PhD position in bioinformatics/evolutionary microbiology

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University constitutes a broad international environment for research and teaching. Research at IMBIM spans biochemistry, molecular and cell biology, structural biology, tumor biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is focused on basic science with strong relevance to the mechanisms behind health and disease in both animals and humans. More information: Forskning – Institutionen för medicinsk biokemi och mikrobiologi – Uppsala universitet

We are seeking a highly motivated PhD student for the project ”A two billion year long history of infections: evolution of host adaptation in early gammaproteobacteria”, funded by Vetenskapsrådet and led by Lionel Guy. The PhD student will be placed at Biomedicinskt centrum (BMC) in Uppsala.

Project description

The ability to subsist on other organisms through phagocytosis is a crucial step in eukaryotic evolution and a prerequisite for food webs, multicellularity, and probably also the acquisition of mitochondria. It also paved the way for intracellular parasitism, as certain bacteria avoided being broken down by their hosts and instead multiplied in the nutrient-rich cytoplasm.

Here we focus on Deep-branching Intracellular Gammaproteobacteria (DIG), a large group of related bacteria (e.g., Legionella and Francisella) with a wide variation of strategies for host adaptation. Our hypothesis is that the last common ancestor of DIG emerged during eukaryogenesis two billion years ago and was among the first bacteria to infect eukaryotes.

In the project, the PhD student will collect a solid selection of DIG genomes, including isolates from 30 new Legionella species, reconstruct their evolutionary history, assess their metabolic potential, and identify their genes for host adaptation. The PhD student will search the genomes for horizontal gene transfer from early eukaryotes or Asgard archaea, and specifically analyze the evolution within the genus Legionella.

A better understanding of the relationships between the first eukaryotes and their early invaders will shed light on eukaryogenesis, and particularly on the role of phagocytosis.

Qualification requirements

Eligible for postgraduate studies is the person who has

obtained a degree at the advanced level in bioinformatics, molecular biology, microbiology, microbial ecology, or a related field or completed at least 240 higher education credits, of which at least 60 higher education credits are at the advanced level including an independent project of at least 15 higher education credits, or in some other way acquired substantially equivalent knowledge.

The degree must be obtained, or expected to be obtained, before March 2027.

Documented programming skills in Python or R. Experience in using and/or developing methods within metagenomics and molecular evolution Basic understanding of and interest in microbial evolution Good knowledge of English, both oral and written Ability to independently plan, conduct, and complete research projects Creativity and good collaborative skills

Other desirable/merit-based qualifications

Experience in building pipelines for high-performance computing clusters (HPC) Competence in handling large datasets Experience in DNA extraction and preparation of sequencing libraries

The selection will be based on the following criteria: fulfillment of the above qualifications, grades in relevant courses, the relevance of the courses to the research program, as well as previous experience of work and research within the broader field addressed by the project. An overall assessment of the applicant will be made to hire the best possible candidate, who can undertake the doctoral education and contribute to a positive development of the research program. Great importance is placed on personal qualities such as analytical ability, precision, flexibility, and collaborative skills.

Provisions for doctoral students can be found in Högskoleförordningen 5 kap §§ 1-7 as well as in the university's rules and guidelines.

About the employment

The employment is fixed-term, according to HF 5 kap § 7. The scope is full-time. Commencement as soon as possible or by agreement. Location: Uppsala

For more information, contact Universitetslektor Lionel Guy, lionel.guy@imbim.uu.se

Welcome with your application no later than October 29, 2026, UFV-PA 2026/2912.

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