Table_1_Genetic and technological diversity of Streptococcus thermophilus isolated from the Saint-Nectaire PDO cheese-producing area.DOCX

Streptococcus thermophilus is of major importance for cheese manufacturing to ensure rapid acidification; however, studies indicate that intensive use of commercial strains leads to the loss of typical characteristics of the products. To strengthen the link between the product and its geographical area and improve the sensory qualities of cheeses, cheese-producing protected designations of origin (PDO) are increasingly interested in the development of specific autochthonous starter cultures. The present study is therefore investigating the genetic and functional diversity of S. thermophilus strains isolated from a local cheese-producing PDO area. Putative S. thermophilus isolates were isolated and identified from milk collected in the Saint-Nectaire cheese-producing PDO area and from commercial starters. Whole genomes of isolates were sequenced, and a comparative analysis based on their pan-genome was carried out. Important functional properties were studied, including acidifying and proteolytic activities. Twenty-two isolates representative of the diversity of the geographical area and four commercial strains were selected for comparison. The resulting phylogenetic trees do not correspond to the geographical distribution of isolates. The clustering based on the pan-genome analysis indicates that isolates are divided into five distinct groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of the accessory genes indicates that the accessory gene contents of isolates are involved in different functional categories. High variability in acidifying activities and less diversity in proteolytic activities were also observed. These results indicate that high genetic and functional variabilities of the species S. thermophilus may arise from a small (1,800 km2) geographical area and may be exploited to meet demand for use as autochthonous starters.

嗜热链球菌（Streptococcus thermophilus）在奶酪生产中对保障快速酸化具有核心意义；但相关研究显示，商业菌株的过度应用会导致产品典型特性的流失。为强化产品与其地理来源的关联，并提升奶酪的感官品质，各受保护的原产地名称（Protected Designation of Origin, PDO）奶酪产区愈发重视特异性本土发酵剂培养物的研发。因此，本研究针对从某一奶酪原产地保护产区分离的嗜热链球菌菌株的遗传与功能多样性展开探究。研究人员从圣内克泰尔（Saint-Nectaire）奶酪原产地保护产区采集的牛乳及商业发酵剂中，分离并鉴定出疑似嗜热链球菌分离株。对所有分离株进行全基因组测序，并基于泛基因组开展比较分析。研究人员对包括酸化活性与蛋白水解活性在内的重要功能特性展开了检测。研究选取了代表该地理区域菌株多样性的22株分离株，以及4株商业菌株用于对照分析。构建得到的系统发育树与分离株的地理分布并不匹配。基于泛基因组分析的聚类结果显示，分离株可被划分为5个独立类群。对附属基因进行的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）功能注释结果显示，分离株的附属基因集涉及多个不同的功能类别。研究同时观察到，菌株的酸化活性存在较高变异，而蛋白水解活性的多样性则相对较低。上述结果表明，即便在面积仅1800平方千米的狭小地理区域内，嗜热链球菌仍可展现出极高的遗传与功能多样性，该特性可被开发利用以满足本土发酵剂的应用需求。