Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
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
- Diabetic retinopathy Diabetic Retinopathies,diabetic retinopathy,retinal abnormality - diabetes-related,Retinopathies, Diabetic,Retinopathy, Diabetic,Diabetic retinopathy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals diagnosed with type 2 diabetes Mellitus
- 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 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- 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, sex, region, diet
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
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
