Metagenome analysis of polymicrobial diseases and its application to clinical fields

指状乳头状瘤性皮炎（Papillomatous数字式皮炎，PDD）是由包括不可培养菌种在内的多种细菌引起的疾病，是一种多微生物性疾病，是一类新的传染病。在本项目中，我们开发了一种适用于PDD宏基因组分析的DNA提取方案和基因组序列组装器。通过使用它们，我们获得了高质量的参考宏基因组序列，可用于重建PDD主要病原体的基因组。对于可培养的pdd相关物种噬菌体密螺旋体（Treponema phagedenis），我们测定了1株pdd衍生菌株和1株人源标准菌株的全基因组序列，以及5株pdd衍生菌株的高质量草图序列。通过比较这些基因组，我们揭示了这种微生物通过IS和MITE元件的爆炸性扩增、多重噬菌体感染以及这些移动遗传元件介导的广泛的基因组重排而进化和多样化的独特机制。

Papillomatous digital dermatitis (PDD) is caused by multiple bacteria including non-cultivable species, and is one of the polymicrobial diseases, a new category of infectious diseases. In this project, we developed a protocol for DNA extraction and a genome sequence assembler, both suitable for metagenome analysis of PDD. By using them, we obtained high quality reference metagenome sequences that can be used to reconstitute the genomes of major causative agents of PDD. As for Treponema phagedenis, a uniquely cultivable PDD-related species, we determined the complete genome sequences of one PDD-derived strain and one human-derived standard strain and, in addition, the high quality draft sequences of 5 PDD-derived strains. By comparing these genomes, we revealed unique mechanisms of evolution and diversification of this microbe via explosive amplification of IS and MITE elements, multiple phage infections, and extensive genome rearrangements mediated by these mobile genetic elements.