Genetic background and analysis of probiotics related genes in Lactobacillus paragasseri IMAU FB017

Abstract:

[Objective] Lactobacillus paragasseri as a closely related species of L. gasseri, is one of the important bacteria in the intestinal and reproductive tract. Our research team previously found that L. paragasseri IMAU FB017 had good tolerance to stomach acid and bile salt. Therefore, we intended to analyze the genetic background of IMAU FB017 from the genome level, explore its functional gene characteristics, and dig into its potential probiotic genes, thereby laying a genetic foundation for its development and utilization. [Methods] In this study, the whole genome of IMAU FB017 was sequenced and assembled using Nanopore and Illumina sequencing technologies, and the genomic sequences of 18 L. paragasseri strains published by National Center for Biotechnology Information (NCBI) were combined for comparative genomic analysis. Roary software was used to identify core gene sets and pan gene sets. The Rapid Annotation using Subsystem Technology website was used for functional annotation of the genome to explore the genomic characteristics of IMAU FB017. [Results] The results showed that IMAU FB017 genome contained a ring chromosome and a plasmid, and the size of the ring chromosome was 1 880 023 bp, with 34.90% of the guanine/cytosine (G/C) content, containing 1 851 protein-coding sequences. The size of the plasmid was 43 639 bp, and the G/C content was 38.00%. A phylogenetic tree was constructed based on 903 core genes identified from 18 L. paragasseri genome sequences. It was found that L. paragasseri population formed three clades. Strain IMAU FB017 belonged to clades Ⅰ, which contained the most strains (13 strains, about 68%), and the strains from the same source had no significant aggregation trend. Functional annotation analysis found that the IMAU FB017 genome encoded genes related to N-acetylgalactosaamine and galactosaamine utilization, as well as probiotic genes related to oxalate catabolism, and contained a complete exopolysaccharide (EPS) gene cluster and three acid and bile salt tolerance gene clusters corresponding to the phenotype. [Conclusion] In this paper, the genetic background of IMAU FB017 has been analyzed at the genomic level, and the potential probiotic genes have been mined to provide references for its development and utilization.