Table_2_Genetic and technological diversity of Streptococcus thermophilus isolated from the Saint-Nectaire PDO cheese-producing area.XLSX

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）在干酪生产中对保障快速酸化具有核心重要性；但相关研究表明，商业菌株的过度使用会导致干酪产品典型特征的流失。为强化产品与产地的关联并提升干酪感官品质，获得地理标志保护（Protected Designation of Origin, PDO）的干酪产区愈发重视开发专属的本土发酵剂培养物。因此本研究针对某地理标志保护干酪产区分离得到的嗜热链球菌菌株，开展遗传与功能多样性相关研究。研究人员从圣讷克泰尔（Saint-Nectaire）地理标志干酪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菌株。对分离菌株进行全基因组测序，并基于泛基因组开展比较基因组分析。同时对菌株的重要功能特性进行了研究，包括酸化活性与蛋白水解活性。研究选取了代表该产区菌株多样性的22株分离菌株，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菌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，分离菌株可划分为5个不同的类群。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）功能注释结果表明，分离菌株的附属基因内容参与了不同的功能类别。研究同时观察到，菌株的酸化活性存在较高变异性，而蛋白水解活性的多样性则相对较低。上述结果表明，嗜热链球菌物种的高度遗传与功能多样性，可源自面积仅1,800 km²的小型地理区域，且该多样性可被开发用于满足本土发酵剂的应用需求。