Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis/Experiment 19

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Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

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

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

Response to diet Response to diet,response to diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Recovery oats Day 0 Abx

Group 1 name Corresponds to the case (exposed) group for case-control studies

Recovery oats Day 14 Post Abx

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Recovery oats without amoxicillin fecal pellets that were collected on day 14

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

4

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

None

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

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).

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

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged