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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- 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
- Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.
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
Description: Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.
Abundance in Group 1: increased abundance in Rifaximin (Rif)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Staphylococcus | ||
| Lactobacillus | ||
| Corynebacterium | ||
| Klebsiella | ||
| Sporosarcina |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 2E
Description: Wilcoxon rank-sum test identified the most differentially abundant phyla and genera between Con group and Rif group.
Abundance in Group 1: decreased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Experiment 2
Subjects
- 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 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 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.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2F
Description: 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)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacterota | ||
| Desulfovibrio | ||
| Helicobacter | ||
| Thermodesulfobacteriota |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 2F
Description: 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: decreased abundance in Rifaximin (Rif)
Revision editor(s): SheikhAlMamun
Experiment 3
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Con_T0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Con_T1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. The top 30 differentially abundant bacterial species before and after treatment in the control group.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 0
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- 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
Statistical Analysis
Signature 1
Source: Figure 7A
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.
Abundance in Group 1: increased abundance in Con_T1
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 7A
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.
Abundance in Group 1: decreased abundance in Con_T1
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus faecium | ||
| Escherichia_coliEscherichia_coli | ||
| Bacteroides stercoris | ||
| Parabacteroides merdae | ||
| Blautia_sporothermoduransBlautia_sporothermodurans |
Revision editor(s): SheikhAlMamun
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- (Lower in RL_T1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- (Higher in RL_T1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
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: Figure 7B
Description: Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
Abundance in Group 1: increased abundance in (Higher in RL_T1)
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 7B
Description: Fig 7 Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
Abundance in Group 1: decreased abundance in (Higher in RL_T1)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter hormaechei | ||
| Streptococcus parasanguinis | ||
| Lachnospiraceae bacterium | ||
| Ruminiclostridium | ||
| Prevotella sp. | ||
| Alistipes putredinis |
Revision editor(s): SheikhAlMamun
Signature 3
Source: Figure 7B
Description: Fig 7 Rifaximin induces specific alterations in the abundance and function of the gut microbiota in patients predicted to SAP. (B) The top 30 differentially abundant bacterial species before and after treatment in the rifaximin group.
Abundance in Group 1: decreased abundance in (Higher in RL_T1)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Bacteroides thetaiotaomicron | ||
| Bacteroides caccae | ||
| Enterocloster bolteae | ||
| Streptococcus parasanguinis | ||
| Enterobacter hormaechei |
Revision editor(s): SheikhAlMamun
