Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT
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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
- Italy
- 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
- graft versus host disease disease, graft-versus-host,disease, graft-VS-host,disease, homologous wasting,disease, runt,diseases, graft-versus-host,diseases, graft-VS-host,graft versus host disease,graft VS host disease,graft VS. host disease,graft-versus-host disease,graft-versus-host disease, resistance to,graft-versus-host disease, susceptibility to,graft-versus-host diseases,graft-versus-host-disease,graft-VS-host disease,graft-VS-host diseases,GVH,GVHD,GVHDS,homologous wasting disease,runt disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre- engraftment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post- engraftment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- malignant or non-malignant disease patients from four transplantation centers (Bologna, Pavia, Rome and Verona) that underwent allogeneic hematopoietic stem cell transplant with or without myeloablative conditioning regimen, who did not develop acute graft-versus-host disease post- enrichment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
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
- 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
Signature 1
Source: Figure 3b, c, d, and supplemental table S1, text
Description: Average relative abundances in pre-HSCT and engrafment samples, of the main discriminant genera between the two time points in subjects who did not develop acute graft-versus- host disease (non-aGvHD)
Abundance in Group 1: decreased abundance in post- engraftment
NCBI | Quality Control | Links |
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Blautia | ||
Dorea | ||
Roseburia | ||
Faecalibacterium | ||
Oscillospira |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- malignant or non-malignant disease patients from four transplantation centers (Bologna, Pavia, Rome and Verona) that underwent allogeneic hematopoietic stem cell transplant with or without myeloablative conditioning regimen, who developed skin acute graft-versus-host disease post- enrichment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3b, c, d, and supplemental table S1, text
Description: Average relative abundances in pre-HSCT and engrafment samples, of the main discriminant genera between the two time points in subjects who developed acute graft-versus- host disease (I-II grade) at a skin level (Skin aGvHD)
Abundance in Group 1: decreased abundance in post- engraftment
NCBI | Quality Control | Links |
---|---|---|
Bifidobacterium | ||
Coprococcus | ||
Dorea | ||
Lachnospira | ||
Roseburia | ||
Ruminococcus | ||
Oscillospira |
Revision editor(s): WikiWorks