Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome
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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
- Systemic inflammatory response syndrome Inflammatory Response Syndrome, Systemic,Sepsis Syndrome,SIRS,Systemic inflammatory response syndrome,systemic inflammatory response syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LPS-induced SIRS (systemic inflammatory response syndrome) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lipopolysaccharide-induced SIRS group represent the disease model receiving treatment. They serve as the primary target for testing the efficacy of therapeutic interventions aimed at reducing inflammation and restoring gut microbiota balance.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
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
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- LPS-induced SIRS (systemic inflammatory response syndrome) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-L Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The (Xuanfei Baidu)XFBD-fed group containing live microbiota
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure S2D
Description: Specific genus variations used for Fecal Microbiota Transplantation effects of SIRS mice.
Abundance in Group 1: decreased abundance in FMT-L Group
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Oscillospiraceae |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-HK Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The (Xuanfei Baidu)XFBD-fed group containing heat-killed microbiota
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S2A
Description: Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.
Abundance in Group 1: increased abundance in FMT-HK Group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: Figure S2D
Description: Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.
Abundance in Group 1: decreased abundance in FMT-HK Group
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Oscillospiraceae |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- MD (cultured model)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- A2.1 (gut microbiome remodeling compound)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 2
Source: Figure S5D
Description: The relative abundance in genus levels after cocktail treatment
Abundance in Group 1: decreased abundance in A2.1 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Enterobacter | ||
| Escherichia/Shigella sp. |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 16
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD2 (Patient sample 2 with DMSO)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PC2 (Patient sample 2 treated with cocktail c)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patient sample treated with cocktail c
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure S6A and S6C
Description: The relative abundance in Phylum and genera levels
Abundance in Group 1: decreased abundance in PC2 (Patient sample 2 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroidia | ||
| Parabacteroides | ||
| Pseudomonadota |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: Figure S6A
Description: The relative abundance level in Phylum levels
Abundance in Group 1: increased abundance in PC2 (Patient sample 2 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD4 (Patient sample 4 with DMSO)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PC4 (Patient sample 4 treated with cocktail c)
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
- unchanged
Signature 1
Source: Figure S6A and S6C
Description: the relative abundance in Phylum and genera levels
Abundance in Group 1: decreased abundance in PC4 (Patient sample 4 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Enterobacter | ||
| Pseudomonadota | ||
| Bacteroidia |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: figure S6A and S6C
Description: The relative abundance in Phylum and genera levels
Abundance in Group 1: increased abundance in PC4 (Patient sample 4 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Escherichia/Shigella sp. |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 20
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PD8 (Patient sample 8 with DMSO)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PC8 (Patient sample 8 treated with cocktail c)
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
Signature 1
Source: Figure S6A and S6C
Description: The relative abundance in Phylum and genera levels
Abundance in Group 1: decreased abundance in PC8 (Patient sample 8 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Escherichia/Shigella sp. |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: Figure S6A and S6C
Description: The relative abundance in Phylum and genera levels
Abundance in Group 1: increased abundance in PC8 (Patient sample 8 treated with cocktail c)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bifidobacterium |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H (Healthy Volunteers)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- P (Patients with SIRS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with SIRS
- 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
- 8
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 8C
Description: Abundance comparison of key genera between SIRS patients and healthy volunteers.
Abundance in Group 1: increased abundance in P (Patients with SIRS)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Lactobacillus | ||
| Bacteroides | ||
| Enterobacter | ||
| Lachnoclostridium | ||
| Escherichia/Shigella sp. | ||
| Akkermansia | ||
| Pseudomonas | ||
| Ralstonia | ||
| Dysgonomonas |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: Figure 8C
Description: Abundance comparison of key genera between SIRS patients and healthy volunteers
Abundance in Group 1: decreased abundance in P (Patients with SIRS)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Streptococcus | ||
| Blautia | ||
| Fusicatenibacter | ||
| Faecalibacterium | ||
| Dorea | ||
| Agathobacter | ||
| Romboutsia |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 22
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- MD (cultured model)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B2.2 (gut microbiome remodeling compound)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
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
- unchanged
Signature 2
Source: Figure S5D
Description: The relative abundance in genus levels after cocktail treatment
Abundance in Group 1: decreased abundance in B2.2 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 26
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- D2.2 (gut microbiome remodeling compound)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure S5D
Description: The relative abundance in genus levels after cocktail treatment
Abundance in Group 1: increased abundance in D2.2 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus |
Revision editor(s): Ifeanyisam, WikiWorks
Signature 2
Source: Figure S5D
Description: The relative abundance in genus levels after cocktail treatment
Abundance in Group 1: decreased abundance in D2.2 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): Ifeanyisam, WikiWorks
Experiment 28
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- E2.2 (gut microbiome remodeling compound)
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
- unchanged
Signature 1
Source: Figure S5D
Description: the relative abundance in genus levels after cocktail treatment
Abundance in Group 1: decreased abundance in E2.2 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Escherichia/Shigella sp. | ||
| Bacteroides |
Revision editor(s): Ifeanyisam, Victoria, WikiWorks
Experiment 29
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F2.1 (gut microbiome remodeling compound)
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
- unchanged
Signature 1
Source: Figure S5D
Description: The relative abundance in genus levels after cocktail treatment
Abundance in Group 1: decreased abundance in F2.1 (gut microbiome remodeling compound)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Bacteroides | ||
| Enterobacter |
Revision editor(s): Ifeanyisam, WikiWorks
