Abstract
A study was conducted on 500 juvenile rainbow trout (122 ± 4 g) fed either a control diet or a treatment diet containing 300 mg/kg of a microencapsulated blend of organic acids and essential oils to elucidate effects on intestinal morphology and microbiome. Proximal intestinal villi length was significantly increased in fish fed the treatment diet. Despite no differences in gut inflammation scores, edema, lamina propria inflammation and apoptosis were completely absent in the distal intestine of fish fed the treatment diet. Next-generation sequencing of the 16S rDNA showed no differences in alpha and beta diversity, and gut bacteria were mainly composed of Firmicutes, Bacteroidetes and Proteobacteria. On the genus level, LefSe analysis of indicator OTUs showed Bacteroides, Sporosarcina, Veillonella, Aeromonas and Acinetobacter were associated with the control diet whereas Streptococcus, Fusobacterium and Escherichia were associated with the treatment diet. Aeromonas hydrophila and Acinetobacter spp. are opportunistic pathogens and several strains have been found to be resistant to antibiotics. The increase in villi length and reduction of specific pathogens indicates that feeding a microencapsulated blend of organic acids and essential oils improves gut health and may serve as a part of an effective strategy to reduce antibiotic use in aquaculture.