Genomic Approaches to Advance the Species Definition for Prokaryotes

推进原核生物物种定义的基因组方法

• 批准号: 0516252
• 负责人: James Tiedje
• 金额: $ 56.25万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-10-01 至 2009-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0516252&HistoricalAwards=false
• 关键词: Genomic; Approaches; Advance; Species; Definition

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.

据估计，地球上最小的生物--细菌和古生菌--的总生物量等于或超过所有陆地和海洋植物的总生物量，是未开发生物多样性的最大储藏库。尽管微生物具有全球重要性，但对其生物学的几个方面仍然知之甚少，包括什么界定了细菌物种。科学界越来越多地发现，目前对细菌的物种定义缺乏。这在传染病病原体的可靠诊断、知识产权、关于病原体运输和拥有的国际和国家法规、生物防御监督、报告和检疫方面产生了更广泛的影响。例如，导致人类严重肠道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被归类在同一物种。如果物种名称没有很好的依据，或者“物种”没有很好地界定表型，就会出现效率低下的情况，在某些情况下可能会导致严重的危害。新的监管程序明显限制了微生物学研究，包括菌株和模式材料的国际交换，这种情况可以通过更准确的细菌物种定义来帮助。这个项目的目标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。目标是确定基因内容是否有潜在的模式，可以用来定义一致的菌株集群，从而确定细菌自然物种边界的生物学证据。对几个细菌基因组家族的比较分析将揭示这些家族之间是否存在进化差异，以反映它们的生态位。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。研究工作还将包括为本科生和博士后科学家提供培训机会。