Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs/Experiment 8
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_7dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw 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 7 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Fig 5E, Suppl fig 5 and text
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw 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: increased abundance in Diarrhoea_7dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Limosilactobacillus reuteri |
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 5C, Suppl fig 3B and text
Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw 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_7dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister massiliensis | ||
| Limosilactobacillus reuteri | ||
| Selenomonadaceae | ||
| Selenomonadales | ||
| Selenomonas sputigena |
Revision editor(s): Fiddyhamma
