PhD fellowship in Interactions between Eukaryotic and Prokaryotic Microbiomes in Pigs

We are offering a PhD fellowship in Interactions between Eukaryotic and Prokaryotic Microbiomes in Pigs commencing on 1st January 2024 or as soon as possible hereafter. The position is funded by two projects, the EU Innovation Action AVANT and the Novo Nordisk Foundation project PIG PARADIGM. The research activities will focus on the use of metagenomics to understand how fungi and protozoa that make up the eukaryotic microbiome of the porcine intestine respond to external stimuli and modulate the bacterial community structure, thereby contributing to pig health and disease.

Our group and research
The PhD student will be a member of the One Health Antimicrobial Resistance (OHAR) research group led by Prof. Luca Guardabassi. Our research focuses on discovery and development of solutions for improving diagnosis and antimicrobial therapy of bacterial infections in veterinary medicine using a One Health approach. For more information: https://ivh.ku.dk/english/research/veterinary_clinical_microbiology/one-health-antimicrobial-resistance/

Project description

The project will investigate the role of fungal and protozoan microeukaryotes as modulators of the intestinal bacterial community structure in pigs. Our hypothesis is that these microorganisms play a key, yet largely neglected role in the assembly and resilience of the bacterial microbiome. The project will benefit from the large amount and diversity of samples and data collected during longitudinal cohort studies conducted on pig farms in the two funding projects. The approach is to combine shotgun metagenomics with amplification and sequencing of the ITS2 region and the 18S rRNA gene, as these methods provide higher sensitivity for studying fungi and protozoa, respectively. Positive associations with pig health will be further validated under controlled experimental conditions by assessing the effects of administering selected fungal or protozoan species. This research will elucidate how inter-kingdom interactions are influenced by diet and antimicrobial therapy, as well as their possible role in the pathogenesis of post-weaning diarrhoea in piglets. Knowledge generated by the project can help develop new strategies for prevention of diarrhoea by manipulating the microeukaryotic fraction of the intestinal microbiota.

Principal supervisor isLuca Guardabassi, Professor with Special Duties (MSO), Department of Veterinary and Animal Sciences, E-mail: [email protected].

Start: 1st January 2024

Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision.

• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. veterinary medicine. biology and biotechnology. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

• The grade point average achieved
• Professional qualifications relevant to the PhD project
• Previous publications
• Relevant work experience
• Other professional activities
• A curious mind-set with a strong interest in bioinformatics and microbial ecology
• Language skills

Place of employment

The place of employment is at the Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories and animal facilities.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years. The start date is 1st of January 2024 or after agreement.

The employment is conditioned upon the applicant’s success­ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 28,900 DKK/Roughly 3,880 EUR (April 2023 level) plus pension.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

4. Publication list (if possible)

Application deadline: 8th October 2023, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in weeks 46 and 47.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Kilde: Jobnet.dk