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.

地球上最小的生物，细菌和古细菌的总生物量估计等于或超过所有陆地和海洋植物的生物量，并且是未探索的生物多样性的最大储层。尽管微生物具有全球重要性，但其生物学的几个方面仍然鲜为人知，包括划界细菌物种的原因。 科学界越来越多地发现缺乏细菌的当前物种定义。这对可靠诊断传染病药物，知识产权，国际和国家的运输和拥有病原体，BiodeFense监督，报告和隔离的法规产生了更大的影响。例如，大肠杆菌O157：H7的高致病性菌株与无害的实验室菌株K12一起在同一物种中分组在一起。如果“物种”的指定不是良好的基础或表型，“物种”效率低下，在某些情况下可能会导致严重的伤害。新的监管过程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，这种情况可以通过细菌物种的更准确的定义来帮助。该项目的目的是使用全基因组序列分型和基因含量细菌的表达模式，以了解密切相关菌株之间的遗传差异。 目的是确定基因含量中是否存在潜在的模式，可用于定义菌株的相干簇，从而证明细菌天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是否反映其生态壁ches的家族之间存在进化差异。最后，这些分子分析可能会导致更好的工具来定义和识别物种。 研究工作还将涉及本科生和博士后科学家的培训机会。