The Population Biology of Vibrio cholerae

点击翻译按钮获取中文摘要

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.**