Enterococcus faecalis is used as a probiotic in animal and human food supplements. Atmospheric and room temperature plasma (ARTP) systems have frequently been used to screen for effective mutant probiotics. In this study, E. faecalis was treated with ARTP, and high-yielding digestive enzyme mutant strains were obtained by measuring the activities of α-amylase, lipase, and neutral protease. A total of 833 mutant strains were obtained after 40–60 s of ARTP treatment, and after screening for digestive enzyme activity, EF-448, EF-798, and EF-804 were obtained. The three strains demonstrated an 180% increase in α-amylase activity, a 30% increase in lipase activity, and a more than 40% increase in neutral protease activity. Furthermore, the enzyme activities remained stable after nine generations. In addition, the strains exhibited high auto-aggregation capacity (over 91%) and high cell hydrophobicity (over 93%). After exposure to simulated intestinal fluid for 6 h, the survival rates of EF-448 and EF-798 were 85.71% and 82.32%, respectively. Moreover, the three mutant strains retained antioxidant capacity and DPPH free radical scavenging ability, and there was no hemolysis. A safety experiment has shown that there is no mortality of Macrobrachium rosenbergii within 14 days after receiving injections of mutant strains at different concentrations. In conclusion, this study obtained three mutant strains with high production of digestive enzymes and stable inheritance through ARTP mutagenesis of E. faecalis, providing an efficient microbial resource.
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