Gut microbiome alterations precede graft rejection in kidney transplantation patients/Experiment 4
From BugSigDB
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
- Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rejection (Sample 1-Pre rejection)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rejection (Sample 2-Post rejection)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the Rejection group were those who showed rejection after kidney transplantation within a timeframe of 90 to 1000 days post rejection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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, chronic kidney disease, time, sex, Matched on: "Donor type" 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.Donor type
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 5d
Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).
Abundance in Group 1: increased abundance in Rejection (Sample 2-Post rejection)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Faecalibacterium |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 5d
Description: Differential abundance analysis of bacterial taxa between Rejection (Pre Rejection) and Rejection (Post Rejection).
Abundance in Group 1: decreased abundance in Rejection (Sample 2-Post rejection)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Streptococcus |
Revision editor(s): MyleeeA
