- Job Title
- Postdoctoral Research Scientist (ONE Health of Gastrointestinal Pathogens)
- Post Number
- Closing Date
- 6 Jan 2019
- Starting Salary
- £31,250 - £38,100
- Hours per week
- Project Title
- Examining the linked population genomics of bacterial pathogen populations found in the environment, animals and in human clinical disease
- Expected/Ideal Start Date
- 01 Feb 2019
- Months Duration
- Interview Date
- 10 Dec 2018
Main Purpose of the Job
Investigate the overlap in bacterial populations found in the environment, animals and human clinical disease. Use this information to predict the likely origin (human, animal, environmental) of both emerging pathogenic lineages and AMR determinants observed in human clinical cases.
This work will involve working directly with other microbiologists and sequencing experts, as well as working with bioinformaticians to identify, develop and deploy analysis tools to examine organisms of interest. The work will also involve elements of ecology, and so may require interactions with ecologists to plan work.
The work also involves key stakeholders within Public Health Wales Microbiology and Health Protection, who will provide data around human clinical disease, as well as expertise around AMR and anaerobic bacterial characterisation and culture.
Main Activities & Responsibilities
- To undertake bioinformatics analyses to characterise and examine the populations being exampled, including integration of data gathered from the environment with data generated/provided by Public Health Wales and Public Health England
- Undertake environmental sampling around the UK, and perform metagenomic/metataxanomic analyses on samples collected
- To culture bacterial isolates from samples collected, speciate organisms and perform DNA extractions for sequencing
- As agreed with line manager, any other duties commensurate with the nature of the post
Education & Qualifications
- A PhD or equivalent in a biological or computational biological science subject
- A BSc or equivalent in a science subject
Specialist Knowledge & Skills
- Molecular biology skills
- Experience/an understanding of metagenomics and/or 16S for community profiling
- Skilled in performing analysis on sequence data
- Knowledge of a programming language
- Culturing microbiological organisms
- Extracting DNA from cultured organisms
- Performing sample collection from the environment
- Laboratory experience handling microbiological organisms
- Performing bioinformatics analysis of molecular data (DNA or protein)
- Using the UNIX commandline
Interpersonal & Communication Skills
- Excellent interpersonal skills, with the ability to work well as part of a team
- Ability to operate independently when required
- Excellent communication skills, both written and verbal
- Promotes equality and values diversity
- Prepared/able to travel to rural locations to collect samples
- Attention to detail
Who We Are
Quadram Institute Bioscience
The Quadram Institute is at the forefront of a new interface between food science, gut biology and health, developing solutions to worldwide challenges in food-related disease and human health.
We are engaged in fundamental and translational food and health research, alongside clinical studies, endoscopy and industry, working together to become a leading international hub for food and health research, combining scientific excellence and clinical expertise, delivering impacts on patient care and accelerating innovation.
In preparation for the full opening of the Quadram Institute in 2018, the Institute of Food Research transitioned into Quadram Institute Bioscience on April 28th 2017.
Microbes in the Food Chain
Dr Connor’s group is focused on examining the population genomics of bacterial pathogens. This work makes use of genomic sequence data to establish how the populations bacteria found in one environment (e.g. human clinical cases) overlap with those found in other contexts (e.g. animals). This work is particularly focused around investigating the elements of pathogen lifecycles that are traditionally understudied – i.e. those that take place outside of the primary host. This work also includes re-examining pathogens in light of genome sequence data to better understand the host range and likely reservoirs of pathogens of interest, with a view to better developing strategies to control or prevent pathogen spread. As part of this work we are also interested in how the genes found in bacterial populations (particularly antimicrobial resistance genes) correlate (or not) with the hosts in which those bacteria are found.
Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Tom Connor at the Quadram Institute Bioscience (QIB), based in Norwich, UK.
The project forms part of the Microbes in the Foodchain Programme at the Quadram Institute, and focuses on understanding bacterial populations found in animals and the environment. The work has two aims 1) To examine and quantify the overlap of key bacteria found in both the environment and animals in human clinical disease 2) To quantify the population structure of emerging pathogens that are, or may be, animal associated.
The role is a mix of wet lab, fieldwork and computational biology. The postholder will undertake environmental sampling to collect and culture bacteria from a range of places including farms, water sources and hospitals. Once cultured, the postholder will sequence and analyse the samples that have been collected, alongside genomic sequence data derived from animals and human clinical cases. The principal organisms that we expect to find/examine are E. coli, Enterococcus, Salmonella, Campylobacter, and C. difficile.
The role will involve working with collaborators (most especially within Public Health Wales NHS Trust), and potentially working across a number of different organisms at once. The work will also involve applying and potentially contributing to the development of new analysis approaches to identify the source (human/animal/environmental) of bacteria and understand bacterial geneflow between different environments.
The ideal candidate:
The ideal candidate could be an environmental microbiologist or a researcher who has experience working on/with bacterial pathogens. The work will include practical elements, and so you should have some lab experience and be comfortable with laboratory activities such as culturing and extracting bacterial DNA. The ideal candidate would also have an interest in (and perhaps experience of) learning how to analyse next generation sequencing data. A PhD in a biological or computational biological science subject is essential.
As part of this position we would expect to train the candidate in bacterial population genomics, phylogenetics and comparative genomics.
Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a fulltime post for a period of 3 years.
We are committed to equal opportunities and welcome applications from all sectors of society. The Institute supports equality of opportunity within the workplace and expects all employees to share and display these values. To support our commitment, we have a range of family, faith and diversity friendly working arrangements to help all staff achieve excellence in their area of work.
As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.
About the Quadram Institute:
The Quadram Institute is a new interdisciplinary research institute at the forefront of a new era in food and health research. Its mission is to understand how food and the gut microbiota are linked to the promotion of health and the prevention of disease. A partnership between Quadram Institute Bioscience (formerly the Institute of Food Research), the University of East Anglia, the Norfolk and Norwich University Hospital and BBSRC, it brings together scientists and clinicians in a new state-of-the-art building. The Quadram Institute is based on the Norwich Research Park, one of Europe’s largest centres of life sciences and home of the John Innes Centre and The Earlham Institute. (https://quadram.ac.uk/).