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

Curated date: 2023/10/29

Curator: Chinelsy

Revision editor(s): Chinelsy, ChiomaBlessing

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 ControlLinks
Haemophilus
Megasphaera
Parabacteroides
Pasteurellaceae
Pasteurellales
Streptococcaceae
Tannerellaceae
Veillonella
unclassified Bacilli

Revision editor(s): Chinelsy, ChiomaBlessing