Exploring With Transcriptomic Approaches the Underlying Mechanisms of an Essential Oil-Based Phytogenic in the Small Intestine and Liver of Pigs.

Phytogenics are plant-based feed additives utilized in animal nutrition to support animal growth and health. Worldwide restrictions and bans on the use of antibiotic growth promoters resulted in an increased demand for in-feed alternatives including phytogenics. However, several challenges remain for technology readiness in animal industry, especially regarding the standardization of the ingredients as well as our knowledge on the cellular mechanisms underlying their biological effects. In the present study, 32 weaned piglets were allocated for 28 days to four experimental diets, a control diet, a phytogenic feed additive (PFA) diet, or the same two diets but with the addition of oxidized oil (OO) at 10%. The last two diets aimed at evaluating the antioxidant properties of PFA. At the end of the trial, the ileum and the liver of the pigs were sampled, and RNA were isolated for profiling their transcriptome via RNA sequencing (RNA-Seq). In the ileum, the gene set enrichment analysis showed that the activity of several immune pathways (NF-kB, interferon α/ß, antimicrobial peptide, and collagen pathways) was reduced in piglets fed PFA compared to the control piglets. As expected, the addition of OO induced strong effects on the liver 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. Collectively, the effects seen at day 28 suggest that substances in the PFA formulation provide anti-inflammatory and antioxidant properties. The use of RNA-Seq in animal nutrition allows exploring and deciphering novel mechanisms of natural growth promoters.

Research Note: Snapshot of the transcriptome via RNA sequencing in the ileum of broiler chickens fed subtherapeutic concentrations of avilamycin.

Antibiotics have played a critical role in sustaining and improving livestock production in the past decades, but the emergence of antimicrobial resistance has led several countries to ban or limit their use. Since then, in-feed alternatives have gained a lot of attention but the development of efficacious alternatives implies a better understanding of the mode of action of antibiotic growth promoters (AGP) when administered at subtherapeutic concentrations. In the present study, 120 broiler chickens per group (8 pens/group) were fed for 35 d with either basal feed (control group) or feed supplemented with avilamycin (AGP group; 10 g/1,000 kg of feed). At the end of the trial, the ileum from the small intestine of 5 birds per group was sampled, and RNA were isolated for profiling their transcriptome via RNA sequencing (RNA-Seq). As expected, the growth of chickens in the AGP group was significantly higher than in the control group. Overall, 66 differentially expressed genes (false discovery rate ≤ 0.05 and fold change ≥ 2 or ≤ -2) were found in the ileum of chickens fed avilamycin in comparison with the control group. The functional analysis showed reduced activity of genes related to signaling by interleukins, with IL-22, SOCS3, and certain antimicrobial peptides found multiple times in these pathways in the AGP group at day 35. In addition, higher activity was predicted in a module of genes related to lipid metabolism and transport in the avilamycin group. The use of RNA-Seq allowed a snapshot of the whole transcriptome at day 35 and aimed at delivering additional data on the host-centric hypothesis regarding the mode of action of AGP (i.e. immunomodulation, reduction of the immunological stress).

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments.