The Genomic Characteristics Of Lactobacillus Reuteri From Different Sources

Lactobacillus reuteri is one of the most important probiotics,which widely exists in human and animal intestines,dairy products,sourdough and meat products.At present,Lactobacillus reuteri has been used as a model to describe the ecology and evolution of vertebrate gut symbionts,but little research has been done on the strains from fermented food.In this study,Illumina Hiseq high throughput sequencing technology was used to sequence 11 strains of Lactobacillus reuteri isolated from fermented food(koumiss and sour porridge).And then we compared the whole genome of 11 Lactobacillus reuteri with 23 Lactobacillus reuteri isolated from sourdough,goat feces,sheep feces,cow feces and horse feces in NCBI database.We aim to analyze the gene diversity and genomic characteristics of different sources of Lactobacillus reuteri.It can provide a theoretical basis for the development of good strains of Lactobacillus reuteri.The main results are as follows:The genome size and GC content of 11 strains were 2.14 MB and 38.77%respectively,which were different from those of the four isolation sources:koumiss,sour porridge,sourdough and herbivore.The genome size and GC content of sourdough strains were higher than those of herbivore strains.The phylogenetic tree was constructed based on the core genome of 34 strains of Lactobacillus reuteri.The results showed that the phylogenetic relationship of isolates from the same source was close.The pan gene set and core gene set of 34 strains were constructed.The results showed that the pan gene set was an open type,including 7242 genes,and the core gene set was a stable type,including 969 genes.There was significant difference in the number of predicted genes among the strains of koumiss,sourdough and herbivores.The most specific genes were found in koumiss isolates.According to the functional classification of four kinds of isolates,the number and types of carbohydrate and amino acid genes were significantly different.According to the phylogenetic relationship,the strains were divided into four categories:A,B,C and D.In the carbohydrate,the number of genes related to glycolysis/gluconeogenes pathway,galactose metabolism pathway,TCA cycle and other metabolic pathways of A branch(koumiss,sour porridge)was the largest.In the protein,there are 12 kinds of amino acid synthesis and metabolism pathways in branch A,and the number is 66,with the largest number and types.In terms of lipids,the fatty acid metabolism pathway of branch A was incomplete.In the vitamin,the specific metabolic pathways of branch A was thiamine metabolism(VB1),niacin and nicotinamide metabolism(VB3),pantothenate and coenzyme A biosynthesis(VB5).In addition,the number of butyric acid metabolizing enzymes in branch A is the largest,and only in branch A there are aromatic compounds degradation,xylene degradation,dioxin degradation payhways.The results of CAZy(carbohydrate active enzyme)annotation showed that the GH3(?-glucosidase,etc.),GH43(?-xylosidase,etc.),CBM 16(binding with cellulose),CBM37(binding with xylan,chitin,etc.)appeared in the strains of fermented food and herbivore.AA3(cellobiose dehydrogenase,etc.)and GH66(glucose transferase,etc.)were specific respectively.The same enzyme families of fermented food and herbivore strains was related to the environment.To sum up,Lactobacillus reuteri from different sources has a wide range of gene diversity,which is closely related to the living environment.The fermented food isolates had the characteristics of herbivore intestinal strains but it had its unique environmental adaptability.The results can deepen the understanding of traditional fermented food and the adaptation of bacterial habitat in the intestinal environment.