Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy/Experiment 1

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

Curated date: 2024/03/12

Curator: Rahila

Revision editor(s): Rahila

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 nephropathy Diabetes with renal manifestations,Diabetes with renal manifestations (disorder),Diabetes-nephrosis syndrome,Diabetes-nephrosis syndrome (disorder),Diabetic Glomerulosclerosis,Diabetic Kidney Disease,diabetic kidney disease,Diabetic Kidney Diseases,Diabetic Nephropathies,diabetic nephropathy,Diabetic renal disease,Diabetic renal disease (disorder),DKD,DMII RENAL UNCNTRLD,DMII RENL NT ST UNCNTRLD,Glomerulosclerosis, Diabetic,Glomerulosclerosis, Nodular,Intracapillary Glomerulosclerosis,Kidney Disease, Diabetic,Kidney Diseases, Diabetic,Kimmelstiel - Wilson disease,Kimmelstiel Wilson Disease,Kimmelstiel Wilson Syndrome,Kimmelstiel-Wilson Disease,Kimmelstiel-Wilson Syndrome,Nephropathies, Diabetic,Nephropathy, Diabetic,Nephrotic syndrome due to diabetes mellitus,Nephrotic syndrome in diabetes mellitus,Nephrotic syndrome in diabetes mellitus (disorder),Nodular Glomerulosclerosis,Renal disorder associated with diabetes mellitus,Syndrome, Kimmelstiel-Wilson,type 1 diabetes nephropathy,type 2 diabetes nephropathy,Diabetic nephropathy

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls (CON)

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). DN is a chronic kidney disease (CKD), which is one of the most common complications of diabetic microangiopathy and the primary cause of end-stage renal disease (ESRD).

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Past 1 month

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

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

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

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

Curated date: 2024/03/12

Curator: Rahila

Revision editor(s): Rahila, ChiomaBlessing

Source: FIG 3 (B)

Description: Differentially abundant taxa identified in the diabetic nephropathy (DN) group compared to the healthy control (CON) group

Abundance in Group 1: increased abundance in Diabetic nephropathy (DN)

Revision editor(s): Rahila, ChiomaBlessing