) - Danish Cohort
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Indian Cohort (IN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Danish Cohort (DK)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Danish Cohort (DK) refers to the normoglycemic and prediabetic groups in Danish subjects.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 278
- Group 1 sample size Number of subjects in the case (exposed) group
- 259
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Additional file 7: Table S5B, Table S5A
Description: Differentially abundant taxa between Indian (IN) and Danish (DK) gut microbiomes identified using a negative binomial Wald test.
Abundance in Group 1: increased abundance in Danish Cohort (DK)
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 7: Table S5B, Table S5A
Description: Differentially abundant taxa between Indian (IN) and Danish (DK) gut microbiomes identified using a negative binomial Wald test.
Abundance in Group 1: decreased abundance in Danish Cohort (DK)
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (NG) controls - Indian & Danish Cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (PD) - Indian & Danish Cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 275
- Group 1 sample size Number of subjects in the case (exposed) group
- 262
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- geographic area
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 9: Table S7
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).
Abundance in Group 1: increased abundance in Prediabetes (PD) - Indian & Danish Cohorts
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 9: Table S7
Description: Differentially abundant OTUs between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort effect).
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Indian & Danish Cohorts
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Location of subjects
- India
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (NG) controls - Indian Cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (PD) - Indian Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes (PD) - Indian Cohort refers to patients in their early stage of prediabetes.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 137
- Group 1 sample size Number of subjects in the case (exposed) group
- 141
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 10: Table S8A
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Indian cohort, identified using a negative binomial Wald test.
Abundance in Group 1: increased abundance in Prediabetes (PD) - Indian Cohort
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 10: Table S8A
Description: Differentially abundant OTUs between NG and PD subjects, belonging to the Indian cohort, identified using a negative binomial Wald test.
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Indian Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae_UCG-002Ruminococcaceae_UCG-002 | ||
| Faecalibacterium | ||
| Alloprevotella | ||
| Prevotella 9Prevotella 9 | ||
| Agathobacter | ||
| Muribaculaceae |
Revision editor(s): KateRasheed
Experiment 6
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "waist-to-hip ratio" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.waist-to-hip ratio, Confounders controlled for: "Systolic BP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Systolic BP, Confounders controlled for: "IL6" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.IL6, Confounders controlled for: "TNFα" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.TNFα, Confounders controlled for: "LBP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.LBP, Confounders controlled for: "IAP" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.IAP
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 10: Table S8B
Description: Differentially abundant OTUs between NG and PD subjects , belonging to the Indian cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP) using a negative binomial Wald test.
Abundance in Group 1: increased abundance in Prediabetes (PD) - Indian Cohort
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 10: Table S8B
Description: Differentially abundant OTUs between NG and PD subjects , belonging to the Indian cohort, identified after correcting for covariates (age, gender, waist-to-hip ratio, Systolic BP, IL6, TNFα, LBP and IAP) using a negative binomial Wald test.
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Indian Cohort
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (NG) controls - Indian & Danish Cohorts
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediabetes (PD) - Indian & Danish Cohorts
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prediabetes (PD) - Indian & Danish Cohorts refers patients in their early stage of prediabetes in both India and Denmark cohorts.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 275
- Group 1 sample size Number of subjects in the case (exposed) group
- 262
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 months
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- geographic area
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 12: Table S10A, Table S10B, Table S10C
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort-effect).
Abundance in Group 1: increased abundance in Prediabetes (PD) - Indian & Danish Cohorts
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 12: Table S10A, Table S10B, Table S10C
Description: Differentially abundant taxa between NG and PD subjects, belonging to the Indian and Danish cohorts (pooled together) identified using a negative binomial Wald test (corrected for geography specific cohort-effect).
Abundance in Group 1: decreased abundance in Prediabetes (PD) - Indian & Danish Cohorts
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota | ||
| Mycoplasmatota | ||
| Verrucomicrobiota | ||
| Cyanobacteriota | ||
| Spirochaetota | ||
| Lentisphaerota | ||
| Synergistota | ||
| Clostridiales vadinBB60 groupClostridiales vadinBB60 group |
Revision editor(s): KateRasheed
