Comparison of changes in fecal microbiota of calves with and without dam/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Bos grunniens
- 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
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Calves with dam on day 65
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Calves without dam on day 65
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Calves without dam on day 65 of the whole 95 days formal experimental period.
- 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
- 8
- 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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.
Abundance in Group 1: increased abundance in Calves without dam on day 65
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lactobacillus | ||
| unclassified Oscillospiraceae |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.
Abundance in Group 1: decreased abundance in Calves without dam on day 65
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae bacterium UCG-005 | ||
| Treponema | ||
| Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group | ||
| unclassified Oscillospiraceae |
Revision editor(s): Folakunmi
