Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial
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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
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Acute pancreatitis acute necrotizing pancreatitis,acute pancreatic necrosis,acute pancreatitis,acute pancreatitis (disorder) [ambiguous],pancreatitis necrotizing,pancreatitis, acute,Acute pancreatitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (Con)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rifaximin (Rif)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice/patients with SAP receiving rifaximin intervention
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
Signature 1
Source: Figure 2E & 2F
Description: (E) Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group. (F) Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis.
Abundance in Group 1: increased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 2E & 2F
Description: (E) Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group. (F) Wilcoxon rank-sum test identified the most differentially decreased phyla and genera between Cer + Bom group and Cer + Bom + Rif group. *P < 0.05, **P < 0.01, and ***P < 0.001. Rif, rifaximin; Cer, caerulein; Bom, bombesin; Con, control; PCoA, principal coordinate analysis.
Abundance in Group 1: decreased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Experiment 2
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7A & 7B
Description: Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (A) The top 30 differentially abundant bacterial species before and after treatment in the control group. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
Abundance in Group 1: increased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 7A & 7B
Description: Rifaximin induces specific alterations in the decrease and function of the gut microbiota in patients predicted to SAP. (A) The top 30 differentially abundant bacterial species before and after treatment in the control group. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
Abundance in Group 1: decreased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Experiment 3
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: Table S7 & Table S8
Description: The abundance of gut microbiota had specific alterations at the phylum, genus, and species levels. At the phylum level, rifaximin decreased Verrucomicrobia and Fibrobacteres (P < 0.05) (Table S7). At the genus level, significant reductions in mucin-degrading genera, such as Akkermansia and Hungatella, were observed in the fecal samples (P < 0.05) (Table S8).
Abundance in Group 1: increased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Signature 2
Source: Table S7 & Table S8
Description: The decreased of gut microbiota had specific alterations at the phylum, genus, and species levels. At the phylum level, rifaximin decreased Verrucomicrobia and Fibrobacteres (P < 0.05) (Table S7). At the genus level, significant reductions in mucin-degrading genera, such as Akkermansia and Hungatella, were observed in the fecal samples (P < 0.05) (Table S8).
Abundance in Group 1: decreased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
