Table_5_Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species.XLSX

Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.

乳酸链球菌（Streptococcus thermophilus）作为乳制品工业的主要发酵剂，具有极高的经济价值。本研究分析了23个乳酸链球菌的完整基因组，旨在揭示该物种在进化、生物学和工艺特性方面的创新点。全基因组分析表明，该物种拥有大量保守基因，且其泛基因组可能即将闭合。根据全基因组系统发育和平均核苷酸一致性（ANI）分析，大多数乳酸链球菌菌株被分为两个主要集群（即集群A和集群B）。具体而言，集群A包括染色体大于1.83兆碱基对（Mbp）的菌株，而集群B则包括染色体小于此阈值的菌株。这一发现表明，属于两个集群的菌株可能通过基因的获得或丢失事件而分化。此外，集群A中的某些菌株还可进一步细分为亚群，例如亚群I（包括ASCC 1275、DGCC 7710、KLDS SM、MN-BM-A02和ND07）、亚群II（包括MN-BM-A01和MN-ZLW-002）、亚群III（包括LMD-9和SMQ-301）以及亚群IV（包括APC151和ND03）。在集群B中，某些菌株形成了一个独特的亚群，即亚群I（包括CNRZ1066、CS8、EPS和S9）。观察到的乳酸链球菌的集群和亚群表明，该物种内存在谱系，这一观点得到了多个基因组特征的分布和/或结构的不同程度支持。这些特征包括外多糖（EPS）基因簇、成簇规律间隔短回文重复序列（CRISPRs）-与CRISPR相关的（Cas）系统、限制修饰（R-M）系统以及基因组岛（GIs）。值得注意的是，组氨酸生物合成簇存在于所有集群A菌株（包括NCTC12958T菌株）中，但在集群B的所有菌株中均不存在。与乳糖/半乳糖降解和尿素代谢、氨肽酶、大多数氨基酸和肽转运蛋白以及氨基酸生物合成途径相关的其他位点在所有菌株中均被发现是保守的，这表明它们在物种中起着核心作用。本研究强调了测序和分析更多乳酸链球菌完整基因组的重要性，以进一步阐明该发酵剂在乳制品工业应用中可能相关的菌株多样性方面的重要方面。