Clostridioides (formerly Clostridium) difficile is a leading cause of healthcare-associated infections. Although considerable progress has been made in the understanding of its genome, the epigenome of C. difficile and its functional impact has not been systematically explored. Here, we perform a comprehensive DNA methylome analysis of C. difficile using 36 human isolates and observe a high level of epigenomic diversity. We discovered an orphan DNA methyltransferase with a well-defined specificity, the corresponding gene of which is highly conserved across our dataset and in all of the approximately 300 global C. difficile genomes examined. Inactivation of the methyltransferase gene negatively impacts sporulation, a key step in C. difficile disease transmission, and these results are consistently supported by multiomics data, genetic experiments and a mouse colonization model. Further experimental and transcriptomic analyses suggest that epigenetic regulation is associated with cell length, biofilm formation and host colonization. These findings provide a unique epigenetic dimension to characterize medically relevant biological processes in this important pathogen. This study also provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomic studies.

中文翻译：

---

艰难梭菌的表观基因组特征发现了一种保守的 DNA 甲基转移酶，可介导孢子形成和发病机制。

艰难梭菌（以前称为梭菌）是导致医疗保健相关感染的主要原因。尽管在对其基因组的理解方面取得了相当大的进展，但尚未系统地探索艰难梭菌的表观基因组及其功能影响。在这里，我们使用 36 个人类分离株对艰难梭菌进行了全面的 DNA 甲基化分析，并观察到高水平的表观基因组多样性。我们发现了一种具有明确特异性的孤儿 DNA 甲基转移酶，其相应的基因在我们的数据集和所有检查的大约 300 个全球艰难梭菌基因组中高度保守。甲基转移酶基因的失活会对孢子形成产生负面影响，这是艰难梭菌疾病传播的关键步骤，这些结果得到多组学数据的一致支持，基因实验和小鼠定植模型。进一步的实验和转录组学分析表明，表观遗传调控与细胞长度、生物膜形成和宿主定植有关。这些发现提供了独特的表观遗传维度来表征这一重要病原体的医学相关生物学过程。本研究还提供了一套比较表观基因组学和综合分析的方法，我们希望这些方法可以广泛适用于细菌表观基因组研究。