High-throughput discovery of novel lanthipeptides and producers by metagenomic mining of isolates population (MMIP) from Chinese spicy cabbage

Abstract

Lanthipeptides are known antimicrobial agents having great potential for application in food preservation. Many lanthipeptide biosynthetic gene clusters (BGCs) were mined in fermented food microbiota, however, it is difficult to obtain the bioactive lanthipeptides and their producing strains. Here, we established a high-throughput strategy designated Metagenomic Mining of Isolates Population (MMIP) to efficiently excavate and obtain novel lanthipeptides, especially their potential producing strains. MMIP procedure involves gathering bacteria isolates using culturable strategy, metagenomic mining for lanthipeptides and screening their producers, and characterization of specific lanthipeptides. 928 biosynthetic gene clusters including 139 ribosomally synthesized and post-translationally modified peptides (RiPPs) gene clusters were discovered in the metagenomic data of the isolates by antiSMASH. Entianin, lactocin S, lichenicidin, and 17 novel lanthipeptides gene clusters corresponding to 29 possible producers were further found from the harvested isolates population. Entianin and a novel two-component lanthipeptide paralicin were purified from Bacillus subtilis C5B1 and Bacillus paralicheniformis BaC1-8, respectively. They showed strong inhibitory activity to food spoilage bacteria Bacillus cereus and Listeria monocytogenes, and have great potential for application in food preservation. A novel lanthipeptide polysacin was also obtained using semi-in vitro biosynthesis. MMIP affords a novel strategy for effectively excavating lanthipeptides, especially their producers from diverse environmental niches.