A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17
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
- Methionine measurement Methionine measurement,methionine measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mice fed control rodent diet.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mice fed American Diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber
- 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
- 5
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- Mann-Whitney (Wilcoxon)
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17
Source: Table 2
Description: Increased abundance of microbial taxa in AD mice compared with control mice
Abundance in Group 1: increased abundance in mice fed American Diet
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus | ||
| Oscillospira | ||
| Ruminococcus | ||
| unclassified Prevotellaceae | ||
| unclassified Clostridiales Family XVII. | ||
| unclassified Bacillaceae | ||
| Bacillus | ||
| Lactococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17
Source: Table 2
Description: Decreased abundance of microbial taxa in AD mice compared with control mice
Abundance in Group 1: decreased abundance in mice fed American Diet
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Erysipelotrichaceae | ||
| Eubacterium sp. | ||
| unclassified Clostridiaceae | ||
| Clostridium | ||
| Prevotella |
Revision editor(s): Claregrieve1, WikiWorks
