Hellenic Agricultural Organization, DEMETER, Institute of Technology of Agricultural Products, Department of Dairy Research, Ethnikis Antistaseos 3, 45221, Ioannina, Greece.
Food Microbiol. 2020 May;87:103392. doi: 10.1016/j.fm.2019.103392. Epub 2019 Nov 26.
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.
利用系统发育、泛基因组和宏转录组分析研究了乳球菌乳亚种的遗传多样性和代谢特性。本研究中使用的基因组可从 GenBank 下载，主要与乳制品中分离的微生物有关，其次与其他食品有关。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，如平均核苷酸同一性、数字 DNA-DNA 杂交、系统发育分析、直系同源簇分析、KEGG 直系同源分析和泛基因组分析。结果表明，基于 16S rRNA 基因序列，乳球菌乳亚种菌株不能充分分为进化枝，基于核心基因组的系统发育分析更为合适。菌株的泛基因组分析表明，核心、辅助和独特基因组分别包含 1036、3146 和 1296 个基因。考虑到泛基因组和 KEGG 直系同源分析的结果，重建了乳球菌乳亚种的代谢网络，考虑了其碳水化合物代谢能力。根据瑞士型马司卡彭干酪在 20°C 和 5°C 成熟过程中的宏转录组数据，表明该微生物进行了混合酸发酵，产生乳酸、甲酸盐、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，参与混合酸发酵的基因受到抑制，而乳酸的产生不受影响，类似于同型乳酸发酵。比较基因组学和宏转录组学分析是了解作为发酵剂使用的乳酸菌的基因组多样性以及发酵乳制品中发生的代谢活性的有力工具。
