The Population Biology of Vibrio cholerae

尽管种群生物学在动物和植物方面已经是一门成熟的科学，但对于微生物来说，它仍然处于起步阶段。大多数群体“微”生物学的基础工作都是用人类病原体进行的，这些病原体并不代表环境细菌。不幸的是，大多数野生细菌很难培养，这限制了我们获得足够多的个体来研究微生物群体水平现象的能力。不依赖培养的方法，如宏基因组学和核糖体小亚基基因测序，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中得到了很好的研究，因为它是人类霍乱疾病的原因，以及水生动物的各种感染。它特别适合于群体生物学研究，因为它具有易于在纯培养中大量选择性分离的独特特性。使用这个新开发的模型系统，我们可以第一次解决基本问题：新的生态类型和物种出现的频率以及它们的稳定性如何？自然种群的突变率、多样性和规模是多少？这些定义人口的参数在时间和地理上是如何变化的？*我们采用两种新的方法，这个模型系统来回答这些问题。第一种是对环境DNA样品进行物种特异性蛋白质编码基因扩增。这种方法提供了更高的分辨率比其他基因标记以前使用的文化独立的研究，如金标准核糖体小亚基基因。它还允许针对单一物种进行特定目标定位，以捕获环境样本中的完整多样性。第二种方法是群体泛基因组学，即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。第一个是在法尔茅斯（MA，美国）的沿海池塘，在那里我们已经确定了一个新的姐妹种V. cholesterol，V. metoecus，以及多个V. cholesterol生态型。该网站的目标是研究新物种和生态类型的出现。第二个地点是孟加拉国的达卡市，我们在那里建立了六个地点的长期直接采样程序。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。来自美国和孟加拉国的种群比较将提供有关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.**