Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Chen H., Wang J., Ouyang Q., Peng X., Yu Z., Wang J., Huang J.
Journal
Frontiers in cellular and infection microbiology
Year
2023
Keywords:
chronic kidney disease, clinical indicators, community composition, end-stage renal disease, gut microbe
Gut microecosystem has been shown to play an important role in human health. In recent years, the concept of the gut-kidney axis has been proposed to explain the potential association between gut microbiota and chronic kidney disease (CKD). Here, a cohort of fecal samples collected from patients with CKD (n = 13) were involved. The composition of gut microbial communities and clinical features in CKD and end-stage renal disease (ESRD) were characterized. Our study focused on the changes in gut microbiome and the correlation with clinical features in patients with CKD and ESRD by analyzing high-throughput sequencing results of collected feces. We elucidated the alterations of gut microbiota in CKD patients at different stages of disease and initially identified the gut microbiota associated with CKD progression. We also combined correlation analysis to identify clinical features closely related to the gut microbiome. Our results offered the possibility of using non-invasive gut microbiome in the early diagnosis of course from CKD to ESRD and provide new insights into the association between clinical features and gut microbiota in CKD.
Experiment 1
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
- 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
- Chronic kidney disease (CKD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- End-stage renal disease (ESRD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with end-stage renal disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
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)
- 0.05
- 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, sex, Matched on: "clinical indicators" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.clinical indicators
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3
Description: Differential abundance between chronic kidney disease (CKD) and end-stage renal disease (ESRD)
Abundance in Group 1: increased abundance in End-stage renal disease (ESRD)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Dubosiella | ||
| Enterococcus | ||
| Faecalitalea | ||
| Geobacter | ||
| Helicobacter | ||
| Raoultibacter | ||
| Staphylococcus |
Revision editor(s): EniolaAde
Signature 2
Source: Figure 3
Description: Differential abundance between chronic kidney disease (CKD) and end-stage renal disease (ESRD)
Abundance in Group 1: decreased abundance in End-stage renal disease (ESRD)
Revision editor(s): EniolaAde
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low HDL_C
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High HDL_C
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High HDL_C in end-stage renal disease
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Spearman Correlation
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure 5
Description: Correlation between genus relative abundance in low HDL_C and high HDL_C
Abundance in Group 1: decreased abundance in High HDL_C
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Revision editor(s): EniolaAde
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low TG
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High TG
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High TG (triglyceride) in end-stage renal disease
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure 3
Description: Correlation between genus relative abundance in low TG and high TG
Abundance in Group 1: decreased abundance in High TG
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Revision editor(s): EniolaAde
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low beta 2-MG
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High beta 2-MG
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High beta 2-MG (beta 2 microglobulin) in end-stage renal disease
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure 3
Description: Correlation between genus relative abundance in low beta 2-MG and high beta 2-MG
Abundance in Group 1: decreased abundance in High beta 2-MG
| NCBI | Quality Control | Links |
|---|---|---|
| Intestinibacter | ||
| Phascolarctobacterium |
Revision editor(s): EniolaAde
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