Genomic characterization of Lactobacillus fermentum DSM 20052
Genomic characterization of Lactobacillus fermentum DSM 20052
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DOI：
10.1186/s12864-020-6740-8
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发表时间：
2020-04-29
期刊：
影响因子：
4.4
通讯作者：
Barrangou, Rodolphe
中科院分区：
文献类型：
--
作者：
Brandt, Katelyn;Nethery, Matthew A.;Barrangou, Rodolphe
发酵乳杆菌是乳酸菌复合体的一员，由于已知的拮抗特性和对评估可能对人类健康有益的菌株的益生菌潜力的兴趣，发酵乳杆菌最近引起了越来越多的关注。结果我们测定了该类型菌株的全基因组序列，并将其与该物种中的37个基因组序列进行了比较。结果揭示了九个分支的遗传多样性，内容可变，包括可移动的遗传元件、CRISPR-CAS免疫系统和基因组岛，以及许多基因组重排。有趣的是，我们在72%的基因组中发现了I型、II型和III型CRISPR-Cas系统的高频率出现，并具有高度的菌株超变性。结论这些发现为具有科学和商业价值的发酵乳杆菌菌株的遗传特征提供了基础。此外，我们的研究使得能够在基因组信息的情况下选择具有特定特征的菌株用于商业产品配方，并为感兴趣的特征的功能表征建立了框架。
BackgroundLactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of select strains that may provide human health benefits. Here, we genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species.ResultsWe determined the polished whole genome sequence of this type strain and compared it to 37 available genome sequences within this species. Results reveal genetic diversity across nine clades, with variable content encompassing mobile genetic elements, CRISPR-Cas immune systems and genomic islands, as well as numerous genome rearrangements. Interestingly, we determined a high frequency of occurrence of diverse Type I, II, and III CRISPR-Cas systems in 72% of the genomes, with a high level of strain hypervariability.ConclusionsThese findings provide a basis for the genetic characterization of L. fermentum strains of scientific and commercial interest. Furthermore, our study enables genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest.