The Research On Niche-specific Evolution And Genetic Diversity Of Lactobacillus Plantarum From Different Sources

Lactobacillus plantarum,a common probiotic species,is widely distributed in nature.Previous studies have shown that different niches and genetic backgrounds of microorganism will cause differences in microbial functional genomics and phenotypes.However,there have been few studies focusing on genetic diversity and the niche-specific evolution of functional genomics of L.plantarum.In this study,the effect of genetic background and isolation niches on the functional genomics of 140 L.plantarum strains was analyzed using comparative genomics and multivariate statistical analysis.Also,the growth abilities of 6 L.plantarum strains in specific niche environments were compared and the genotype-phenotype correlation was analyzed.The main research contents are as follows:Firstly,140 L.plantarum strains were divided into four niche groups,and the difference of the sizes of L.plantarum genome and GC contents under different niche groups were compared.It was found that L.plantarum strains isolated from Drosophila melanogaster habored a larger genome and a lower GC content.Using the core genes of 140 L.plantarum strains to establish a phylogenetic tree,it was found that the genetic background of L.plantarum was not significantly associated with its isolation niche group.According to phylogenetic evolution analysis and ANI analysis,L.plantarum could be divided into 2 subspecies.Functional gene databases were used to perform functional annotations on L.plantarum genomes,and the differences between the functional genomics of L.plantarum in different niche groups and genetic backgrounds were analyzed using multivariate statistical methods.It was found that for the COG annotation profile,the functional genomes of L.plantarum from human and milk sources were similar,but were different from the other two habitats(R2=0.031),and L.plantarum strains from D.melanogaster had more specific COGs.CAZyme annotation results showed that the CAZyme profile of L.plantarum strains from human and vegetable sources were similar,but were different from the other two types of habitats(R2=0.031);L.plantarum strain from D.melanogaster niche group were richer in various carbohydrate metabolism-related genes and Cazymes from milk-derived L.plantarum significantly degenerated.The VFDB annotation results showed that the virulence factors of L.plantarum from 4 niches group are different from each other(R2=0.024),but L.plantarum isolated from D.melanogaster tended to enrich virulence factors.The CARD annotation results showed that the antibiotic resistance gene distribution of L.plantarum isolated from D.melanogaster were significantly different from other niche groups(R2=0.036),and L.plantarum from human harbored a larger antibiotic resistance gene repertoire.The functional genomes of L.plantarum from different genetic backgrounds were very different,and the divergence was greater than that caused by niche.Based on this,a high-accuracy machine learning model for predicting the niche group of L.plantarum was constructed(81%),indicating that the difference in functional genes caused by niche and genetic background is universal.Finally,6 L.plantarum of from different niches were selected,and the growth abilities of these strains in a specific niche were compared.In the pickle environment,most of the L.plantarum strains completed the growth cycle in 32 h,and the maximum biomass of L.plantarum isolated from pickles during the growth process was significantly larger than that of L.plantarum from human,but there was no significant difference in generation time.The maximum biomass was related with some Cazymes and COGs but the generation time was only related with 2 COGs.In the in vitro digestion fermentation medium,different L.plantarum strains has different growth capabilities,but it was irrelavent with the niche group;and the changes in the microbiome structure caused and the inter-correlation among microbiota by different L.plantarum were related to its isolation niche.At the same time,the variation of microbiota could be predicted by the functional genome of L.plantarum.The Cazymes profile had a stronger correlation with the alteration of microbiota wheras the CARD profile had a weaker correlation.In summary,at the genomics level,L.plantarum had a significant genetic diversity,and had undergone a niche-specific evolution for functional genomics to adapt to the habitat.At the phenotypic level,L.plantarum from different sources showed different adaptation and growth abilities in different niches,and the growth capability was significantly related to its functional genomics,which verified the results of genomic analysis.According to the analysis results of genotype-phenotype correlation of L.plantarum with different genetic backgrounds and niche groups,it can give us some guidance from the genomic point of view in screening strains,improving the efficiency of screening the target L.plantarum in the future,and facilitating mining L.plantarum with probiotic properties.