Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes
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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
- 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
- Response to metformin Response to metformin,response to metformin
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Metformin naive T2D (type 2 diabetes) patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Metformin treated T2D (type 2 diabetes) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Species confounded by metformin use in T2D (type 2 diabetes) cases
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina, Ion Torrent, BGISEQ-500 Sequencing
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.10
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "metformin use" 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.metformin use
Signature 1
Source: Extended Data Figure 4B
Description: Meta-analyzed and cohort-specific associations of microbial species with metformin use among T2D (type 2 diabetes) patients
Abundance in Group 1: increased abundance in Metformin treated T2D (type 2 diabetes) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus intestini | ||
| Bilophila wadsworthia |
Revision editor(s): Tosin
Signature 2
Source: Extended Data Figure 4B
Description: Meta-analyzed and cohort-specific associations of microbial species with metformin use among type 2 diabetes (T2D) patients
Abundance in Group 1: decreased abundance in Metformin treated T2D (type 2 diabetes) patients
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Metformin naive T2D patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Metformin treated T2D patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Species associated with both metformin use and T2D cases
Lab analysis
Statistical Analysis
Signature 1
Source: Extended data Fig. 4B
Description: Meta-analyzed and cohort-specific associations of microbial species associated with both metformin use and T2D
Abundance in Group 1: increased abundance in Metformin treated T2D patients
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Enterocloster bolteae |
Revision editor(s): Fiddyhamma
Signature 2
Source: Extended data Fig. 4B
Description: Meta-analyzed and cohort-specific associations of microbial species associated with both metformin use and T2D
Abundance in Group 1: decreased abundance in Metformin treated T2D patients
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. CAG:182 | ||
| Clostridium sp. CAG:167 |
Revision editor(s): Fiddyhamma
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diabetes mellitus Diabetes,diabetes,diabetes mellitus,diabetes mellitus (disease),Diabetes mellitus (disorder),Diabetes mellitus, NOS,Diabetes NOS,DM,DM - Diabetes mellitus,Diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increased normoglycemic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Decreased normoglycemic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Signature 1
Source: Figure 2a and Supplementary Table 3
Description: Heatmap for the meta-analyzed associations of microbial species with T2D. The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D) and adjust for age, sex, FDR with a target of 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic
Revision editor(s): YokoC
Signature 2
Source: Figure 2a and Supplementary Table 3
Description: Heatmap for the meta-analyzed associations of microbial species with T2D. The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D) and adjust for age, sex, FDR with a target of 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic
Revision editor(s): YokoC
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Signature 1
Source: Figure 2a and Supplementary Table 3
Description: Heatmap for the meta-analyzed associations of microbial species with T2D. The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D) and adjust for age, sex, FDR with a target of 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic
Revision editor(s): YokoC
Signature 2
Source: Figure 2a and Supplementary Table 3
Description: Heatmap for the meta-analyzed associations of microbial species with T2D. The blue-to-red gradient represents the magnitude and direction of the associations quantified by a linear mixed model that includes disease status as an ordinal variable (normoglycemic controls, prediabetes or T2D) and adjust for age, sex, FDR with a target of 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic
Revision editor(s): YokoC
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with type 2 diabetes (diabetes mellitus).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 2277
- Group 1 sample size Number of subjects in the case (exposed) group
- 1851
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Signature 1
Source: Extended data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2D)
Revision editor(s): Fiddyhamma
Signature 2
Source: Extended Data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2D)
Revision editor(s): Tosin, Fiddyhamma
Experiment 6
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Signature 1
Source: Extended data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2D)
Revision editor(s): Fiddyhamma
Signature 2
Source: Extended Data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2D)
Revision editor(s): Tosin, Fiddyhamma
Experiment 7
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: "metformin use" 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.metformin use
Signature 1
Source: Extended data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2D)
Revision editor(s): Fiddyhamma
Signature 2
Source: Extended Data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2D)
Revision editor(s): Tosin, Fiddyhamma
Experiment 8
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "metformin use" 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.metformin use
Signature 1
Source: Extended data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2D)
Revision editor(s): Fiddyhamma
Experiment 9
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "metformin use" 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.metformin use, Confounders controlled for: "insulin use" 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.insulin use
Signature 1
Source: Extended data Figure 3B and Supplementary Table 2
Description: Meta- analyzed associations of individual microbial species with type 2 diabetes (T2D) phenotype from the binary (b) models.The binary model modeled the disease status as a binary variable (T2D or controls) and used data from T2D patients and normoglycemic controls.
Abundance in Group 1: increased abundance in Type 2 diabetes (T2D)
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea sp. CAG:317 | ||
| Escherichia coli | ||
| Flavonifractor plautii | ||
| Streptococcus parasanguinis | ||
| Streptococcus salivarius |
Revision editor(s): Fiddyhamma
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increased normoglycemic (ordinal model)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Decreased normoglycemic (ordinal model)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "metformin use" 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.metformin use
Signature 1
Source: Figure 2A, Extended Data Figure 3A and Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI), and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic (ordinal model)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Enterocloster bolteae | ||
| Enterocloster citroniae | ||
| Escherichia coli | ||
| Flavonifractor plautii | ||
| Streptococcus parasanguinis | ||
| Streptococcus salivarius |
Revision editor(s): Tosin
Signature 2
Source: Figure 2A, Extended Data Figure 3A and Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI), and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic (ordinal model)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. CAG:167 | ||
| Coprococcus eutactus | ||
| Desulfovibrio piger | ||
| Firmicutes bacterium CAG:238 | ||
| Oscillibacter sp. 57_20 | ||
| Roseburia sp. CAG:182 | ||
| Turicibacter sanguinis |
Revision editor(s): Tosin
Experiment 11
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (diabetes mellitus).
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "metformin use" 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.metformin use, Confounders controlled for: "insulin use" 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.insulin use
Signature 1
Source: Extended Data Figure 3A, Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI),metformin use (metf) and insulin use. For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic (ordinal model)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Enterocloster bolteae | ||
| Enterocloster citroniae | ||
| Escherichia coli | ||
| Flavonifractor plautii | ||
| Streptococcus parasanguinis | ||
| Streptococcus salivarius |
Revision editor(s): Tosin
Signature 2
Source: Extended Data Figure 3A, Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex, body mass index (BMI),metformin use (metf) and insulin use. For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic (ordinal model)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. CAG:167 | ||
| Coprococcus eutactus | ||
| Desulfovibrio piger | ||
| Firmicutes bacterium CAG:238 | ||
| Oscillibacter sp. 57_20 | ||
| Roseburia sp. CAG:182 | ||
| Turicibacter sanguinis |
Revision editor(s): Tosin
Experiment 12
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with decreasing normoglycemic condition, which finalizes in type 2 diabetes (T2D) mellitus
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "metformin use" 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.metformin use
Signature 1
Source: Figure 2A, Extended Data Figure 3A and Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic (ordinal model)
Revision editor(s): Tosin, Fiddyhamma
Signature 2
Source: Figure 2A, Extended Data Figure 3A and Supplementary Table 3
Description: Meta-analyzed associations of microbial species with type 2 diabetes (T2D) based on 8,117 metagenomes from 1,851 T2D patients, 2,770 individuals with prediabetes, and 2,277 normoglycemic controls. The blue-to-red gradient represents the magnitude and direction of the associations quantified by linear mixed models that include disease status as an ordinal variable (normoglycemic controls, prediabetes, or T2D) and adjust for age, sex and metformin use (metf). For multiple comparison correction, we controlled the false discovery rate (FDR) with a target rate of 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic (ordinal model)
Revision editor(s): Tosin
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increased normoglycemic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Decreased normoglycemic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as an ordinal variable (type 2 diabetes, prediabetic, normoglycemic controls).
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, Confounders controlled for: "metformin use" 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.metformin use
Signature 1
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): YokoC
Signature 2
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. CAG:167 |
Revision editor(s): YokoC
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T2D (type 2 diabetes)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female patients with type 2 diabetes (diabetes mellitus) from a binomial model (type 2 diabetes and normoglycemic controls).
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an binomial variable (normoglycemic controls or T2D). FDR < 0.10.
Abundance in Group 1: increased abundance in T2D (type 2 diabetes)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli |
Revision editor(s): YokoC
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Increased normoglycemic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Decreased normoglycemic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as an ordinal variable (type 2 diabetes, prediabetic, normoglycemic controls).
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.
Abundance in Group 1: increased abundance in Decreased normoglycemic
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Collinsella aerofaciens | ||
| Enterocloster asparagiformis | ||
| Enterocloster bolteae | ||
| Enterocloster citroniae | ||
| Eubacterium ventriosum | ||
| Flavonifractor plautii |
Revision editor(s): YokoC
Signature 2
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an ordinal variable (normoglycemic controls, prediabetes or T2D). FDR < 0.10.
Abundance in Group 1: decreased abundance in Decreased normoglycemic
| NCBI | Quality Control | Links |
|---|---|---|
| marine bacterium JAMB33 | ||
| Oscillibacter sp. 57_20 | ||
| Clostridium sp. CAG:253 | ||
| Desulfovibrio piger |
Revision editor(s): YokoC
Experiment 16
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T2D (type 2 diabetes)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as a binomial variable (type 2 diabetes or normoglycemic controls).
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 11
Description: Heatmap of meta-analyzed associations of microbial species with T2D (type 2 diabetes). The blue-to-red gradient represents the magnitude and direction of the associations quantified by Maaslin2, where the disease status is an binomial variable (normoglycemic controls or T2D). FDR < 0.10.
Abundance in Group 1: increased abundance in T2D (type 2 diabetes)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterocloster citroniae |
Revision editor(s): YokoC
Signature 2
Source: Supplementary Table 11
Description: Male patients with type 2 diabetes (diabetes mellitus), from a model where the disease status was treated as a binomial variable (type 2 diabetes or normoglycemic controls).
Abundance in Group 1: decreased abundance in T2D (type 2 diabetes)
| NCBI | Quality Control | Links |
|---|---|---|
| Firmicutes bacterium CAG:238 | ||
| Coprococcus eutactus CAG:665 |
Revision editor(s): YokoC
