Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia

Abstract

Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC). All 229 isolates could be allocated to 171 unique sequence types, including 25 clonal complexes and 71 singletons. The high index of association value (1.3524) and standardized index of association value (0.1503) indicate the formation of an underlying clonal population by all the isolates. However, split-decomposition, relative frequency of occurrence of recombination and mutation, and relative effect of recombination and mutation in the diversification values confirm that recombination may have occurred, and were more frequent than mutation during the evolution of Lb. casei. Results from Structure analyses (version 2.3; http://pritch.bsd.uchicago.edu/structure.html) demonstrated that there were 5 lineages in the Lb. casei isolates, and the overall relatedness built by minimum spanning tree showed no clear relationship between the clonal complexes with either the isolation sources or sampling locations of the isolates. Our newly developed MLST scheme of Lb. casei was an easy and valuable tool that, together with the construction of an MLST database, will contribute to further detailed studies on the evolution and population genetics of Lb. casei from various niches.

The Lactobacillus casei Group: History and Health Related Applications

“…The study determined that PFGE was an effective method for discriminating isolates, even where MLST was unsuccessful ( Cai et al, 2007 ). Another MLST study of 224 L. casei isolates from fermented foods using 10 housekeeping genes found no correlation with geographic location or food source, implying a complex evolutionary history and contradicting previous studies ( Bao et al, 2016 ). Other single target genes used for species discrimination include housekeeping genes such as the chaperone protein gene, dnaJ ( Huang et al, 2015 ), dnaK ( Huang and Lee, 2011 ), yycH ( Huang et al, 2014 ), and mutL ( Bottari et al, 2017 ).…”

Molecular typing tools for identifying and characterizing lactic acid bacteria: a review

“…plantarum (de las Rivas et al, 2006 ; Xu et al, 2015 ), St. thermophiles (Delorme et al, 2017 ), the Lb. casei group (Bao et al, 2016 ; Diancourt et al, 2007 ; Feng et al, 2018 ), and Oenococcusoeni (De Las Rivas et al, 2004 ; Yu et al, 2018 ). Our research group used the MLST tool to differentiate the Leu.…”

Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

“…To explore the metabolism, evolution and speciation, high-throughput methods (e.g., site sequence typing (MLST) and OmniLog (Biolog) phenotyping (Di Cagno et al, 2010) have been used to analyze genotype and phenotype (Bao et al, 2016). Comparative genomic analysis is a common tool in bioinformatics (Kant et al, 2011) that is able to identify the association between strains and their origins as well as to evaluate the gene distribution of specific species (Kelleher et al, 2017).…”