The Population Biology of Vibrio cholerae

虽然种群生物学在动物和植物方面是一门发达的科学，但在微生物方面仍处于起步阶段。群体“微”生物学的大部分基础工作都是针对人类病原体进行的，而这些病原体并不代表环境细菌。不幸的是，大多数来自野外的细菌很难培养，这限制了我们获得足够的个体来研究微生物种群水平现象的能力。独立于培养的方法，如宏基因组学和小核糖体亚基基因测序，也取得了有限的成功，因为它们缺乏物种水平或更低水平的分辨率。***我的团队开发了一个独特的模型系统来研究细菌的种群生物学：无处不在的水生细菌霍乱弧菌。该物种的遗传学和生理学在实验室得到了很好的研究，因为它是人类腹泻病霍乱以及水生动物各种感染的原因。它特别适合于群体生物学研究，因为它具有易于在纯培养物中大量选择性分离的独特特性。利用这个新开发的模型系统，我们可以第一次解决一些基本问题：新的生态型和物种出现的频率有多高，它们有多稳定？自然种群的突变率、多样性和大小是什么？这些定义人口的参数在时间和地理上是如何变化的？****我们对这个模型系统应用了两种新的方法来回答这些问题。首先是在环境DNA样本上进行物种特异性蛋白质编码基因扩增。这种方法提供了比以前在培养独立研究中使用的其他基因标记（如金标准小核糖体亚基基因）更高的分辨率。它还允许对单个物种进行特定的靶向，以捕获其在环境样品中的完整多样性。第二种方法是群体泛基因组学，对来自单个样本的数百个分离株的完整基因组进行测序，现在可以通过下一代测序以低成本实现。霍乱弧菌的种群生物学研究将在两个主要地点进行。第一个是法尔茅斯（马萨诸塞州，美国）的一个沿海池塘，我们在那里发现了霍乱弧菌的一种新的姊妹种，metoecus，以及多种霍乱弧菌生态型。该站点的目标是研究新物种和生态型的出现。第二个地点是孟加拉国的达卡市，我们在那里建立了一个长期的六个地点的夜间采样程序。在每次采样时，收集霍乱弧菌分离株和环境DNA，并测量许多环境参数。这种时间研究将使我们能够研究细菌种群基本参数的变异性。比较来自美国和孟加拉国的种群将提供关于细菌物种如何适应不同环境的见解

Although population biology is a well-developed science for animals and plants, it is still in its infancy for microbes. Most of the foundational work for population "micro" biology has been performed with human pathogens, which are not representative of environmental bacteria. Unfortunately, most bacteria from the wild are hard to culture, limiting our ability to get enough individuals to study population-level phenomena for microbes. Culture-independent methods, such as metagenomics and small ribosomal subunit gene sequencing, have also had limited success, because of their lack of resolution at the species level or below.***My team has developed a unique model system to study the population biology of bacteria: the ubiquitous aquatic bacteria Vibrio cholerae. The genetics and physiology of this species are well studied in the laboratory, as it is the cause of the diarrheal disease Cholera in humans, as well as various infections in aquatic animals. It is especially suited for population biology studies, as it has the singular characteristic of being easy to selectively isolate in pure culture in large numbers. Using this newly developed model system, we can for the first time address fundamental questions: How often do novel ecotypes and species emerge and how stable are they? What are the mutation rates, diversity and sizes of natural populations ? How do these parameters defining populations vary temporally and geographically ?****We apply two novel approaches to this model system to answer these questions. The first is species-specific protein-coding gene amplification on environmental DNA samples. This method provides far greater resolution than other gene markers previously used in culture-independent studies, such as the gold standard small ribosomal subunit gene. It also allows the specific targeting of a single species to capture its complete diversity in environmental samples. The second approach is population pangenomics, the sequencing of the complete genomes of hundreds of isolates from a single sample, which is now possible at low cost with next-generation sequencing.***Population biology studies of V. cholerae will take place at two principal locations. The first is a coastal pond in Falmouth (MA, USA), where we have identified a novel sister species to V. cholerae, V. metoecus, as well as multiple V. cholerae ecotypes. The goal at this site is to study the emergence of novel species and ecotypes. The second site is Dhaka city in Bangladesh, where we have set-up a long-term forthnightly sampling routine of six sites. At each sampling, V. cholerae isolates and environmental DNA are collected and numerous environmental parameters are measured. This temporal study will allow us to investigate variability of fundamental parameters of bacterial populations. Comparison of populations from the USA and Bangladesh will provide insight on how bacterial species adapt to different environments.**