Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Curated date: 2023/10/29
Curator: Chinelsy
Revision editor(s): Chinelsy, Peace Sandy, ChiomaBlessing
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
- Retinopathy eye disease of retina,retina eye disease,retinal disease,retinopathy,Retinopathy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- diabetes mellitus (DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who identify as diabetic patients without retinopathy (DM)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- 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-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Source: Fig.4
Description: Relative abundance of the bacterial community in diabetic patients without retinopathy (DM) and healthy controls (HC)
Abundance in Group 1: increased abundance in diabetes mellitus (DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Megasphaera | ||
| Parabacteroides | ||
| Pasteurellaceae | ||
| Pasteurellales | ||
| Streptococcaceae | ||
| Tannerellaceae | ||
| Veillonella | ||
| unclassified Bacilli |
Revision editor(s): Chinelsy, ChiomaBlessing
