Study On The Genome Evolution And Community Stability Of Lactic Acid Bacteria In Natural Fermented Milk Niches

Natural fermentation is an important way of preserving raw milk,and naturally fermented dairy products are an important part of everyday diets around the world.As people of all ethnic groups have passed on traditional production techniques of fermented dairy products from generation to generation,the microorganisms involved have also been passed on and evolved over generations.Thousands of years of heritage have led to the retention of microorganisms well-adapted to naturally fermented dairy products,including strains with excellent probiotic and production properties that can reduce fermentation time and improve fermentation quality.At the same time,the relatively small number of microorganisms in fermented milk provides an opportunity to dissect the mechanisms of microbial community formation and population genetics as a comparatively simple,reproducible,culturable,and easily manipulated microbial ecosystem.However,there have been few reports on the drivers of lactic acid bacteria genome evolution.Therefore,systematic analysis of the evolutionary mechanism of lactic acid bacteria genomes under microbial community ecology is of great significance for the exploitation of lactic acid bacteria resources.In this study,636 strains of lactic acid bacteria were isolated from 12 samples of koumiss,tarag milk,khoormog,and kurut milk from Inner Mongolia of China,Xinjiang of China,Tibet of China,Kyrgyzstan,Tajikistan,Morocco,and Mongolia,yielding 214 strains of Lactobacillus helveticus,97 strains of Lactococcus lactis subsp.lactis,and 325 strains of Lactobacillus delbrueckii subsp.bulgaricus for population genetics and metagenomics analyses.The following conclusions were obtained:(1)The genetic diversity of Lactobacillus helveticus,Lactococcus lactis subsp.lactis,and Lactobacillus delbrueckii subsp.bulgaricus was studied at the genome-wide level.The results of phylogenetic and genetic distance analyses showed that the genetic diversity of isolates in different samples was rather different;the genetic distance between evolutionary branches was greater than within branches;the bacterial community structure showed obvious geographical clustering patterns;and lactic acid bacteria in the same sample exhibited high degree of intra-species heterogeneity and were evolved from multiple lineages.Further pan-genome analysis found that the degree of open closure of pan-and core-genomes varied between strains in different samples,and that the higher the genetic diversity of the strains in the sample,the more open the pan-genome.Comparison of carbohydrate-active enzymes(CAZy)between strains revealed that the CAZy distribution was related to genetic distance,and strains with closer genetic distance shared more CAZy genes.(2)Species with high genetic diversity in a single sample have more genes specific to their evolutionary branches.Bioinformatics analysis and identification of genes underwent horizontal gene transfer(HGT)and their sources found that HGT occurred in multiple species in the environment,mostly in congenic and closely related species.Thus,HGT between closely related species might facilitate rapid adaptation of bacteria to new environments.(3)Correlation analysis between the composition of microbial community and genetic diversity of lactic acid bacteria found that the relative abundance of a specific species in fermented milk was negatively correlated with its genetic diversity.The lower the relative content,the higher the genetic diversity was.In addition to the species itself,other key species in the metagenome also influenced the microbial genetic diversity.This study studied the internal mechanism of natural fermented milk habitat community stability and strain evolution from the levels of flora,strains and strains,and explored the change rule of the genetic diversity of lactic acid bacteria in the natural fermented milk niche,which is a group of complex ecosystems,providing a theoretical basis and guiding significance for future population genetics studies and the development and utilization of lactic acid bacteria multi-strain starter.