Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.

中文翻译：

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乳酸乳球菌亚种的基因组特征和碳水化合物的代谢活性研究。瑞士型奶酪成熟期间的乳酸菌。

乳酸乳球菌亚种的遗传多样性和代谢特性。使用系统发育，全基因组和转录组分析方法对乳酸菌进行了研究。当前研究中使用的基因组可以从GenBank获得和下载，这些基因组主要与从乳制品中分离出的微生物有关，其次与其他食品中分离出的微生物有关。为了研究微生物的遗传多样性，使用了各种生物信息学工具，例如平均核苷酸同一性，数字DNA-DNA杂交，系统发育分析，直系同源群分析，KEGG正交分析和泛基因组分析。结果表明，Lc。乳酸亚种 根据16S rRNA基因序列，无法将乳酸菌充分分离为系统发育谱系，基于核心基因组的系统发育分析更为合适。菌株的全基因组分析表明，核心，辅助基因组和独特基因组分别由1036、3146和1296个基因组成。考虑到全基因组和KEGG正交分析的结果，Lc的代谢网络。乳酸亚种 就其碳水化合物的代谢能力而言，乳酸菌正在重建。根据瑞士型Maasdam奶酪在20°C和5°C熟化过程中的转录组数据，表明微生物进行了混合酸发酵，产生乳酸，甲酸，乙酸盐，乙醇和2，3-丁二醇。在较高的成熟温度下，混合酸发酵更为明显。在较低的成熟温度下，与混合酸发酵有关的基因受到抑制，而乳酸的产生却不受影响，类似于纯乳酸发酵。