Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments
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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
- Denmark
- 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
- Clostridium difficile infection clostridium difficile disease,Clostridium difficile infection,clostridium difficile infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice Before Clostridioides difficile infection (CDI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Survived mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 7A
Description: Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.
Abundance in Group 1: increased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Bacillota | ||
| Clostridioides difficile | ||
| Clostridium | ||
| Turicibacter sanguinis |
Revision editor(s): Tosin
Signature 2
Source: Figure 7A
Description: Differential abundance of significantly different bacterial taxa Between Before CDI (Clostridioides difficile infection) and Survived mice.
Abundance in Group 1: decreased abundance in Survived mice
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Euthanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that reached a humane endpoint and were euthanized before the intended study termination date.
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 7B
Description: Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and euthanized mice.
Abundance in Group 1: increased abundance in Euthanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Bacteroides | ||
| Clostridioides difficile |
Revision editor(s): Tosin
Signature 2
Source: Figure 7B
Description: Differential abundance of significantly different bacterial taxa between Before CDI (Clostridioides difficile Infection) and euthanized mice.
Abundance in Group 1: decreased abundance in Euthanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillus taiwanensis | ||
| Ligilactobacillus animalis | ||
| Limosilactobacillus vaginalis | ||
| Parasutterella excrementihominis | ||
| Turicibacter sanguinis |
Revision editor(s): Tosin
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Euthanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Survived mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 7C
Description: Differential abundance of significantly different bacterial taxa between euthanized and survived mice.
Abundance in Group 1: increased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridium | ||
| Lactobacillus taiwanensis | ||
| Ligilactobacillus animalis | ||
| Limosilactobacillus vaginalis | ||
| Turicibacter sanguinis |
Revision editor(s): Tosin
Signature 2
Source: Figure 7C
Description: Differential abundance of significantly different bacterial taxa between euthanized and survived mice.
Abundance in Group 1: decreased abundance in Survived mice
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice before Clostridioides difficile infection (CDI)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 7D
Description: Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.
Abundance in Group 1: increased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| VOC5VOC5 | ||
| Tubulavirales | ||
| Crassvirales |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 7D
Description: Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Survived mice.
Abundance in Group 1: decreased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| VOC1VOC1 | ||
| unidentified virus | ||
| unclassified viruses | ||
| Norzivirales | ||
| Durnavirales |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Euthanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that reached a humane endpoint and were euthanized before the intended study termination date.
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 7E
Description: Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Euthanized mice.
Abundance in Group 1: increased abundance in Euthanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Tubulavirales | ||
| Petitvirales |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 7E
Description: Differential abundance of significantly different viral taxa between Before CDI (Clostridioides difficile Infection) and Euthanized mice.
Abundance in Group 1: decreased abundance in Euthanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| unidentified virus | ||
| Norzivirales | ||
| Durnavirales |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Euthanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Survived mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that survived a Clostridioides difficile infection (CDI) followed by one of 4 FVT (fecal virome transplantation), FMT (fecal microbiota transplantaiton) or saline treatments until study termination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 7F
Description: Differential abundance of significantly different viral taxa between Euthanized and Survived mice.
Abundance in Group 1: increased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| VOC5VOC5 |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 7F
Description: Differential abundance of significantly different viral taxa between Euthanized and Survived mice.
Abundance in Group 1: decreased abundance in Survived mice
| NCBI | Quality Control | Links |
|---|---|---|
| Petitvirales | ||
| Durnavirales |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clostridium difficile [Clostridium] difficile,Bacillus difficilis,Clostridium difficile,clostridium difficile
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FVT-UnT (Untreated Fecal Virome Transplantation)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received untreated donor fecal virome material (Before second treatment).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- PCR
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- RT-qPCR
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Linear Regression
Signature 1
Source: Figure 4B
Description: Evaluation of C. difficile abundance by qPCR.
Abundance in Group 1: decreased abundance in FVT-UnT (Untreated Fecal Virome Transplantation)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FVT-ChP (Chemostat-Processed Fecal Virome Transplantation)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received fecal virome material reproduced through chemostat fermentation (Before second treatment).
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Evaluation of C. difficile abundance by qPCR.
Abundance in Group 1: decreased abundance in FVT-ChP (Chemostat-Processed Fecal Virome Transplantation)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FVT-SDT (Solvent-Detergent Treated Fecal Virome Transplantation)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received fecal virome material subjected to solvent-detergent treatment to inactivate enveloped viruses (Before second treatment).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Evaluation of C. difficile abundance by qPCR.
Abundance in Group 1: decreased abundance in FVT-SDT (Solvent-Detergent Treated Fecal Virome Transplantation)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received fecal virome material subjected to solvent-detergent treatment to inactivate enveloped viruses (At termination).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Evaluation of C. difficile abundance by qPCR.
Abundance in Group 1: decreased abundance in FVT-SDT (Solvent-Detergent Treated Fecal Virome Transplantation)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile |
Revision editor(s): Aleru Divine
