Abstract
BackgroundLactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections.ResultsThe results showed that 179 isolates and seven reference isolates could be assigned to 73 different sequence types (STs), forming ten clonal complexes (CCs) and 23 singletons. There were 158 polymorphic sites detected in total, and the nucleotide diversity per site varied from 0.00401 in clpX to 0.03220 in groEL. The minimum spanning tree analyses suggested that the evolution of L. plantarum isolates have little relationship with ecological sources have similar nucleotide diversity. Phylogenetic trees and structure indicated that there were six lineages in the L. plantarum isolates used in our study. Split-decomposition and ClonalFrame analysis indicated that recombination had occurred throughout the population of L. plantarum, but it occurred at a low frequency in these eight loci.ConclusionWe deduced that L. plantarum isolates from the same ecological niches have similar genetic diversity and population structure. The MLST scheme presented in this study provides abundant sequence data for L. plantarum and enabled global comparisons of isolates associated with various environmental origins to be made. This will further advance our understanding of the microbial ecology of this industrially important LAB.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0584-4) contains supplementary material, which is available to authorized users.
Highlights
Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food
It is clear that recombination plays a driving role in the evolution of bacteria [34], but little was known about the details of the recombination process within L. plantarum
These events may have facilitated rapid adaptation of L. plantarum to different environments. This is in agreement with previous reports that recombination is an important source of diversity in LAB [16]
Summary
Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. The genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections. Technological, probiotic, antimicrobial and sensorial attributes are strain-specific and so it is important to be able to distinguish between isolates with different properties [13] For this reason, a great number of, molecular, techniques have been developed for the identification and typing of L. plantarum isolates. These include randomly amplified polymorphic DNA, pulsed-field gel electrophoresis, amplified fragment length polymorphism, repetitive element PCR and multilocus sequence typing (MLST) [13,14,15,16,17]
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