Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.
BMC Genomics. 2018 Mar 20;19(1):205. doi: 10.1186/s12864-018-4586-0.
Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities.
Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident.
The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.
副干酪乳杆菌存在于许多不同的环境中，包括乳制品和植物材料以及人类和动物的肠道。它们对各种小生境的适应与基因组和代谢水平上的种内多样性有关。在这项研究中，我们比较了从成熟切达干酪中分离出的三株副干酪乳杆菌菌株的基因组序列，其中两株（DPC4206 和 DPC4536）通过 PFGE 具有相同的基因组指纹，但表现出不同的代谢能力。
基因组大小从 DPC2071 的 2.9 Mbp 变化到 DPC4206 的 3.09 Mbp 和 DPC4536 的 3.08 Mpb。质粒的存在是菌株之间的一个区别特征，菌株 DPC2071 拥有异常数量的质粒（多达 11 个），而 DPC4206 有一个质粒，DPC4536 则没有质粒。每个菌株都具有其他两个分析菌株所没有的特定基因。这三个菌株在糖转化基因的丰度以及可作为能源使用的糖的类型上存在差异。还检测到了与乳制品小生境通常不相关的糖代谢基因，如肌醇和普鲁兰，但菌株不能利用这些糖。三个菌株的遗传内容在精氨酸和含硫氨基酸代谢的特定基因以及对重金属离子抗性的基因方面存在差异。此外，噬菌体残余物和噬菌体保护系统的存在存在明显的可变性。
本研究的结果证实了副干酪乳杆菌菌株之间存在相当大的异质性，即使是从同一小生境分离的菌株也是如此。
