Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy/Experiment 3

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-5

Curated date: 2024/03/13

Curator: Rahila

Revision editor(s): Rahila, 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

Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

type 2 diabetes mellitus (T2DM)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Diabetic nephropathy (DN)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with diabetic nephropathy (DN).

Group 0 sample size Number of subjects in the control (unexposed) group

12

Group 1 sample size Number of subjects in the case (exposed) group

12

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

Past 1 month

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

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

2.0

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Richness Number of species

unchanged