Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Chronic kidney disease chronic kidney disease,chronic kidney failure,Chronic Kidney Insufficiencies,Chronic Kidney Insufficiency,chronic renal disease,Chronic Renal Failure,chronic renal failure syndrome,Chronic Renal Insufficiencies,chronic renal insufficiency,CKD,CKD - chronic kidney disease,Disease, End-Stage Kidney,Disease, End-Stage Renal,END STAGE KIDNEY DIS,End Stage Kidney Disease,END STAGE RENAL DIS,End Stage Renal Disease,End-Stage Kidney Disease,End-Stage Renal Disease,End-Stage Renal Failure,ESRD,kidney disease, chronic,Kidney Disease, End-Stage,Kidney Failure, Chronic,Kidney Insufficiencies, Chronic,Kidney Insufficiency, Chronic,RENAL DIS END STAGE,Renal Disease, End Stage,Renal Disease, End-Stage,renal failure - chronic,Renal Failure, Chronic,Renal Failure, End Stage,Renal Failure, End-Stage,Renal Insufficiencies, Chronic,Renal Insufficiency, Chronic,Chronic kidney disease
- 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
- Chronic Kidney Disease (CKD G3-G4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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: increased abundance in Chronic Kidney Disease (CKD G3-G4)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Parasutterella | ||
| Ruminococcus | ||
| Thomasclavelia | ||
| Clostridiales Vadin groupClostridiales Vadin group | ||
| Unknown genusUnknown genus | ||
| Cyanobacteriota |
Revision editor(s): MyleeeA
Signature 2
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: decreased abundance in Chronic Kidney Disease (CKD G3-G4)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Parabacteroides | ||
| [Ruminococcus] torques | ||
| Ruminococacceae NK4A214Ruminococacceae NK4A214 |
Revision editor(s): MyleeeA
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- 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 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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 Control | Links |
|---|---|---|
| Acetanaerobacterium | ||
| Bacteroides | ||
| Barnesiella | ||
| Citrobacter | ||
| Dielma | ||
| Thomasclavelia |
Revision editor(s): MyleeeA
Signature 2
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 Control | Links |
|---|---|---|
| Cyanobacteriota | ||
| Actinomycetota | ||
| Mycoplasmatota | ||
| Subdoligranulum | ||
| Tyzzerella | ||
| Fusicatenibacter | ||
| Bifidobacterium | ||
| Unknown genusUnknown genus |
Revision editor(s): MyleeeA
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Kidney transplant Kidney transplant,kidney transplant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Kidney transplantation (KT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients after successful KT, at an earliest of 4 weeks after KT, without a history of rejection or chronic graft failure, and an eGFR of >60 ml/min per 1.73 m2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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: increased abundance in Kidney transplantation (KT)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacterium | ||
| Parabacteroides | ||
| Bacteroides | ||
| Barnesiella |
Revision editor(s): MyleeeA
Signature 2
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: decreased abundance in Kidney transplantation (KT)
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus |
Revision editor(s): MyleeeA
Experiment 4
Subjects
- 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
- Chronic Kidney Disease (CKD)
- 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
- 7
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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 Control | Links |
|---|---|---|
| Barnesiella | ||
| Escherichia/Shigella sp. |
Revision editor(s): MyleeeA
Signature 2
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)
Revision editor(s): MyleeeA
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chronic kidney disease chronic kidney disease,chronic kidney failure,Chronic Kidney Insufficiencies,Chronic Kidney Insufficiency,chronic renal disease,Chronic Renal Failure,chronic renal failure syndrome,Chronic Renal Insufficiencies,chronic renal insufficiency,CKD,CKD - chronic kidney disease,Disease, End-Stage Kidney,Disease, End-Stage Renal,END STAGE KIDNEY DIS,End Stage Kidney Disease,END STAGE RENAL DIS,End Stage Renal Disease,End-Stage Kidney Disease,End-Stage Renal Disease,End-Stage Renal Failure,ESRD,kidney disease, chronic,Kidney Disease, End-Stage,Kidney Failure, Chronic,Kidney Insufficiencies, Chronic,Kidney Insufficiency, Chronic,RENAL DIS END STAGE,Renal Disease, End Stage,Renal Disease, End-Stage,renal failure - chronic,Renal Failure, Chronic,Renal Failure, End Stage,Renal Failure, End-Stage,Renal Insufficiencies, Chronic,Renal Insufficiency, Chronic,Chronic kidney disease
- 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
- Chronic Kidney Disease (CKD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic Kidney Disease (CKD) stage G3–G4 and an eGFR of 15–60 ml/min per 1.73 m2.
- 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
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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 Chronic Kidney Disease (CKD)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Eubacterium coprostanoligenes | ||
| Holdemanella | ||
| Parasutterella | ||
| Clostridiales vadin groupClostridiales vadin group |
Revision editor(s): MyleeeA
Signature 2
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: decreased abundance in Chronic Kidney Disease (CKD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): MyleeeA
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- 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 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
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 Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Barnesiella | ||
| Butyricimonas | ||
| Faecalitalea | ||
| Prevotella |
Revision editor(s): MyleeeA
Signature 2
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 Control | Links |
|---|---|---|
| Subdoligranulum | ||
| Ruminococcus | ||
| Cyanobacteriota | ||
| Ruminiclostridium | ||
| Unknown genusUnknown genus |
Revision editor(s): MyleeeA
