New molecule of nonribosomal peptide synthesis mechanism from Lactiplantibacillus plantarum LMG100 probiotic bacteria

Abstract

Background The huge increasing on gastrointestinal illness by spreading of resistance pathogens requires to develop alternative antimicrobial agents. Nonribosomal peptides are considered one of these alternatives which produced by wild spectrum of bacteria. Objective Detection of nonribosomal peptide synthesis from Lactiplantibacillus plantarum LMG100 probiotic strain isolated from traditional lactic fermenting foods as alternative antimicrobial agent is important to human health and immune system. Materials and methods The identification of isolated strains using 16S rDNA technique was performed and followed by bioinformatics analysis tools; AntiSmash, PKS-NRPS analysis website, LSI based A-domain function predictor, NRPS predictor2, clustering using PhyML 3.0 to detect adenylation domain substrate specificity of NRP synthetases genes cluster of Lactiplantibacillus plantarum LMG100. To prove the presence of the NRP synthetases genes cluster, degenerate primers protocol and three sets of primers covered the five gene cluster were designed based on the original reference strain L. plantarum WCFS1. Antibacterial activity of the isolated strain was detected against bacterial strains from coliform group of the enteric genera of Escherichia, Salmonella and Shigella which formed the ordinary gastrointestinal tract infection. Results and conclusion The isolated L. plantarum LMG100 strain showed 99.96% of identity to 16S rDNA partial gene sequence of Lactiplantibacillus plantarum WCFS1 strain and bioinformatics analysis tools revealed the presence of NRPS gene cluster of five genes; two biosynthetic genes npsA and npsB from the five genes encoded for polypeptide of six amino acids, but six different predictors programs couldn’t assign the specificity of all adenylation domains except A4 serine and A5 glycine. The use of degenerate primers confirmed the presence of the NRPS in the isolated strain L. plantarum LMG100 compared to the standard strain WCFS1. Three sets of primers covering the five gene cluster were designed based on the original reference strain L. plantarum WCFS1 complete genome sequence confirmed the same organization of the putative gene cluster. In general, the approach of degenerated primers proved the presence of polypeptide NRPs gene presence in lactobacilli isolates. The new polypeptide NRP produced from the strain LMG100 showed maximum inhibition zones against G-ve short-rods bacterial strains from the coliform group of the enteric genera of Escherichia, Salmonella and Shigella which formed the ordinary gastrointestinal tract infection, and the minimal inhibitory concentrations (MIC) for G-ve bacterial strains was approximately of 125 mg.ml−1. The obtained results revealed that the selected probiotic Lactiplantibacillus strain is suitable candidate for use as bio-preservative starter or probiotic for human consumption in food and pharmaceutical industries.