van Eijk Erika, Anvar Seyed Yahya, Browne Hilary P, Leung Wai Yi, Frank Jeroen, Schmitz Arnoud M, Roberts Adam P, Smits Wiep Klaas
Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
BMC Genomics. 2015 Jan 31;16(1):31. doi: 10.1186/s12864-015-1252-7.
Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.
In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.
Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.
艰难梭菌菌株630Δerm是通过在无抗生素培养基中连续传代获得的参考菌株630的自发红霉素敏感衍生物。它被广泛用作明确且易于处理的艰难梭菌菌株。尽管它与原始菌株在很大程度上相似，但它表现出的表型差异可能是潜在基因变化的结果。在此，我们基于单分子实时测序进行了从头组装，并分析了主要甲基化模式。
除了单核苷酸多态性和各种插入缺失外，我们发现移动元件CTn5存在于编码甲基转移酶rumA的基因中，而非参考菌株中其所在的粘附素CD1844基因中。
本研究中鉴定出的遗传特征可能有助于至少部分解释表型差异。该实验室菌株的注释基因组序列，包括对主要甲基化模式的首次分析，将成为艰难梭菌基因研究的宝贵资源。
