Myroides属模式种的比较基因组学、种的分化及其与环境适应的关系

Till now, it's not clear which genes are initially changed in the bacterial speciation process and what's the relationship between these genes and bacterial environmental adaptation. This project intends to answer this question by studying the genus Myroides. Currently, this genus harbors 6 species that can be classifed into two groups, three of which were isolated from marine conditions and three of which were isolated from human body. We'll sequence the genomes of all the type strains of the species of this genus. Two representatives, M. profundi D25 (from ocean) and M. odoratimimus LMG 12837 (from human body), were choosed from each group for detailed study.These two strains are different speceis from the bacterial classification standard but with close relationship considering the 16S rRNA gene identity and average nucleotide identity. They can be regarded as incipient differentiated species. Comparative genomic analyses of this two strains can reveal which genes are firstly differentiated and how these gene are produced as well as what's the functions of these genes. Bacterial transcriptomic analyses can indicate the transcription level of these differentiated genes. The phenotypic characters of these differentiated genes can be predicted using bioinformatic methods and verified by designed experiments. Taken together the results from this project, we could investigate the detailed process of bacterial incipient speciation and construct the relationship between speciation and environmental adaptation of the genus Myroides. We can also answer the questions of how different strains of this genus can thirve in so different two conditons and the speciation routines of two groups. Extant bacterial speciation models will be discussed to find which model can explain the data. If all the current models can not explain the data, we will build new bacterial speciation mode from the reults of this project.

目前，对于细菌的种在分化过程中哪类基因最先开始发生变化及变化的基因在环境适应中的作用还不清楚。本项目拟以Myroides属的模式种为例研究种的分化与环境适应的关系。该属目前正式发表的种有6个，其中3个分离自海洋环境， 3个分离自人体环境。本项目首先对该属所有已经鉴定的模式种进行基因组测序和比较基因组学分析，揭示该属细菌的基因组特性。在此基础上，重点对其中2个亲缘关系较近的菌株M. profundi D25（海洋环境）和M. odoratimimus LMG 12837（人体环境）进行研究。探索在种的分化过程中最先出现变化的基因以及其产生机制。进一步利用转录组学技术分析变化基因的转录状况。预测转录基因对应的菌株表型并实验验证，建立种的分化与菌株环境适应之间的关系模型，阐明Myroides属的菌株适应不同环境的演化历程。最终揭示细菌种的初始分化过程与机制。

每年都有大量的微生物被外力从陆地转移到海洋。大部分陆地来源的微生物不能在海洋中生存，但毫无疑问有部分能存活下来。对于这部分陆地来源的微生物如何在海洋中生存和进化现在还不了解。拟杆菌门细菌Myroides profundi D25分离自距离中国大陆很近的冲绳海槽深海沉积物环境。本项目对其基因组进行了测序，结果表明其与人类条件致病菌Myroides odoratimimus具有很高的基因组相似性和共线性。系统发育和生理性质分析表明两个菌株的共同祖先位于陆地且两者分化时间较短，M. profundi D25是在较近的时间内从陆地转移到海洋并开始适应海洋环境。这为研究细菌在适应一个全新环境的初始过程中基因组的进化和种的分化提供了一个很好的研究对象。盐度是影响细菌生存的一个非常重要的因素，而高盐度是海洋环境的一个重要特征。对两个菌株从低盐环境转移到高盐环境下的转录组进行了测序。比较基因组学和比较转录组学分析表明M. profundi D25在适应高盐环境的初始阶段，通过基因横向转移获得的外源基因所起的作用较小，起主要作用的是纵向遗传的保守基因，通过调控保守基因的转录水平来适应新的高盐环境。该研究表明一些人类的致病菌可以在海洋环境下生存，这也为海滨区域公共卫生控制提供了重要的信息。.基因横向转移获得的外源基因通常认为在细菌适应新的环境方面起重要的作用。而本项目研究结果表明纵向遗传的保守基因在细菌适应全新环境的初始阶段发挥着比横向转移基因更为重要的作用。细菌可以通过调控保守基因的转录以很快的适应一个全新的环境，这丰富了对细菌环境适应方式的认识。