Wels Michiel, Siezen Roland, van Hijum Sacha, Kelly William J, Bachmann Herwig
NIZO Food Research B.V., Ede, Netherlands.
TI Food and Nutrition, Wageningen, Netherlands.
Front Microbiol. 2019 Jan 31;10:4. doi: 10.3389/fmicb.2019.00004. eCollection 2019.
is one of the most important micro-organisms in the dairy industry for the fermentation of cheese and buttermilk. Besides the conversion of lactose to lactate it is responsible for product properties such as flavor and texture, which are determined by volatile metabolites, proteolytic activity and exopolysaccharide production. While the species consists of the two subspecies and their taxonomic position is confused by a group of strains that, despite of a genotype, display a phenotype. Here we compared and analyzed the (draft) genomes of 43 strains, of which 19 are of dairy and 24 are of non-dairy origin. Machine-learning algorithms facilitated the identification of orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation. This allowed the unambiguous categorization of the genotype/phenotype disparity of ssp. and ssp. strains. A detailed analysis of phenotypic properties including plasmid-encoded genes indicates evolutionary changes during niche adaptations. The results are consistent with the hypothesis that dairy isolates evolved from plant isolates. The analysis further suggests that genomes of phenotype strains are so eroded that they are restricted to a dairy environment. Overall the genome comparison of a diverse set of strains allowed the identification of niche and subspecies specific genes. This explains evolutionary relationships and will aid the identification and selection of industrial starter cultures.
是乳制品行业中用于奶酪和酪乳发酵的最重要的微生物之一。除了将乳糖转化为乳酸外，它还负责产品的风味和质地等特性，这些特性由挥发性代谢产物、蛋白水解活性和胞外多糖的产生所决定。虽然该物种由两个亚种组成，但其分类地位却被一组菌株所混淆，这些菌株尽管具有基因型，但却表现出表型。在这里，我们比较并分析了43株菌株的（草图）基因组，其中19株来自乳制品，24株来自非乳制品来源。机器学习算法有助于识别蛋白质序列直系同源组（OGs），这些直系同源组可作为分类地位或分离源的预测指标。这使得对亚种和亚种菌株的基因型/表型差异能够进行明确分类。对包括质粒编码基因在内的表型特性的详细分析表明了生态位适应过程中的进化变化。结果与乳制品分离株从植物分离株进化而来的假设一致。分析还表明，表型菌株的基因组已被严重侵蚀，以至于它们仅限于乳制品环境。总体而言，对多种菌株的基因组比较使得能够识别生态位和亚种特异性基因。这解释了进化关系，并将有助于工业发酵剂培养物的鉴定和选择。
