Genomic Approaches to Advance the Species Definition for Prokaryotes

据估计，地球上最小的生物，即细菌和古细菌的总生物量等于或超过所有陆地和海洋植物的总生物量，是尚未开发的生物多样性的最大储存库。尽管微生物在全球具有重要意义，但人们对其生物学的几个方面仍然知之甚少，包括细菌种类的界限。科学界越来越发现，目前对细菌的物种定义是缺乏的。这对传染病病原体的可靠诊断、知识产权、关于运输和拥有病原体的国际和国家条例、生物防御监督、报告和检疫等方面产生了更广泛的影响。例如，导致人类严重肠出血性感染的高致病性大肠杆菌O157:H7菌株与无害的实验室菌株K12归为同一物种。如果物种名称没有很好地建立，或者“物种”没有很好地限定表型，就会出现效率低下的情况，在某些情况下可能导致严重的危害。新的监管程序明显限制了微生物学研究，包括菌株和类型材料的国际交流，这种情况可以通过更准确的细菌物种定义来帮助。该项目的目的是利用细菌的全基因组序列分型和基因含量和表达模式来了解密切相关菌株之间的遗传差异。目的是确定基因内容中是否存在潜在的模式，可以用来定义菌株的连贯簇，从而为细菌的自然物种边界提供生物学证据。对几个家族的细菌基因组进行比较分析，将揭示这些家族之间是否存在反映其生态位的进化差异。最后，这些分子分析可能会带来更好的工具来定义和识别物种。这项研究还将为本科生和一名博士后提供培训机会。

The total biomass of the smallest organisms on Earth, the bacteria and the archaea, is estimated to equal or exceed that of all terrestrial and marine plants, and is the largest reservoir of unexplored biodiversity. Despite the global importance of microbes, several aspects of their biology remain poorly understood, including what delimits bacterial species. Increasingly, the scientific community is finding the current species definition for bacteria to be lacking. This has broader impacts with regard to reliable diagnosis of infectious disease agents, intellectual property rights, international and national regulations for transport and possession of pathogens, biodefense oversight, reporting, and quarantine. For instance, the highly pathogenic strains of Escherichia coli O157:H7, which causes severe enterohaemorrhagic infections in humans, are grouped together in the same species with the innocuous laboratory strain K12. If species designations are not well founded or phenotype not well circumscribed by the "species", inefficiencies occur and in some cases could result in serious harm. New regulatory processes have noticeably constrained microbiological research, including the international exchange of strains and type material, a situation that could be aided by a more accurate definition for bacterial species.The objective of this project is to use whole-genome sequence typing and gene content and expression patterns of bacteria to understand the genetic differences among closely related strains. The goal is to determine if there are underlying patterns in gene content that can be used to define coherent clusters of strains, and hence biological evidence for a natural species boundary for bacteria. Comparative analyses on several families of bacterial genomes will reveal if there are evolutionary differences among the families that reflect their ecological niches. Finally, these molecular analyses may lead to better tools to define and identify species. The research effort will also involve training opportunities for undergraduate students and a postdoctoral scientist.