Gut microbiota dysbiosis and diarrhea in kidney transplant recipients
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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
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea Diarrhea,Diarrhoea,Watery stool
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls (No Diarrhea Group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhea Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Applicable, but exact duration not specified
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 2
Description: Differential microbial abundance between Controls and Diarrhea group
Abundance in Group 1: decreased abundance in Diarrhea Group
Revision editor(s): Ufuoma Ejite
Signature 2
Source: Figure 2
Description: Differential microbial abundance between Controls and Diarrhea group
Abundance in Group 1: increased abundance in Diarrhea Group
NCBI | Links |
---|---|
Enterococcus � | |
Escherichia � | |
Lachnoclostridium � |
Revision editor(s): Ufuoma Ejite
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antibiotic-excluded Controls (No Diarrhea Group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic-excluded Diarrhea Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Antibiotic-excluded diarrheal group; Kidney transplant recipients that developed post-transplant diarrhea within the first 3 months after transplantation
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Applicable; but exact duration not specified
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.15
- 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
- antibiotic exposure
Signature 1
Source: Table S2
Description: Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group
Abundance in Group 1: decreased abundance in Antibiotic-excluded Diarrhea Group
NCBI | Links |
---|---|
Eubacterium � | |
Coprococcus � | |
Anaerostipes � | |
Romboutsia | |
Dorea � | |
Faecalibacterium � | |
Ruminococcus � | |
Fusicatenibacter � | |
Bifidobacterium � | |
Oscillibacter � | |
Ruminiclostridium |
Revision editor(s): Ufuoma Ejite
Signature 2
Source: Table S2
Description: Differential microbial abundance between Antibiotic-excluded Controls and Antibiotic-excluded Diarrhea group
Abundance in Group 1: increased abundance in Antibiotic-excluded Diarrhea Group
NCBI | Links |
---|---|
Lachnoclostridium � | |
Escherichia � |
Revision editor(s): Ufuoma Ejite
Signature 3
Source:
Description:
Abundance in Group 1:NCBI | Links |
---|---|
Revision editor(s): Ufuoma Ejite
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 1000 mg/day MMF Dosage No Diarrhea Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2000 mg/day MMF Dosage No Diarrhea Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2000 mg/day MMF Dosage administered to the No Diarrhea Group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- intake of diabetes medication
Signature 1
Source: Table S4
Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage No Diarrhea Group
Abundance in Group 1: decreased abundance in 2000 mg/day MMF Dosage No Diarrhea Group
NCBI | Links |
---|---|
Erysipelotrichaceae |
Revision editor(s): Ufuoma Ejite
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 1000 mg/day MMF Dosage Diarrhea Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 1000 mg/day MMF Dosage administered to the Diarrhea Group
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Table S5
Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group
Abundance in Group 1: decreased abundance in 1000 mg/day MMF Dosage Diarrhea Group
NCBI | Links |
---|---|
Bacteroides � | |
Eubacterium � | |
Oscillibacter � | |
Dorea � | |
Ruminococcus � | |
Anaerostipes � | |
Faecalibacterium � | |
Romboutsia | |
Fusicatenibacter � |
Revision editor(s): Ufuoma Ejite
Signature 2
Source: Table S5
Description: Differential microbial abundance between 1000 mg/day MMF Dosage No Diarrhea Group and 1000 mg/day MMF Dosage Diarrhea Group
Abundance in Group 1: increased abundance in 1000 mg/day MMF Dosage Diarrhea Group
NCBI | Links |
---|---|
Enterococcus � | |
Escherichia � |
Revision editor(s): Ufuoma Ejite
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2000 mg/day MMF Dosage No Diarrhea Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2000 mg/day MMF Dosage Diarrhea Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2000 mg/day MMF Dosage administered to the Diarrhea Group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Signature 1
Source: Table S6
Description: Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group
Abundance in Group 1: decreased abundance in 2000 mg/day MMF Dosage Diarrhea Group
NCBI | Links |
---|---|
Eubacterium � | |
Coprococcus � | |
Anaerostipes � | |
Ruminococcus � | |
Faecalibacterium � | |
Romboutsia | |
Ruminiclostridium | |
Dorea � | |
Oscillibacter � | |
Bifidobacterium � | |
Fusicatenibacter � | |
Blautia � |
Revision editor(s): Ufuoma Ejite
Signature 2
Source: Table S6
Description: Differential microbial abundance between 2000 mg/day MMF Dosage No Diarrhea Group and 2000 mg/day MMF Dosage Diarrhea Group
Abundance in Group 1: increased abundance in 2000 mg/day MMF Dosage Diarrhea Group
NCBI | Links |
---|---|
Enterococcus � |
Revision editor(s): Ufuoma Ejite