Center for Bioinformatics and Computational Genomics, School of Biology, and School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7200-5. doi: 10.1073/pnas.1015622108. Epub 2011 Apr 11.
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.
定义细菌物种仍然是一个具有挑战性的问题，即使对于模式细菌大肠杆菌也是如此，这对可靠诊断传染病病原体以及有关经济重要生物的运输和持有规定具有重大的实际意义。传统上认为大肠杆菌生活在人类和其他温血动物的胃肠道内，并且不会在宿主外长时间存活；这种理解是将其广泛用作粪便污染指标的基础。在这里，我们报告了 9 个适应环境的菌株的基因组序列，这些菌株在表型和分类上与典型的大肠杆菌（共生或致病）无法区分。然而，我们发现共生基因组编码了更多对在人类肠道中适应至关重要的功能，它们与环境同类之间不交换遗传物质，因此不符合最近提出的碎片化物种形成模型。这些发现与当前定义相比，对细菌物种的定义更加严格和具有生态学意义，并为用基于组学的方法取代传统的定义独特表型的方法来定义新物种提供了手段。它们对可靠诊断和监管致病性大肠杆菌以及大肠菌群计数测试也具有重要意义。
