Study On The Genetic Diversity Of Lactobacillus Plantarum Strains From Traditional Fermented Dairy Products

There are diverse lactic acid bacteria(LAB)strains in traditional fermented dairy products,which have excellent fermentation characteristics.Lactobacillus plantarum,a member of LAB,has been reported to have multiple probiotic properties and can be studied as a potential commercial strain.In this study,a multilocus sequence typing(MLST)scheme based on seven housekeeping genes(pheS,groEL,ileS,recA,recG,murC and murE)was constructed to provide an insight on the genetic diversity,phylogenetic relationships,genetic evolution and population structure of 61 L.plantarum strains isolated from traditional fermented dairy products from the Inner Mongolia and Tibet Autonomous Region supplemented with 30 reference strains.Then,whole genome sequencing was performed on L.plantarum LJ 26 for genome composition,functional genes and comparative genome analysis.The results of this study are presented as follows:(1)The numbers of alleles per gene ranged from seven(recG)to 15(pheS).The?values varied from 0.00234(groEL)to 0.00887(ileS).The numbers of polymorphic sites ranged between eight(recG)and 18(pheS).The mean G+C%contents for each locus varied between 42.73%(murC)and 50.95%(murE).Tajima's D values ranged from-1.82269(murC)to-0.39648(murE).The d_N/d _S ratios for each individual gene varied between 0.020(recG)and 0.105(pheS).The index of association(I_A)and the standardized index of association(I_A~S)were 1.4364 and 0.2394,respectively.These results indicated that the selected housekeeping genes were relatively conserved with a clonal structure under a stable selection,and suitable for MLST analysis.(2)From 91 L.plantarum isolates,47 sequence types(STs)were identified,and ST-1 was the predominant one.47 STs were divided into 10 clonal complexes(CCs)and 13 singletons using eBURST.The predominant clonal complex,CC1,considering ST-1 as the original sequencing type contained eight STs occupying 42.86%of all isolates.(3)47 STs were resolved into seven clusters by phylogenetic analysis and seven ancestral populations were revealed by STRUCTURE.Two clusters were single ancestral source and the remaining clusters(half of all isolates)contained mixtures of ancestral sources,which suggested high genetic heterogeneity.(4)Split decomposition analysis was used to investigate the recombination amongst the isolates.The split graphs for pheS and murE were parallelogram-shaped structures and the combined split graph of the seven concatenated gene fragments displayed a network-like structure with several parallelograms,indicative of the occurrence of recombination in its evolution history.Additionally,the P-value showed significant evidence for recombination(P=2.06E-4).The values of?/?and r/m indicated that recombination happened more frequent and effective than mutation(?/?=1.25;r/m=3.95).(5)The L.plantarum LJ 26 genome was about 3.26 Mb and comprised of a circular chromosome and four circular plasmids.There were 3289 predicted genes containing 16 rRNA operons,71 tRNAs,six sRNAs,16 genomics islands(GIs)and several repeat sequences in the genome.Functional genes were investigated for further verifying the related probiotic properties of L.plantarum LJ 26 at the genome level.Teichoic acid related genes,cps clusters and plantaricin biosynthesis related genes were identified.(6)Comparative genomic analysis revealed that there were 4560 pan genes,1886 core genes and 2674 dispensable genes in the 11 L.plantarum genomes.L.plantarun LJ 26 contained 448specific genes among 1173 specific genes,and most of the genes distributed in GIs,which was probably due to the horizontal gene transfer.