Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Ireland
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- 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
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-medicated control (CT) global data set
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic (Ab) global data set
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Piglets treated with antibiotics Global data set involves both consistency and Day post weaning (dpw) factors
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).
- relative abundances
- Statistical test
- LEfSe
- 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
Signature 1
Needs review
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: increased abundance in Antibiotic (Ab) global data set
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera elsdenii | ||
| Megasphaera | ||
| Negativicutes | ||
| Veillonellaceae | ||
| Veillonellales | ||
| Limosilactobacillus reuteri |
Revision editor(s): Fiddyhamma
Signature 2
Needs review
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: decreased abundance in Antibiotic (Ab) global data set
Revision editor(s): Fiddyhamma
