基于天然特征对细菌进行分类是科学界尚未完全解决的问题，其焦点是如何界定细菌的物种及物种形成的机制。目前所用的DNA杂交和16S rRNA序列比对方法具有划时代意义，但因其参数都是连续性的，因此难以清晰区分近缘细菌。我们最近鉴定出了能清晰划定细菌种系群的遗传界限，其产生源自基因组歧化，与细菌新物种的形成密切相关。然而，由这种遗传界限所区分的细菌之间，可鉴定出上千种基因组歧化事件，但其中哪些可能导致了遗传界限的产生尚不清楚。在本项目中，我们拟以大肠菌和沙门菌为主要模型，探讨遗传界限的产生及其导致新物种形成的分子基础，并进一步验证其有关参数是否可广泛用于细菌天然物种的界定。我们所用细菌来自正常儿童、成年人和长寿老人，感染症和癌症患者，以及多种野生动物。这些细菌之间已经初显不同清晰度的遗传界限，适于细菌新物种的形成过程及其分子机制研究。我们对这个问题的探讨，将为细菌分类学的发展提供新的视角和理念。

Since the discovery of bacteria, scientists have attempted defining bacterial species but natural properties that can be used to clearly delineate bacteria on an evolutionary basis remain to be identified and characterized. The current criteria include DNA-DNA re-association rate at 70% and 16S rRNA sequence similarity at 97%. However, because both kinds of data are continuous, clear-cut genetic boundaries can hardly be determined among bacteria to define then as species. As a result, the current bacterial species tend to contain genetically as well as biologically quite diverse bacteria, making a name of bacteria meaningless. We have recently identified and characterized genetic boundaries among representative Salmonella lineages. In this application, we propose to experimentally validate these findings and determine whether the concept of genetic boundaries might be extended to other bacteria and whether the genetic boundaries can be used to define natural species of bacteria. We will use bacteria in the E. coli complex as the experimental system. We have a special E. coli resource, including a collection of strains isolated from more than 80 mammalian species and some birds. We already discovered genetic boundaries among the E. coli strains and here propose to find out whether E. coli from different host species may be defined as different natural species. This study may not only contribute to the bacterial taxonomy studies but also to evolutionary biology investigations.