Whole genome sequencing of two Lactobacillus plantarum strains isolated from human milk

Abstract:

[Background] Breast milk is an important screening database for probiotics, among which Lactobacillus plantarum is a one that is adaptable and widely used. Different strains of Lactobacillus plantarum show differences in functions, but the existing physiological and biochemical methods have limited research on its potential probiotic characteristics. Identify probiotics with good specificity by high-throughput method has become a hot topic in probiotics, research. [Objective] Combining with the biochemical characteristics of the bacterial strains, the potential functions of the two strains of Lactobacillus plantarum were predicted based on the whole genome sequencing and analysis. We explored the phenotype of the bacterial strains based on the genomic structure. In particular, we searched for genes related to intestinal fluid tolerance and bacteriocin synthesis. [Methods] We separated two strains of Lactobacillus plantarum (MP55, MP37) from human milk, used the Illumina genome analyzer to sequence whole genomes of the two strains, annotated the genomes by Prokka software, adopt carbohydrate-active enzymes (CAZy), and performed functional annotation using the koyto encyclopedia of genes and genomes (KEGG) and clusters of orthologous genes (COG) databases. Coding sequences and ribosomal RNA were predicted using Prodigal, RNAmmer and other tools, and the genome ring map of the bacterial strain was plotted using CGView software. [Results] The whole genome information of two strains of Lactobacillus plantarum was obtained through gene assembly. The genome sizes of Lactobacillus plantarum MP37 and MP55 were 3 204 421 bp and 3 299 180 bp, respectively. (G+C)mol% contents were 44.36% and 44.46%, respectively. The genome contained 3 012 and 3 101 DNA coding sequences, and four genes related to intestinal fluid tolerance and a cluster of genes related to bacteriocin synthesis were found by combining the biochemical characteristics of the bacterial strain. Raw genomic sequence data and splicing results have been submitted to the “gcMeta” platform. [Conclusion] Through high-throughput sequencing analysis, this study revealed the possible mechanism of MP55 and MP37 activity of Lactobacillus plantarum in the intestinal tract and inhibition of pathogenic bacteria. Lactobacillus plantarum MP55 and MP37 are two potential candidate strains of probiotics. The results of this experiment provide genome information for further elucidation of the functional mechanism of the probiotics.

Key words:Lactobacillus plantarum, Probiotics, Whole genome sequencing, Breast milk, Bacteriocin