Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs/Experiment 12
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_14dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_14dpw 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 14 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: Fig 5D, Suppl fig 4 and text
Description: Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_14dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus fermentans | ||
| Clostridium sp. SY8519 | ||
| Agathobacter rectalis |
Revision editor(s): Fiddyhamma
