Evolution of Microbial Host Specificity in E. coli

大肠埃希氏菌是人类和动物正常肠道微生物区系的一部分。人们普遍认为，大肠杆菌可以在不同动物之间传播，因此被认为是一种宿主通才。然而，越来越多的文献表明，许多菌株是宿主专家，这种细菌物种可能代表一个物种复合体(即，由许多细菌物种组成)。因此，它的遗传多样性可能反映了这种微生物对各种动物和非动物宿主环境的进化辐射。大肠杆菌在动物肠道的定植能力取决于其对宿主肠道微环境的生理条件的感知和反应能力，并与内源微生物群竞争生存和复制的能力。据推测，这种感觉基因组，或调节组，将面临强大的进化选择压力，作为一种适应性和决定性的力量，驱动宿主特异性。基于我们最近发表的论文(由一年的NSERC资助)，我们通过对调节组[基因间隔区(ITGRs)]中DNA序列变异的逻辑回归分析，确定了与宿主特异性相关的新的大肠杆菌单核苷酸多态(SNP)生物标记物。这些数据支持我们的假设，即ITGRs带有宿主特有的信息。这与传统的生物信息学方法(即无监督学习)不同，传统的生物信息学方法通常无法解决这些复杂的宿主特定生物标志物模式。在目前的提案中，我们打算通过使用基因篡改方法检测宿主特异性菌株(通过ITGR生物标记物分析鉴定)在不同实验室动物(小鼠、沙鼠和仓鼠)之间交叉传播的能力来进一步研究大肠杆菌的宿主特异性。此外，我们建议使用全基因组测序(WGS)和有针对性的ITGR测序方法在从广泛的动物宿主收集的大量大肠杆菌分离物中识别宿主特异性生物标志物。*这项研究将有助于表征与该物种向不同动物宿主的进化辐射相关的群体遗传结构，并确定宿主选择压力下基因组的关键区域。这些发现非常重要，因为它们可以用来识别可能从一个动物宿主传播到另一个动物宿主(即产生志贺毒素的大肠杆菌)的新出现的致病大肠杆菌菌株的宿主来源。这项研究还将有助于确定可用于追踪水/食品环境中粪便污染宿主来源的遗传目标--环境科学家/监管者/行业专业人员可利用这些工具改进微生物风险评估，并制定风险缓解措施以控制水/食品的污染(即水源保护)。

Escherichia coli is part of the normal microbial gut flora of humans and animals. It is generally believed that E. coli can transmit between different animals and is therefore considered a host-generalist. However, a growing body of literature demonstrates that many strains are host-specialists and that this bacterial species may represent a species-complex' (i.e., comprised of many bacterial species). Consequently, its genetic diversity may be reflective of the evolutionary radiation of this microbe into a wide variety of animal and non-animal host environments. The ability of E. coli to colonize the gut of an animal depends on its ability to 'sense-and-respond' to the physiological conditions of the host gut microenvironment and compete with endogenous microflora for survival and replication. It is hypothesized that this sensory genome, or regulome, would be under strong evolutionary selection pressure as an adaptive and deterministic force that drives host-specificity. Based on our recent publications (funded through a 1 yr NSERC), we have identified novel single nucleotide polymorphic (SNP) biomarkers of E. coli that correlate with host-specificity using logic regression analysis of DNA sequence variations in the regulome [intergenic regions (ITGRs)]. The data support our hypothesis that ITGRs are embossed with host-specific information. This is unlike traditional bioinformatic approaches (i.e., unsupervised learning) that have generally fail to resolve these complex host-specific biomarker patterns. In the current proposal we intend to further study the host-specific nature of E. coli by examining the ability of host-specific strains (identified by ITGR biomarker analysis) to cross-transmit between different laboratory animals (mice, gerbils and hamsters) using gene doctoring methods. Furthermore, we propose to use whole genome sequencing (WGS) and a targeted ITGR sequencing approach to identify host-specific biomarkers in a large library of E. coli isolates collected from a wide range of animal hosts. *** The research will be instrumental in characterizing population genetic structures of E. coli that are associated with the evolutionary radiation of this species into different animal hosts, and identify key areas of the genome under host-selection pressure. These findings are critically important, as they can be used to identify host-sources of emergent disease-causing E. coli strains that may transmit from one animal host into another animal host (i.e., shigatoxin producing E. coli). This research will also help identify genetic targets useful for tracking host sources of fecal pollution in water/food environments - tools that are useful for environmental scientists/regulators/industry professionals for improving microbial risk assessment and developing risk mitigation measures to control contamination of water/food (i.e., source water protection).