Differences In Genomics And Physiological Characteristics Of Lactobacillus Paracasei From Different Sources

Lactobacillus paracasei(L.paracasei)is a species in the Lactobacillus casei group that has a wide range of niches.Different habitats may confer different genomic and physiological characteristics to L.paracasei.Based on the studies of genotypes and phenotypes,the genetic evolution relationship and carbohydrate utilization of L.paracasei have been analyzed.However,most of the existing researches focus on strains isolated from dairy products,and only for a few strains or individual typical genes.In this study,L.paracasei were screened from pickle and intestine samples to explore the differences in genomics and physiological characteristics of strains in different habitats.The main findings are as follows:(1)121 strains of L.paracasei were successfully screened from 508 samples and combined with 27 strains of NCBI published strains(multiple separation sources),whose genome size and GC content ranged from 2.65 to 3.90 Mb and 45.98% to 47.97%,respectively.There is no significant correlation between habitat and the basic characteristics of the genome.The pan-genome curve indicates that L.paracasei has an open pan-genome,and the core gene annotation results show that they are mainly involved in important functions such as translation,DNA replication,and carbohydrate metabolism.Results of comparative genomics show the differences in the genetic evolution of L.paracasei in different habitats.The evolutionary directions of strains isolated from dairy products and pickle are obviously separated.The intestinal strains have a variety of evolutionary directions.For human intestinal isolates,the evolutionary pathway is influenced by the age,region and ethnicity of the host.(2)Based on the genotypic and phenotypic analysis of carbohydrate utilization,the L.paracasei genomes contain 82 carbohydrate active enzyme genes,including 37 glycohydrolase(GH),17 glycosyltransferase(GT),13 carbohydrate binding modules(CBM)and other gene families.There are 22 species that differ significantly in intestinal and kimchi-derived strains.Strains of L.paracasei from different habitats show a difference in the utilization ability of fructooligosaccharide,xylooligosaccharide and D-glucitol.Intestinal strains are more likely to ferment them,which is consistent with its complete gene cluster for sugar utilization.(3)Based on the genotypic and phenotypic analysis of antibiotic tolerance,the L.paracasei genomes contain 45 to 49 antibiotic resistance-related genes.The number of genes is not significantly related to the habitat of strain.However,some of the resistance genes are only found in intestinal strains,which also showed high levels of antibiotic resistance.The antibiotic tolerance of the intestinal strains was generally higher than that of the pickle strains,reflecting the effect of habitat on the antibiotic resistance of L.paracasei.For tetracycline,erythromycin,clindamycin and streptomycin,highly resistant strains are present and are regulated by their tetM,ermB,rpsL genes respectively.(4)Based on the analysis of acid and salt tolerance,L.paracasei strains have good environmental stress tolerance and are able to grow at pH 3.0 and 7.0% salinity.The acid tolerance is related to various amino acid metabolism genes,and the salt tolerance is related to genes of Dnak,GroEL and trehalose active enzyme.The salt tolerance of strains isolated from pickle were generally higher than that of the intestinal strains,revealing the adaptability of L.paracasei in different habitats.The six strains with the best salt tolerance are related to their kdp gene cluster and trkA gene.