功能性前噬菌体数据挖掘及数据库的建立

Functional prophages play an important role in pathogenicity and adaptive evolution of bacteria, as well as ensuring efficient and harmless phage therapy. However, obtaining the complete sequence of a functional phage genome is very difficult, regardless of wet lab experiments performed or computational prediction tools used. Because of this difficulty, few complete genome sequences of functional prophages are known, which hampers the progress of related research. In previous work, we established a unique functional prophage prediction method based on bacterial genome sequencing data, our experiments showed that this method is accurate and reliable. In this project, we aim to optimize the prediction method devised in our previous work and establish an intelligent prediction platform. Our goal is that functional prophage genome sequences can be quickly and accurately predicted from massive bacterial genome sequencing data. Furthermore, we will build a comprehensive functional prophage database and increase the number of known complete functional phage genomes 20-fold. With this database, we will systematically analyze five common pathogenic genera. This includes analyzing their functional prophages, summarizing the patterns of genome integration and lateral gene transfer, and researching the interaction between functional prophage and its host from the perspective of evolution. This project will provide big data support for research on phage-mediated transduction in bacteria as well as comparative genomics and evolution of functional prophages.

功能性前噬菌体在细菌毒力、适应性、进化及保证噬菌体治疗安全性中具有重要作用，但常规研究手段难以准确获得完整的、可被诱导的功能性前噬菌体基因组序列，导致其已知数量非常有限，影响了相关研究顺利进行。我们前期已建立了独特的基于细菌基因组测序数据的功能性前噬菌体预测方法，实验证明该方法准确可靠。为进一步降低该方法的漏检率并实现自动化，本项目拟继续优化和完善该方法，建立智能化预测平台，从海量细菌基因组测序数据中实现大规模功能性前噬菌体基因组的准确预测，并建立综合性的功能性前噬菌体数据库，将目前功能性前噬菌体全基因组序列数量扩充20倍以上，极大丰富噬菌体基因组多样性。在此基础上，重点针对五种常见病原菌属开展功能性前噬菌体基因组分析，归纳其整合规律及基因水平转移规律，从进化角度研究其与宿主间的相互作用关系。本项目的开展将为噬菌体介导的细菌毒力进化机制、噬菌体基因组及功能基因的研究提供大数据支持。

功能性前噬菌体在细菌毒力、适应性、进化及保证噬菌体治疗安全性中具有重要作用，有助于控制致病性、调节群落结构和维持肠道稳态。完整的功能性前噬菌体基因组序列对于理解噬菌体生物学是必不可少的。传统的噬菌体空斑技术不适用于功能性前噬菌体。其具有的溶原性导致采用常规研究手段，难以获得完整的、可被诱导的功能性前噬菌体基因组序列。现有的噬菌体预测生物信息学工具通常无法检测准确和完整的功能性前噬菌体基因组。本研究通过一种新的计算功能性前噬菌体检测方法（TemPhD）挖掘整合的活性噬菌体及其自发诱导形式，从细菌二代测序数据中获得了192，326个完整的功能性前噬菌体基因组，将现有的完整功能性前噬菌体基因组数量扩大了100倍以上。湿实验结果表明，我们的方法TemPhD可以准确获得功能性前噬菌体的完整基因组序列，具有精确的插入位点，优于其他现有的噬菌体预测方法。我们的分析表明，功能性前噬菌体可能通过以下方式在微生物进化中发挥作用：1）交叉感染不同的细菌宿主物种;2）转移抗生素耐药性和毒力基因;3）通过限制修饰和CRISPR/抗CRISPR系统与宿主相互作用。本研究成果提供了全面完整的功能性前噬菌体基因组数据库和相关信息，可为噬菌体研究提供宝贵的数据资源和支撑。