Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-2-11
Curated date: 2024/03/19
Curator: Barrakat
Revision editor(s): WikiWorks, Svetlana up, Victoria, Barrakat, Tosin, KateRasheed
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
- Response to diet Response to diet,response to diet
- 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
Reviewed Marked as Reviewed by Svetlana up on 2025-2-11
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 Always Dextrose oats Day 5 Abx
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-2-11
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 Always Dextrose oats Day 5 Abx
Revision editor(s): Barrakat, KateRasheed, WikiWorks
