Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs/Experiment 10
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
- Abnormal sample abnormal tissue sample,altered sample,Abnormal sample,abnormal sample
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_0dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_0dpw AB(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 0 post weaning from piglets treated with antibiotics
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: Suppl fig 3A and text
Description: Species associated with each dietary treatment in the analysis of Faecal_0dpw species data, according to LEfSe(Linear discriminant analysis Effect Size), most likely explaining the differences among dietary treatments.
Abundance in Group 1: decreased abundance in Diarrhoea_0dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola salanitronis |
Revision editor(s): Fiddyhamma
