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

Abstract

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).

Keywords: avilamycin; gene set enrichment analysis; ileum; poultry; transcriptomics.

Figure 1

Modular coexpression analysis of the RNA-Seq data set with CEMiTool. (A) Profile plots of the modules M1 to M6. The black line represents the mean expression of all genes for that module across the samples. Samples are shown in the x-axis and colored by treatments (control and avilamycin). (B) Gene set enrichment analyses showing the module activity for each treatment. A positive normalized enrichment score (NES) indicates higher activity or expression of the genes from this module, and a negative NES indicates lower activity or expression of the genes from this module. (C) Over-representation analysis of modules M1 and M4. Bar graphs show the -log₁₀ (adjusted P-value) of the enrichment between genes in modules and gene sets from Reactome pathway database. (D) Gene networks of modules M1 and M4. The most connected genes (hubs) are labeled and colored based on their “origin”: if originally present in the CEMiTool module, they are colored blue; if inserted from the interactions file, they are colored red. The size of the node is proportional to its degree.