title: Multilocus sequence typing of Lactococcus lactis from naturally fermented milk foods in ethnic minority areas of China.
abstract: To determine the genetic diversity and phylogenetic relationships among Lactococcus lactis isolates, 197 strains isolated from naturally homemade yogurt in 9 ethnic minority areas of 6 provinces of China were subjected to multilocus sequence typing (MLST). The MLST analysis was performed using internal fragment sequences of 12 housekeeping genes (carB, clpX, dnaA, groEL, murC, murE, pepN, pepX, pyrG, recA, rpoB, and pheS). Six (dnaA) to 8 (murC) different alleles were detected for these genes, which ranged from 33.62 (clpX) to 41.95% (recA) GC (guanine-cytosine) content. The nucleotide diversity (π) ranged from 0.00362 (murE) to 0.08439 (carB). Despite this limited allelic diversity, the allele combinations of each strain revealed 72 different sequence types, which denoted significant genotypic diversity. The dN/dS ratios (where dS is the number of synonymous substitutions per synonymous site, and dN is the number of nonsynonymous substitutions per nonsynonymous site) were lower than 1, suggesting potential negative selection for these genes. The standardized index of association of the alleles IA(S)=0.3038 supported the clonality of Lc. lactis, but the presence of network structure revealed by the split decomposition analysis of the concatenated sequence was strong evidence for intraspecies recombination. Therefore, this suggests that recombination contributed to the evolution of Lc. lactis. A minimum spanning tree analysis of the 197 isolates identified 14 clonal complexes and 23 singletons. Phylogenetic trees were constructed based on the sequence types, using the minimum evolution algorithm, and on the concatenated sequence (6,192 bp), using the unweighted pair-group method with arithmetic mean, and these trees indicated that the evolution of our Lc. lactis population was correlated with geographic origin. Taken together, our results demonstrated that MLST could provide a better understanding of Lc. lactis genome evolution, as well as useful information for future studies on global Lc. lactis structure and genetic evolution, which will lay the foundation for screening Lc. lactis as starter cultures in fermented dairy products.
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Xu
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Liu
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Jie
authors.initials: J
authors.lastname: Yu
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Song
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lv
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Jiachao
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Yuyu
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China.
authors.forename: Bilige
authors.initials: B
authors.lastname: Menghe
authors.affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, P. R. China. Electronic address: hepingdd@vip.sina.com.
authors.forename: Heping
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002681:China; D043302:Cultured Milk Products / Q000382:microbiology*; D019143:Evolution, Molecular; D014644:Genetic Variation; D013294:Lactococcus lactis / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Lactococcus lactis; housekeeping gene; multilocus sequence typing; traditional fermented milk food