Department Microbiology, University College Cork, Ireland.
Microb Cell Fact. 2011 Aug 30;10 Suppl 1(Suppl 1):S13. doi: 10.1186/1475-2859-10-S1-S13.
The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade.
The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group.
The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli.
乳杆菌属的特点是表型和基因型多样性极高，最近的基因组分析进一步突出了这一点。然而，用于测序的物种选择不是随机的，分布也不均匀，迄今为止，仅 L. salivarius 分支有一个代表基因组。此外，没有数据可以促进对乳杆菌运动的功能基因组分析，而这种特性仅限于 L. salivarius 分支。
牛源分离株 Lactobacillus ruminis ATCC 27782 的 2.06 Mb 基因组由单个圆形染色体组成，GC 含量为 44.4%。计算机分析鉴定了 1901 个编码序列，包括细菌素样素、单个大型胞外多糖相关簇、两个 sortase 酶、两个 CRISPR 基因座和许多 IS 元件和假基因的基因。鉴定出与假定菌毛相关的基因簇，并在体外证明其转录。从人类分离的 L. ruminis 菌株 ATCC 25644 的基因组高质量草案组装表明，基因组略大，为 2.138 Mb，与 ATCC 27782 基因组具有高度的同线性。相比之下，对 L. ruminis 和 L. salivarius 的比较分析表明，这两个密切相关的物种之间缺乏长程同线性。将 L. salivarius 分支核心蛋白与分布在 4 个主要系统发育群的其他 9 个乳杆菌属物种的核心蛋白进行比较，确定了共享蛋白组和每个组特有的蛋白组。
L. ruminis 的基因组为指导 L. salivarius 分支其他成员的功能分析提供了一个比较工具，并增加了对这个独特的乳杆菌系与其他共生乳杆菌系分化的理解。基因组序列提供了一个明确的资源，以促进这些运动性肠道乳杆菌的遗传学、生物化学和宿主相互作用的研究。
