Probiogenomic pipeline for new promising probiotic Streptococcus thermophilus strains

International audience

英语. Introduction and objectivesProbiotics are a good way to promote health benefits through diet. Low-cost and socially accepted foods with high probiotic content include dairy products such as yogurt, cheese, and fermented milk. Streptococcus thermophilus (STH) is a lactic acid bacterium with a long history of use in the traditional and industrial manufacture of fermented dairy products. Recently, STH has been the subject of research fordiscovering and assessing new probiotics. Probiogenomic analyses are helpful for identifying desired probiotics from a molecular perspective. Also, evaluating strains from various sources enriches the genetic knowledge of STH and the correlation of probiotic to food produtcs. Therefore, this research aims to apply a probiogenomics pipeline to STH genomes to identify new potential probiotic strains from diversesources and sites.Materials and MethodsPublic available genomes of STH were downloaded from NCBI (106) and GenoScope (3). They were annotated using Prokka, and their annotation features were compared to reference strain CIRM-BIA65. For taxogenomic classification, an average nucleotide identity was calculated considering a 96% threshold, using pyANI, with MUMmer method. To uncover shared and unique genes in the genomes,the pangenome was calculated using four different tools: Roary, OrthoFinder, PPanGGOLiN and BPGA. The virulome and resistome were predicted using PanViTa, against VFDB and CARD databases. Finally, genomic plasticity was assessed using GIPSY2.0.Results, discussion and conclusionsAll downloaded genomes belonged to STH species. The high similarity between the genome sequences is due to the clonality of the species. The number of genes per genome varied from 1750 to 2363, with an average of 2030 genes, while CIRM-BIA65 presented 1961 genes. All pangenomic tools revealed that STH is within an almost closed pangenome, with diverse accessory and unique genomes contributing to different carbohydrate and amino acid metabolisms. The patterns of gene sharing were corroborated with the clades into which the strains fit. A high number of metabolic genomic islands was found for some genomes, but not for all. The small virulome and resistome of STH revealed genes related to immunomodulation and cell adhesion, which are also useful in the context of probiosis.