Evolution of Microbial Host Specificity in E. coli

大肠杆菌是人类和动物正常肠道菌群的一部分。一般认为，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，许多菌株是宿主专门性的，这种细菌可能代表一种“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在各种动物和非动物宿主环境中的进化辐射。大肠杆菌在动物肠道中定植的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，以及与内源性微生物群竞争生存和复制的能力。据推测，这种感觉基因组或规则组将在强大的进化选择压力下作为驱动宿主特异性的适应性和确定性力量。基于我们最近的出版物（通过为期1年的NSERC资助），我们已经确定了新的大肠杆菌单核苷酸多态性（SNP）生物标志物，这些标志物与宿主特异性相关，使用逻辑回归分析规律组[基因间区（ITGRs）]的DNA序列变化。这些数据支持我们的假设，即itgr具有宿主特定信息。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异性生物标志物模式。在目前的提案中，我们打算进一步研究大肠杆菌的宿主特异性，通过检测宿主特异性菌株（通过ITGR生物标志物分析鉴定）在不同实验动物（小鼠，沙鼠和仓鼠）之间使用基因治疗方法交叉传播的能力。此外，我们建议使用全基因组测序（WGS）和靶向ITGR测序方法，从广泛的动物宿主收集的大肠杆菌分离物的大型文库中鉴定宿主特异性生物标志物。***该研究将有助于表征大肠杆菌种群遗传结构，这些遗传结构与该物种向不同动物宿主的进化辐射有关，并确定宿主选择压力下基因组的关键区域。这些发现至关重要，因为它们可用于确定可能从一个动物宿主传播到另一个动物宿主的突发致病性大肠杆菌菌株的宿主来源（即产生志贺毒素的大肠杆菌）。这项研究还将有助于确定有助于追踪水/食物环境中粪便污染宿主来源的遗传靶点——这些工具对环境科学家/监管机构/行业专业人员改进微生物风险评估和制定风险缓解措施以控制水/食物污染（即水源保护）非常有用。

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).