GSE159583
Exploring with transcriptomic approaches the underlying mechanisms of essential oils-based phytogenic in the small intestine and liver of pigs
Purpose:  The study aims the evaluation by RNA-Seq of the anti-oxidant properties of PFA on ileum and liver of pigs. At day 28, for both tissues, 6 biological replicates per groups Method : Ileum & liver mRNA profile of 28-day-old pigs were generated by NextSeq sequencing (2*75, 30 Mio per strand). Sequenced reads were trimmed by bbmap, aligned by STAR on the SusScrofa 11.1 reference genome. Quantification was performed by HTSeq-count. RT-qPCR validation was performed using TaqMan and SYBR green assays. Results: In the ileum, the gene set enrichment analysis showed that the activity of several immune pathways (NF-kB, interferon a/ß, antimicrobial peptide, collagen pathways) was reduced in piglets fed PFA compared to the control piglets. In the liver, the addition of OO induced strong effects on the transcriptome, and most likely accounted for the significant growth impairment. The likelihood ratio test across the four diets revealed a global response driven by the oxidative stress challenge with hundreds of genes associated with fatty acid ß-oxidation and peroxisome in the liver. The expression levels of those genes in the piglets fed OO+PFA were much less affected by the challenge. Conclusions : The effects seen at day 28 suggest that substances in the PFA formulation provide anti-inflammatory and -oxidant properties. Overall design: Ileum & liver mRNA from 28 day old pigs. For each tissue, 6 biological replicates (= 6 pigs) per groups (Control, Phytogenics Feed Additive, Oxidized Oil, Phytogenics Feed Additive+Oxidized Oil).