In Vitro and In Vivo Evaluation of Autochthonous Probiotics and Their Effects on the Mucosal Health of Nile Tilapia (Oreochromis niloticus)

The host microbiome is a promising source of probiotics for aquaculture species including Nile tilapia. In this study, the probiotic potential of autochthonous bacterial isolates from Nile tilapia and carp mid-intestines were screened <i>in vitro</i>. Two isolates (C61 and T70), closely related to <i>Bacillus subtilis</i>, exhibited antagonistic activity against multiple pathogen species and demonstrated multiple digestive enzyme activities. Their antagonistic activity in <i>Aeromonas hydrophila</i> assays remained even under simulated intestinal juice (SIJ) exposure. Subsequently, C61 (PT1) and T70 (PT2) were added to experimental diets at log 7 CFU/g of diet, and fed to Nile tilapia (5.32 ± 0.12 g) for 40 days. There were no significant differences observed in the growth performance across treatments. Despite limited <i>Bacillus</i> intestinal recovery levels, 16S rRNA gene metabarcoding revealed subtle shifts in the intestinal microbial community composition of the probiotic-fed groups. In addition, the PT1 group showed significantly longer mucosal fold length, elevated intestinal and skin goblet cell levels, and higher skin goblet cell coverage compared to the control. These results indicate the potential benefits of the isolates as functional feed additives for enhancing the mucosal health of Nile tilapia, but their benefits were likely achieved through transient activity given the low level of <i>Bacillus</i> recovery in the intestine.