Two PhD Positions in Blastocystis and Gut Microbiome

Parazitologický ústav

Evoluční parazitologie

Laboratoř genomiky a diverzity protist

Pracovní smlouva

Biology Centre of the Czech Academy of Sciences (BC CAS, https://www.bc.cas.cz/en), University of South Bohemia in Ceske Budejovice (USB, https://www.jcu.cz/en/) and University of Stavanger (UIS, https://www.uis.no/en) invite applicants for two fully funded, joint PhD Fellowships in researching interactions between Blastocystis and gut microbiome at the Faculty of Science, Department of Molecular Biology and Genetics (https://www.prf.jcu.cz/en/faculty/departments/department-of-molecular-biology-and-genetics).

This is a trainee position that will give promising researchers an opportunity for academic development through a PhD education leading to a doctoral degree. The appointment is for three years with research duties exclusively.

The PhD Fellow will be affiliated with the following Norwegian Research Council funded project: The role of Blastocystis in inflammatory bowel disease (324516). This is a large interdisciplinary project with collaborators at the University Hospital Stavanger, the Staten Serum Institute in Copenhagen, Denmark, and the Institute of Parasitology in Ceske Budejovice (IP, https://www.paru.cas.cz/en/), Czech Republic. See the Norwegian Research Council for details: https://tinyurl.com/2p86fyfv. The PhD student will be part of a team including Postdoctoral Fellows and several other PhD students.

Project background: In the clinic, microbial eukaryotes are usually treated as parasites. However, recent data suggest a possible beneficial and/or commensal role for intestinal eukaryotes such as Blastocystis. Given the widespread distribution of Blastocystis in the general population and our preliminary data, we hypothesise that this intestinal microbe plays a beneficial role in human intestinal health and inflammatory bowel disease (IBD) in particular. The current literature on IBD and the gut microbiome has mainly focused on the bacterial microbiome while ignoring microbial eukaryotes. Therefore, it remains unknown whether gut microbial eukaryotes such as Blastocystis are associated with clinical outcomes such as disease activity, gut inflammation, treatment response, or quality of life and fatigue in patients with IBD.
This project will thoroughly address our current lack of understanding of the role of the intestinal protist Blastocystis in intestinal health and inflammatory bowel disease (IBD) in particular. Our hypothesis is that the IBD gut is unfavourable for strict anaerobes such as Blastocystis. Currently, there is controversy in the literature as to whether this organism is harmful, commensal, or beneficial. As these studies were based on small cohorts, it is important to finally address this knowledge gap using larger cohorts. Using the cohort of patients from the Stavanger University Hospital Inflammatory Bowel Disease study (SUSI) will finally provide us with solid information on the presence of Blastocystis in IBD patients.

Detailed work description:
• Most of the worktime will be spent on bioinformatic analyses of next-generation sequencing data. Specifically, metagenomics, metatranscriptomics, differential expression. You will be responsible for managing very large datasets.
• In the laboratory, you will work at processing of the raw biological materials for next-generation sequencing. Including, but not limited to, nucleic acid extractions next-generation library preparation.
• You should also be capable of basic culturing techniques and be able to maintain regularly transferred microbial cultures.

• We are looking for applicants with a strong academic background who have completed master degree within the biological sciences, preferably bioinformatics, molecular biology (specifically next-generation sequencing), microbiology or parasitology or microbial ecology.
• The emphasis will be placed on candidates previous experienced with molecular biology, next-generation sequencing, bioinformatics and microbial ecology methods or microbiome research.
• Candidates' motivation to work on the project and learn new methods as stated in their motivation letter is also important part of the evaluation.
• Candidate has to be able to work independently and in a team, be innovative and creative.
• Candidates need to be capable of fluently communicating in English language.

• 5 weeks of paid holiday per year in total for 1 FTE
• Subsidized lunches in our own canteen
• Standard health insurance and social security
• Benefits from Social fund and student benefits
• Working in a stable, prestigious research institution of international importance
• Welcome service and further support for foreigners (HR Award)
• Friendly & stimulating international working environment
• Work-life balance in a middle-sized university city offering options for outdoor, sport & cultural activities
• Free language classes (Czech for foreigners, English for Czechs)
• Opportunity to take part in mentoring programmes as a mentor or a mentee
• Concessionary mobile tariff and banking services at the contractual operator and bank
• Access to accommodation in dormitories at the campus shared by the Biology Centre and the University of South Bohemia (for PhD students)

The position is vacant from 1 March 2023 and is funded by the University of Stavanger for 3 years.

The research will be carried out at the Institute of Parasitology, Biology Centre CAS in Ceske Budejovice, Czech Republic. The students will be joining laboratories of Dr. Martin Kolisko (https://www.paru.cas.cz/en/sections/organismal-and-evolutionary-parasitology/laboratory-of-genomics-and-diversity-of-protists/) and Dr. Katerina Jirku (https://www.paru.cas.cz/en/sections/opportunistic-disease/laboratory-of-parasitic-therapy/), respectively. Currently, there are 3 postdocs and 2 PhD students working in the group of Dr. Martin Kolisko and 1 postdoc and 2 PhD students in laboratory of Dr. Katerina Jirku. It is assumed that the appointee will work full time on the project and that she/he will participate in the academic community.

We are looking for two PhD candidates. The committee will select three top candidates that will be interviewed online. Successful candidates will be informed within a week of after interview.

The Biology Centre of the Czech Academy of Sciences holds the HR Excellence in Research Award. Our selection process meets European standards for recruitment of researchers (https://www.bc.cas.cz/en/employees/candidates/otm-r/) and we provide our employees from abroad with welcome service (visa application, administration, relocation & settlement support).

Ceske Budejovice (2 hours south of the capital Prague) is a middle-sized city with ca. 100K inhabitants, relaxed atmosphere, over 750 years of tradition and a breathtaking countryside around. Both the town and the surrounding countryside provide numerous opportunities for research and leisure activities. There is also a growing international expert community at the Biology Centre CAS (BC CAS, https://www.bc.cas.cz/en/) and the University of South Bohemia (USB, https://www.jcu.cz/en/). In addition to that, the living costs are still low by international standards. Check out our Guide for Expats (https://www.bc.cas.cz/en/employees/) to read about life in the city and the Czech Republic.

To apply for this position, please submit the following documents via the REPLY button below:
• Cover letter explaining your motivation and fit to the project;
• CV with a full summary of your education and experience;
• References, certificates/diplomas and other documentation that you consider relevant;
• List of publications or other relevant research work.

More information on the position can be obtained from Dr. Martin Kolisko (kolisko@paru.cas.cz) and/or Dr. Katerina Jirku (pomajbikova@paru.cas.cz).