The influence of liver transplantation on the interplay between gut microbiome and bile acid homeostasis in children with biliary atresia
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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
- Austria
- 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
- Biliary atresia atresia of bile duct,Atresia of bile ducts,atresia of bile ducts,biliary atresia,biliary atresia, congenital,congenital biliary atresia,isolated atresia of bile ducts,isolated biliary atresia,Non-syndromic biliary atresia,non-syndromic biliary atresia,Biliary atresia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Children with BA before - [pre]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post24 + m
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The impact of LT and reestablishment of bile flow on gut microbiome–bile acid homeostasis in children with BA for more than 24 months (post24 + m) after liver transplantation (LT)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
- LEfSe
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: FIGURE 3
Description: Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m
Abundance in Group 1: increased abundance in Post24 + m
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Clostridia | ||
| Coriobacteriales | ||
| Coriobacteriia | ||
| Deltaproteobacteria | ||
| Desulfovibrionales | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Eubacteriales |
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 3
Description: Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (C) Cladogram of LEfSe analysis results of pre and post24 + m groups on the taxonomic order level. Over-representation of taxa is color-coded in red (post24 + m) and green (pre). Radiating circle depicts phylum to order level. (E) Barchart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m
Abundance in Group 1: decreased abundance in Post24 + m
| NCBI | Quality Control | Links |
|---|---|---|
| Micrococcales | ||
| Campylobacterales | ||
| Bacillales | ||
| Lactobacillales | ||
| Bacilli |
Revision editor(s): Peace Sandy
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- post 24 + m Control
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: FIGURE 3
Description: Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (D) Cladogram of LEfSe analysis results of post24 + m and age-matched control groups (p24 + m control) on the taxonomic order level. Over-representation of taxa is color-coded in red (p24 + m control) and green (post24 + m). Radiating circle depicts phylum to order level. Bar chart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m in (F)
Abundance in Group 1: increased abundance in Post24 + m
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Gammaproteobacteria |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3
Description: Differential abundances and linear discriminant effect size analysis (LEfSe) of gut microbiota. (D) Cladogram of LEfSe analysis results of post24 + m and age-matched control groups (p24 + m control) on the taxonomic order level. Over-representation of taxa is color-coded in red (p24 + m control) and green (post24 + m). Radiating circle depicts phylum to order level. Bar chart of LDA values with significantly different abundances to order level is shown comparing pre versus post24 + m, and healthy versus post24 +m in (F)
Abundance in Group 1: decreased abundance in Post24 + m
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriales | ||
| Actinomycetota | ||
| Eubacteriales | ||
| Clostridia |
Revision editor(s): Peace Sandy
