Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
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DOI：
10.1073/pnas.1015622108
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发表时间：
2011-04-26
影响因子：
11.1
通讯作者：
Konstantinidis, Konstantinos T.
中科院分区：
文献类型：
--
作者：
Luo, Chengwei;Walk, Seth T.;Konstantinidis, Konstantinos T.
定义细菌种类仍然是一个具有挑战性的问题，即使是模式细菌大肠杆菌，并具有重大的实际后果，可靠的诊断传染病病原体和法规的运输和拥有的生物体的经济意义。E.大肠杆菌传统上被认为生活在人类和其他温血动物的胃肠道内，并且不能在其宿主之外长时间存活;这种理解是其作为粪便污染指示剂的广泛使用的基础。在这里，我们报告了9个环境适应菌株的基因组序列，这些菌株在表型和分类学上与典型的大肠杆菌没有区别。大肠杆菌（大肠杆菌或致病性）。然而，我们发现，哺乳动物基因组编码更多的功能，这些功能对人类肠道的适应性很重要，不与环境中的对应物交换遗传物质，因此不会根据最近提出的碎片化物种形成模型进化。这些发现与比当前定义更严格的细菌物种生态定义一致，并提供了开始用基于组学的程序取代定义新物种独特表型的传统方法的方法。它们对致病性大肠杆菌的可靠诊断和调控也有重要意义。大肠杆菌和大肠菌群细胞计数试验。
Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.