The present study investigated the effects of three probiotic strains viz. Bacillus coagulans ATCC 7050 (BC), Bacillus licheniformis ATCC 11946 (BL), and Paenibacillus polymyxa ATCC 842 (PP) on growth, immune response and antioxidant enzyme activities, intestinal microbiota, and resistance against isolated Vibrio harveyi HY99 in juvenile northern whiting fish, Sillago sihama. Three hundred and sixty juvenile S. sihama fish (initial weight 0.67 ± 0.002 g) stocked in 12 fiberglass tanks were fed with basal diet void of probiotic inclusion (control, B0), and BC, BL, and PP at 1012 CFU kg−1 feed. After the 56-day experimental period, regardless of the probiotic strain used, there were significant increase (P < 0.05) in the survival rate, final weight, weight gain rate, specific growth rate, protein efficiency ratio, hepatosomatic index, viscerosomatic index; crude protein, crude lipid content in the whole body; superoxide dismutase, alkaline phosphatase, acid phosphatase, glutathione peroxidase levels in the liver and a significant decrease in the feed conversion ratio; aspartate aminotransaminase, alanine aminotransaminase, malondialdehyde levels in the liver (P < 0.05) of the probiotic treated group than the untreated. Congruently, a significantly high (P < 0.05) intestinal villi height, villi width, crypt depth, and muscle thickness, were detected in the probiotic treated groups than the control with the PP group experiencing the highest. Probiotics’ supplementations in diets also revealed a significantly high (P < 0.05) relative abundance of Proteobacteria than the control group contrast to as observed in Firmicutes. Additionally, the PP and BL groups were found to have a significant (P < 0.05) increase in Bacteroidetes and Gemmatimonadetes abundance than the BC and B0 groups. At the genus level, all fish supplemented with probiotic diet had a significantly (P < 0.05) lower abundance of some purportedly pathogenic genera such as Enterovibrio and Shewanella as well as significantly (P < 0.05) higher abundance of purportedly beneficial genera such as Ruegeria, Phyllobacterium, Sphingomonas, and Lactobacillus. Challenge with V. harveyi in a 14-day study revealed highly significant (P < 0.05) protection of probiotic groups than the control; thus, the B0, BC, BL, and PP groups obtained 78 %, 58 %, 53 %, and 43 % cumulative mortality, respectively. Collectively, these results suggest that dietary supplementation of probiotics viz. BC, BL, and PP at 1012 CFU kg−1 feed exert positive effects; however, PP at a similar dosage is recommended due to its highest improvement in the growth, immune response, antioxidant activities, intestinal health, and disease resistance against V. harveyi.
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