The Diversity Of Lactic Acid Bacteria In Naturally Fermented Milk And Comparative Genomic Analysis Of The Dominant Strains From Morocco

There are many traditionally fermented foods with geographic characteristics in the whole world.Lactic acid bacteria is one of the kind of bacteria widely studied in all kinds of fermented foods.Morocco is a country in northwest Africa close to Western Sahara.Animal husbandry is one of the pillars of traditional agriculture in Morocco.Many animals were raised here including cattle,sheep,camels etc.Thus,naturally fermented milk were very popular in the local area,the cow and camels milk were used as raw materials to fermentation.The naturally fermented dairy products were regarded as good habitat for lactic acid bacteria.In the process of natural curing,lactic acid bacteria with excellent characteristics are retained.In order to analyze the diversity of lactic acid bacteria in naturally fermented milk from Morocco,the thesis combined the pure culture and PacBio SMRT sequencing technology to analyze the bacterial diversity of naturally fermented cow milk and camel milk.Besides,based on the comparative genomics approach,the genetic evolution and functional genomics of dominant isolates from in Morocco naturally fermented dairy products.The main research results are as follows:1.The viable count of lactic acid bacteria in 13 naturally fermented dairy products ranged from 5.89×10~5 to 8.33×10~6CFU/m L.247 strains of lactic acid bacteria were isolated from naturally fermented dairy products,which were identified as 5 genera and11 species.The results showed that there was different kinds of lactic acid bacteria in different types of naturally fermented milk in Morocco.The most dominant strain was Lactococcus lactis,which accounted for 51.82%of the all isolates.Lactobacillus helveticus and Lactobacillus kefiranofaciens accounted for 9.74%and 9.31%respectively.Lactococcus,Lactobacillus and Streptococcus were the dominant strains in naturally fermented cow milk,accounting for 45.22%,40.12%and 12.11%of the isolates.Lactococcus and Lactobacillus were the dominant strains in natural fermented camel milk,accounting for 64.33%and 26.67%of the total isolates.There were certain differences in the composition of lactic acid bacteria in naturally fermented cow milk and camel milk.2.Based on analysis the PacBio SMRT sequencing technology,the bacteria isolated from 13 naturally fermented milk in Morocco were identified into 9 bacteria,132 genera and 246 strains.The Firmicutes and Proteobacteria were the dominant bacteria in naturally fermented cow milk and camel milk,the relative abundance were 68.63%,29.79%.Lactococcus and Lactobacillus were the dominant genera with relative contents of 40.89%,17.36%.The relative contents of Streptococcus thermophilus,Lactobacillus helveticus,and Lactobacillus kefiranofaciens were 6.97%,6.72%,4.47%.In addition to above-mentioned main strains,some potential pathogen bacteria with low relative abundance were also detected,such as Escherichia fergusonii,Klebsiella oxytocai,which appeared in individual samples.3.In this thesis,52 strains of Lactococcus lactis were selected to re-sequence for comprehensive study.The results showed that all strains belonged to Lactococcus lactis subsp.lactis.Thus,the strain Lactococcus lactis subsp.lactis ATCC 19435~Twas used as the type strain to analyze the whole genome basic information of Lactococcus lactis subsp.lactis.The genomic length and GC content of Lactococcus lactis subsp.lactis showed that the average length of Lactococcus lactis subsp.lactis genome was 5.48±0.18 Mb,and the average GC content is 35.13±0.40%.The core gene set and pan gene set were constructed.The pan gene set contained 9542 gene families;the core gene set contained 1283 genes.In this case,the pan gene sets was an open pan gene set,namely its number was also going up.In this thesis,the pure culture method and the Pacbio SMRT sequencing technology were used to understand the bacterial diversity in naturally fermented cow milk and camel milk.In addition,the functional characteristics of Lactococcus lactis subsp.lactis were analyzed based on functional genomics method,which provided a reference theory for the industrial production of naturally fermented milk,and obtained a scientific guidance for the excavation of subspecies of Lactococcus lactis with excellent production characteristics.