Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream () Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization.

New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal and was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of associated with the presence of . The intestinal gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and ) and metal-reducing ( and ) bacteria. Other inflammatory markers (α) were up-regulated in PAP fish, positively correlating the intestinal gene with the inflammasome activator , whereas the systemic expression of and α was negatively correlated with the Bacilli class in PAP fish and positively correlated with in non-PAP fish. Overall changes in the expression pattern of , galectins (), and toll-like receptors () reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of - and -mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.