Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis
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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
Curated date: 2024/03/19
Curator:
Revision editor(s):
Subjects
- Location of subjects
- United States of America
- 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
- Cecum mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Always Dextrose oats Day 5 No Antibiotics (Abx)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Always Dextrose oats Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cecal pellets collected on day 5 from mice that were fed diet supplemented with Always Dextrose oats as a preventive measure during amoxicillin treatment
- 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
- 10
Lab analysis
- Sequencing type
- WMS
- 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).
- 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
Signature 1
Source: Figure 3
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: decreased abundance in
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Signature 2
Source: Figure 3
Description: Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: increased abundance in
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Prophylactic oats Day 5 No Abx
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prophylactic oats Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment
- 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
Signature 1
Source: Fig. 3
Description: Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: increased abundance in Prophylactic oats Day 5 Abx
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 3
Description: Differential abundance in microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: decreased abundance in Prophylactic oats Day 5 Abx
Revision editor(s): KateRasheed, WikiWorks
Experiment 23
Curated date: 2025/02/11
Curator:
Revision editor(s):
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Always Dextrose Day 5 No Abx
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Always Dextrose Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellets collected on day 5 from mice that were fed diet supplemented with always dextrose oats as a preventive measure during amoxicillin treatment
- 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
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
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)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 24
Curated date: 2025/02/11
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Prophylactic oats Day 5 No Abx
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prophylactic oats Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellets collected on day 5 from mice that were fed diet supplemented with Prophylactic oats as a preventive measure during amoxicillin treatment
- 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
Signature 1
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Bacteroidota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 25
Curated date: 2025/02/11
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Always oats Day 5 No Abx
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Always oats Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellets collected on day 5 from mice that were fed diet supplemented with Always oats as a preventive measure during amoxicillin treatment
- 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
Statistical Analysis
Signature 1
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 2B
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by Mann-whitney
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Bacteroidota | ||
| Bacillota |
Revision editor(s): KateRasheed, WikiWorks
