Evaluation of probiotic characteristics and whole genome analysis of Bacillus velezensis R-71003 isolated from the intestine of common carp (Cyprinus carpio L.) for its use as a probiotic in aquaculture

Abstract

Probiotics have been widely used in aquaculture and may serve as a potential alternative to antibiotics. Diverse sources of probiotics have different effects on the host, and the application of native probiotics isolated from target fish may play a better role. This study was conducted to evaluate the probiotic potential of the bacteria isolated from the gut of common carp (Cyprinus carpio L.). Based on morphological, 16 S rRNA sequencing and whole-genome sequencing analysis, an isolated strain that simultaneously produces protease, mannanase, amylase, and cellulose was identified as Bacillus velezensis R-71003. This strain showed antagonistic activity against various pathogens. Further studies showed that B. velezensis R-71003 was susceptible to ampicillin, gentamicin, penicillin G, erythromycin, chloramphenicol, amikacin, cefamezin, sulfamethoxazole, ciprofloxacin and norfloxacin. Additionally, B. velezensis R-71003 met the safety criteria based on safety evaluation results, such as haemolytic activity and biosafety tests in common carp. Moreover, B. velezensis R7–1003 was resistant to low pH (2) and higher bile salt concentration (0.3 %) and showed higher viability ability after high temperature exposure (60, 70, and 80 °C), as well as higher auto-aggregation and cell-surface hydrophobicity. In addition, the challenge test showed that B. velezensis R-71003 significantly increased the survival rate of common carp after challenged with Aeromonas hydrophila. Finally, the growth-promoting effects of sodium gluconate on B. velezensis R-71003 were evaluated. The results indicated that a low concentration of sodium gluconate could promote the growth of B. velezensis R-71003 and increase the expression levels of dnaA and yabD. Whole-genome analysis revealed that genome contains genes related to the biosynthesis of antibacterial substances, digestive enzymes, amino acids and vitamins, as well as stress resistance. The results collectively suggest that B. velezensis R-71003 exhibited good probiotic potential, and its combined application with sodium gluconate may be used to improve the health status of aquatic animals.