Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy
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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
Curated date: 2021/07/05
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, Claregrieve1, WikiWorks
Subjects
- Location of subjects
- India
- 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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, diet, region, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table 2, Table 3
Description: Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls
Abundance in Group 1: decreased abundance in Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Blautia | ||
| Comamonas | ||
| Coprococcus | ||
| Thermoproteota | ||
| Elusimicrobiota | ||
| Fusobacteriota | ||
| Haemophilus | ||
| Lachnospira | ||
| Phascolarctobacterium | ||
| Roseburia | ||
| Sutterella | ||
| Turicibacter |
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Source: Table 2, Table 3
Description: Increased abundance of microbial communities in individuals with Type 2 Diabetes compared to healthy controls
Abundance in Group 1: increased abundance in Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Butyricimonas | ||
| Enterobacter | ||
| Escherichia | ||
| Methanobacteriota | ||
| Lachnobacterium | ||
| Lentisphaerota | ||
| Methanobrevibacter | ||
| Spirochaetota | ||
| Synergistota | ||
| Treponema | ||
| Weissella |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diabetic retinopathy Diabetic Retinopathies,diabetic retinopathy,retinal abnormality - diabetes-related,Retinopathies, Diabetic,Retinopathy, Diabetic,Diabetic retinopathy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, region, diet
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2021/07/05
Curator: Madhubani Dey
Revision editor(s): Fatima, Madhubani Dey, Claregrieve1
Source: Table 2, Table 4
Description: Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR)
Revision editor(s): Fatima, Madhubani Dey, Claregrieve1
Signature 2
Curated date: 2021/07/05
Curator: Madhubani Dey
Revision editor(s): Fatima, Madhubani Dey, Claregrieve1
Source: Table 2, Table 4
Description: Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR)
Revision editor(s): Fatima, Madhubani Dey, Claregrieve1
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals diagnosed with type 2 diabetes Mellitus
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 2, Table 5
Description: Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes
Abundance in Group 1: decreased abundance in Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR)
Revision editor(s): Madhubani Dey, Claregrieve1
Signature 2
Source: Table 2, Table 5
Description: Differential microbial abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes
Abundance in Group 1: increased abundance in Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alistipes | ||
| Cloacibacillus | ||
| Elusimicrobiota | ||
| Enterococcus | ||
| Phascolarctobacterium | ||
| Shigella | ||
| Synergistota | ||
| Verrucomicrobiota |
Revision editor(s): Madhubani Dey, Claregrieve1
