Research Scientist (Metagenomics of AMR in soil)
Post Details
Job Title
Research Scientist (Metagenomics of AMR in soil)
Post Number
1004468
Closing Date
15 Jun 2023
Grade
SC6
Starting Salary
£33,050 - £40,750
Hours per week
37
Expected/Ideal Start Date
01 Dec 2023
Months Duration
12

Job Description

Main Purpose of the Job

Applications are invited for a Research Scientist to join the group of Professor Alison Mather at the Quadram Institute Bioscience (QIB), based in Norwich, UK.

Antimicrobial resistance (AMR) has evolved in environmental bacteria over billions of years, producing a vast reservoir of AMR genes that can potentially be transferred to clinical pathogens. Agricultural soils are exposed to antibiotics through the use of manures or sewage sludge as fertiliser, or irrigation with reclaimed water. There is a concern that such exposure may promote AMR in food producing environments, increasing the likelihood of AMR transmission to the human microbiome via contaminated crops or environmental matrices. The field scale trials undertaken at Agriculture and Agri-Food Canada (AAFC) over the last 10-20 years offers a unique opportunity to investigate the effects of antibiotic application on soil communities and AMR, and how soils recover from long-term application of antibiotics.

The post holder will join a fun, international and supportive group with expertise in bioinformatics, microbiology, molecular ecology and epidemiology. Working closely with our collaborators at the University of Exeter and AAFC, the post holder will use state of the art metagenomic and bioinformatic approaches to determine the evolutionary effects of antibiotic residues on the soil resistome.

Key Relationships

Internal: With the line manager, Prof Alison Mather, group members and other researchers and research
support staff across the Institute. External: Collaborators at the University of Exeter and Agriculture and Agri-Food Canada

Main Activities & Responsibilities

Bioinformatics analysis of shotgun metagenome sequence data and other sequence data from soils, including micobial taxa and AMR analysis
Statistical analysis of metagenomic data and relevant epidemiological data
Preparation and submission of manuscripts for publication in peer-reviewed journals
Present research findings at internal and external meetings/events
Ensure research and record keeping are carried out in accordance with good practice, scientific integrity and in compliance with local policies and any legal requirements
Contribute to the smooth running of the group, including the effective use of resources and supervision of visitors to the laboratory, encouraging scientific excellence
As agreed with the line manager, any other duties commensurate with the nature of the post

Person Profile

Education & Qualifications

Requirement
Importance
A PhD in a relevant subject (e.g. Computational Biology, Microbiology, Molecular Genetics, Bioinformatics, Epidemiology or related discipline)
Essential

Specialist Knowledge & Skills

Requirement
Importance
Bioinformatics skills
Essential
Expertise using analytical programmes eg R, Python
Essential
Understanding of high-throughput sequencing and microbial (meta)genomics
Essential
Good publication record in peer-reviewed scientific journals commensurate with experience
Desirable
Understanding of antimicrobial resistance in bacteria
Desirable

Relevant Experience

Requirement
Importance
Hands-on experience with microbial genome and/or metagenome sequencing and analysis
Essential
Proven record in scientific writing commensurate with experience
Essential
Experience with quantitative data analysis
Essential
Experience with large sequence datasets
Desirable
Experience of oral research presentations
Desirable
Experience with command-line and cloud-computing environment
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Ability to think creatively, contribute new ideas, troubleshoot
Essential
Accurate record keeping
Essential
Ability to collaborate with internal and external stakeholders
Essential
Excellent communication skills, both written and oral, including the ability to present complex information with clarity
Essential
Good interpersonal skills, able to work as part of a team
Essential

Additional Requirements

Requirement
Importance
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Ability to maintain confidentiality and security of information where appropriate
Essential
Willingness to work outside standard working hours when required
Essential
Attention to detail
Essential
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
Essential
Promotes equality and values diversity
Essential
Willingness to undertake any necessary training for the role
Essential
Ability to undertake occasional travel (national/international) related to collaborations and/or seminars
Desirable

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.

The Quadram Institute is a diverse and multicultural scientific community. We thrive on our international and European links, appointing staff from across the world. Any candidate who would like further information on current or anticipated immigration requirements can contact the HR Team on +44 (0)1603 450888 or nbi.recruitment@nbi.ac.uk.

For more information about working at Quadram Institute Bioscience, please click here.

Department

Microbes and Food Safety

Group Details

Quadram Institute Bioscience:
QIB provides a vibrant and exciting setting composed of multiple research teams working on metagenomics, microbial genomics, molecular epidemiology and microbial communities. We offer the chance to work with world leading, cutting edge technologies both in sequencing and computational biology and give you the opportunity to broaden your skills using open source technologies, and bringing together biological, epidemiological and bioinformatics data. You will gain experience of working with large sequence datasets and with academic and government department collaborators, and have the opportunity to publish excellent science in leading peer-reviewed journals.

Living in Norfolk

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Research Scientist (Metagenomics of antimicrobial resistance in soils)

Applications are invited for a Research Scientist to join the group of Professor Alison Mather at Quadram Institute Bioscience (QIB), based in Norwich, UK.

Quadram Institute Bioscience:

QIB provides a vibrant and exciting setting composed of multiple research teams working on metagenomics, microbial genomics, molecular epidemiology, and microbial communities. We offer the chance to work with world leading, cutting edge technologies both in sequencing and computational biology and give you the opportunity to broaden your skills using open-source technologies, and bringing together biological, epidemiological and bioinformatics data. (https://quadram.ac.uk/).

Background:

Antimicrobial resistance (AMR) has evolved in environmental bacteria over billions of years, producing a vast reservoir of AMR genes that can potentially be transferred to clinical pathogens. Agricultural soils are exposed to antibiotics through the use of manures or sewage sludge as fertiliser, or irrigation with reclaimed water. There is a concern that such exposure may promote AMR in food producing environments, increasing the likelihood of AMR transmission to the human microbiome via contaminated crops or environmental matrices. The field scale trials undertaken at Agriculture and Agri-Food Canada (AAFC) over the last 10-20 years offers a unique opportunity to investigate the effects of antibiotic application on soil communities and AMR, and how soils recover from long-term application of antibiotics.

The post holder will join a fun, international and supportive group with expertise in bioinformatics, microbiology, molecular ecology and epidemiology. Working closely with our collaborators at the University of Exeter and AAFC, the postholder will use state of the art metagenomic and bioinformatic approaches to determine the evolutionary effects of antibiotic residues on the soil resistome.

The role:

The successful post holder will analyse and interpret shotgun metagenome sequence data and other sequence data to investigate the effects of different antibiotic residues on the soil microbial communities and AMR at three timepoints: short-term exposure (7 & 30 days after application); long-term exposure (after 10 years of annual exposure); and after cessation of antibiotic application (1, 2, and 3 years post-exposure). The post holder will lead and/or contribute to the preparation of written reports and research publications and present research findings at project meetings, scientific conferences and outreach/translation events. They will contribute to the smooth running of the group, including the effective use of resources and occasional supervision of visitors to the laboratory, encouraging scientific excellence.

The ideal candidate:

Candidates should have a PhD in a relevant subject (e.g. Computational Biology, Microbiology, Molecular Genetics, Bioinformatics, Epidemiology or related discipline), and experience in analysing microbial (meta)genome sequence data. The candidate must value teamwork and collaboration, be able to work independently, and have excellent communication and interpersonal skills. 

You will gain experience of working with large sequence datasets and with academic and government department collaborators, and have the opportunity to publish excellent science in leading peer-reviewed journals.

Additional information:

Salary on appointment will be within the range £33,050 to £40,750 per annum depending on qualifications and experience. This is a full-time post for a contract of 12 months, with an ideal start date of 1 December 2023 (flexible).

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.

The closing date for applications will be 15 June 2023

The Quadram Institute Bioscience is a registered charity (No. 1058499) and is an Equal Opportunities Employer.