Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance/Experiment 6

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-5-5

Curated date: 2025/04/22

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects
Germany
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
Clinical treatment Clinical treatment,clinical treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Kidney transplantation (KT)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Hemodialysis (HD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Chronic Kidney Disease stage G5D, receiving maintenance Hemodialysis (HD), and enrolled at an earliest of 4 weeks after initiation of Hemodialysis (HD).
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
8
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).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-5-5

Curated date: 2025/04/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2D

Description: Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.

Abundance in Group 1: increased abundance in Hemodialysis (HD)

NCBI Quality ControlLinks
Alistipes
Bacteroides
Barnesiella
Butyricimonas
Faecalitalea
Prevotella

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-5-5

Curated date: 2025/04/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2D and Supplementary Figure 2

Description: Taxonomic changes in the abundance of taxa on the genus, family, and phylum level. The heatmap shows significant changes in abundance using the DESeq2.

Abundance in Group 1: decreased abundance in Hemodialysis (HD)

NCBI Quality ControlLinks
Subdoligranulum
Ruminococcus
Cyanobacteriota
Ruminiclostridium
Unknown genusUnknown genus

Revision editor(s): MyleeeA