| Pediococcus pentosaceus,as a natural producer of pediocin,is widely used in the fermentation industry.Recently,much importance has been attached to its probiotic functions,such as inhibiting food-borne pathogens,regulating intestinal immunity and lowering cholesterol.However,it was found that some individual strains might raise the level of pro-inflammatory cytokines and aggravate the inflammatory response when relieving diarrhea in mice caused by pathogenic bacteria.This means that there exists significant strain specificity among the species,which requires further in vivo verification.Currently,only a few P.pentosaceus is available with limited origins,in hence,this study aims to increase the number of P.pentosaceus strains,enrich the genomes,in order to analyze the general characteristics of P.pentosaceus and perform comparative genomic analysis.Based on the results of genomic analysis,strains with different genotype were selected to investigate and compare their influence on the intestinal microenvironment in healthy mice to analyze the potential correlation between their genetics and benefits,which might provide a theoretical basis for further explore the probiotic P.pentosacues.The main findings are as follows:65 strains of P.pentosacues were isolated from 400 fermented food and feces sampled from different regions.Comparative genomic analysis showed that pangenome was open indicating P.pentosaceus exchanged genes with environment frequently;and core genome were mainly related to its life activities,among which 24 genes were related to defense mechanisms;ANI values were above 0.98,proving that all those 65 strains were P.pentosacues and without any subspecies.By constructing a phylogenetic tree based on homologous genes,the clustering of P.pentosaceus on the tree had no correlation with their original source.Further comparative analysis of functional genes found that the genetic differences in P.pentosacues mainly reflected in the genes related to carbohydrate utilization,horizontal gene transfer(CRISPR/Cas and prophage)and bacteriocins.The differences in carbohydrate utilization ability were due to genetic variation,including deletion and rearrangement of key genes.CRISPR/Cas IIA was predicted in 32 strains,and the correlation analysis with the prophage indicated that the repeat sequence of P.pentosacues CRISPR were close to that in Lactobacillus,and the spacer sequence were consistent with bacteriophages derived from Listeria and Lactobacillus,confirming that P.pentosacues might have frequent gene exchange with its neighboring genus and species.Furthermore,totally four kinds of bacteriocins were predicted including pediocin,penocin,enterolysis A and Bac.These four bacteriocins were all related to mobile genetic elements(eg.plasmids).In addition,the genes encoding bacteriocin were conservative,which showed that presence and absence of bacteriocin might be responsible for the differences of P.pentosaceus.Based on the results from comparative genomic analysis,14 P.pentosaceus strains with different genotypes were selected to further explore their different impacts on the intestinal microenvironment in mice.The results showed that P.pentosaceus with different genotypes had different effects on colon cytokines but without significant effect on colon morphology and CD4~+CD25~+Foxp3~+regulatory T cells in mesenteric lymphocytes,and some individual strains could significantly increase fecal acetate;according to the correlation analysis between fecal microbiota,cytokines and short-chain fatty acids,P.pentosaceus differed in regulating cytokines and short-chain fatty acids production possibly because of different modulation of gut microbiota composition;further analysis found that the functional genes related to synthesis and secretion of bacteriocin in the fecal flora metabolic pathways were highly enriched and significantly different,which indicated that the differently microecological influence might be related to the diversity of bacteriocin. |
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