Overview

Vibrios are a diverse genera of Gram-negative bacteria that are widespread in the marine environment. The most well-known Vibrio species is Vibrio cholerae, as the causative agent of cholera. However, the majority of Vibrios are not known to be pathogenic. In some oceanic regions Vibrio blooms are known to increase Vibrio abundance to account for ~20% of the total bacterial community (1), with abundance known to correlate with temperature and salinity. Vibrios serve an important role in the remineralisation of organic matter, forming biofilms that allow the recycling of carbon and nitrogen (2). These biofilms also provide an environment for inter-species genetic exchange, expanding the substrates that can be utilised for growth and increasing the virulence of Vibrios (2). Thus, having consequences for nutrient cycling and human health.

With the advent of high-throughput sequencing, there has been a rapid increase in the number of Vibrio genomes that have been sequenced. Currently, there are > 4,500 Vibrio genomes that are publicly available, with representatives from a range of Vibrio species. We have recently analysed these genomes for the presence of prophages, which were found to be widespread. Prophages are generally known to cause alterations to bacterial physiology expanding host metabolism (3) and are important in V. cholerae where the toxin gene causing cholera is carried by a prophage (4). At present, it is not known how prophages differ between different Vibrio spp or how widespread virulence factors or genes that expand host metabolism are in vibriophages.

We have recently found antibiotic resistance genes in a range of Vibrio prophages, suggesting they could be a reservoir of resistance genes. Therefore, prophages have a potential role in the horizontal gene transfer (HGT) of virulence and antimicrobial resistance genes, via specialised transduction.

In addition to prophages, many lytic bacteriophages are known to infect Vibrio spp. The role these phages have in HGT is equally unknown. How rates of generalised transduction and host range between different vibriophages varies, and how these parameters may affect HGT is unknown.

This project will seek to understand the role bacteriophages have in horizontal gene transfer in marine Vibrios. As the acquisition of new genes provides Vibrios with the potential to adapt to different environmental niches.

A) TEM of a marine bacteriophage. B)Colonies of Vibrio vulnificus. C) Diversity of Vibrio spp , D) Comparative genomics of bacteriophages

Methodology

This project will utilise existing Vibrio spp. genomes to begin to understand the diversity of prophages present in Vibrio spp and how prophage carriage may expand the metabolic function of Vibrio sp. This will involve the development of bioinformatic pipelines for the identification, annotation, and development of  a classification system for prophages in Vibrio spp. 

A model for the spread of genes by phages will be produced. The model will include infection of sensitive cells by phage, detailed timing of the lytic cycle, proportions of transducing or ARG-containing phage progeny, and population dynamics of the free virus particles. Three paradigms will be developed and compared: ordinary differential equations as a baseline; spatially homogeneous stochastic models; and spatially explicit stochastic models. Simulations will be carried out using established software packages, including Matlab and StochS.

“Wet lab” experimental work will include one-step growth experiments to determine latent period and burst size of a range of bacteriophages, to be used in modelling.

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.  This project will provide excellent training in bioinformatics, microbiology and modelling. It will use cutting edge bioinformatics and modelling to determine the role bacteriophages have in the horizontal gene transfer between Vibrio spp.

Timeline

Year 1: Annotation of prophages in ~6, 500 Vibrio genomes.

Comparative analysis of prophage genomes.

Year 2 -3: Classification of prophage genomes in Vibrios

Identification of virulence and antibiotic resistance genes in prophages. Development of stochastic models based on existing data.

One step experiments to determine burst size, latent period. Determination of transduction rates, using antibiotic resistance as a marker to detect transduction. Further model development and simulations using the range of emperically derived parameters.

Partners and collaboration (including CASE)

Dr A Millard has > 15 years experience in the sequencing and annotation of bacteriophage genomes, having lead the sequencing and analysis of the first cyanomyovirus and more recently developed methods for the high-throughput analysis of bacteriophage genomes. With his lab studying bacteriophages that infect a range of bacteria from E. coli to Synechococcus. The project will benefit from the expertise of Dr D. Stekel who has a background in the mathematical modelling of biological systems, including the modelling of antimicrobial resistance. Prof D Scanlan has >25 years’ experience in marine microbiology. 

Further Details

APPLICANTS should possess a BSc or MSc in Microbiology/Bioinformatics/Mathematics. With a particular interest in bioinformatics/modelling.  Experience and/or familiarity of using a linux computing environment is required.

Informal enquiries can be made to Dr Andrew Millard (adm39@le.ac.uk ) details of current research can be found here (www.millardlab.org) and details for additional supervisors labs can be obtained from http://www2.warwick.ac.uk/fac/sci/lifesci/people/dscanlan/, and https://dovlab.wordpress.com/