Integrated multi-omics approach reveals novel associations in the rapeseed diet-microbiota-host axis in pigs

Diet-mediated host-microbiota interplay is a key factor in optimizing the gut function and overall health of the host. Gaining insight into the biological mechanisms behind this relationship is fundamental to finding sustainable, environment-friendly feed solutions in livestock production systems. Here, we apply a multi-omics integration approach to elucidate sustainable diet-associated host-gut microbiota interactions in pigs and we demonstrate novel and biologically relevant host-microbe associations in the gut, driven by a rapeseed meal-based feed (RSF). Interestingly, RSF-diet promoted the abundance of segmented filamentous bacteria Candidatus Arthromitus that was associated with the maintenance of mucosal immunity in the ileum of pigs. In the colon, RSF diet affected host mRNA splicing functions, which may result in different host gene products, through host-microbiota associations, particularly with the Faecalibacterium population, and through the interaction of dietary components such as sinapic acid with the host cells. Moreover, telomere maintenance and organization functions that may determine the overall health of the host were upregulated and notably associated with Subdoligranulum population in the colon of RSF diet-fed pigs. This integrative multi-omics approach provides more insight into the diet-microbiota-host axis, and a better understanding of mechanisms and opportunities to find new strategies for modulating host health and potentially improving caloric and nutritional efficiency in animal production. Graphical AbstractThe most remarkable associations identified between bacterial groups or sinapic acid and host functional pathways in the ileum and colon of the rapeseed diet fed pigs, compared to control diet fed pigs. Bidirectional arrows indicate the associations between the variables (bacteria, sinapic acid, or functional pathways) identified by the multi-omics integration analysis. The upward arrows next to the variable names indicate the higher levels of these variables in ileum or colon of the RSF diet-fed pigs compared to the CON diet-fed pigs. Bacterial groups were shown in green circles, host functional pathways in purple circles, and sinapic acid in blue circle. Created by BioRender.com.