PhD position/s in medical science with a specialization in gut microbiota

Umeå University, Faculty of Medicine

Umeå University is one of Sweden’s largest higher education institutions with over 37,000 students and about 4,700 employees. The University offers a diversity of high-quality education and world-leading research in several fields. Notably, the groundbreaking discovery of the CRISPR-Cas9 gene-editing tool, which was awarded the Nobel Prize in Chemistry, was made here. At Umeå University, everything is close. Our cohesive campuses make it easy to meet, work together and exchange knowledge, which promotes a dynamic and open culture.

The ongoing societal transformation and large green investments in northern Sweden create enormous opportunities and complex challenges. For Umeå University, conducting research about – and in the middle of – a society in transition is key. We also take pride in delivering education to enable regions to expand quickly and sustainably. In fact, the future is made here.

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The Faculty of Medicine, which consists of 12 departments, is responsible for biomedical research and courses in the field of nursing and health care and has an extensive research and graduate education in more than 80 subjects.

Umeå University’s Department of Clinical Microbiology is looking for up to two PhD student/s within the field of medical science with a focus on bioinformatics. We offer an international, stimulating, and collaborative research environment where your scientific career development is promoted.

The project aims to track strain wide differences within human gut bacteria species across different populations. Our goal is to improve the understanding of adaptive mechanisms employed by different gut bacteria at a high resolution to guide next generation microbiota aided therapies.

Project description

Studying functional potential to assess fitness of human gut bacteria strains across populations

The gut microbiota is crucial for maintaining human health, and disease-specific alterations in our gut microbiota are now well-documented across populations. However, the overall composition and relative abundance of specific strains of the human gut microbiota may also naturally fluctuate with diet, geography, lifestyle factors, and age, both within an individual and across different populations. This knowledge is based on studies obtained from large scale shotgun sequencing of the human gut microbiome, only in the last few years.

The candidate/s will primarily develop and use methods for abundance and prevalence detection of human gut associated bacteria at the strain level. A major task will be to perform large scale shotgun metagenomic analysis (on up to 50000 samples) and to capture the distribution of strains and map their functions across human populations. The candidate/s will define the potential ecological functions and differential fitness with an aim to characterize strain wide differences within several species of human gut bacteria.

In addition to bioinformatics, candidate/s may have the opportunity to work on bacterial isolation from fecal samples, in vitro strain characterization, and high-throughput single-cell studies in the laboratory, depending on the interest.

Keywords: PhD position, Metagenomics, human gut microbiota, shotgun metagenomics, microbiota evolution, microbiome, long read sequencing, Metagenome assembled genomes, strain level metagenomics, high resolution metagenomics

You who are admitted to doctoral studies at the Faculty of Medicine will be part of the faculty-wide doctoral education programme. The doctoral programme comprises 25 credits and is offered in two study variants: 25 credits spread over 8 terms (a total of 4 years) or over 12 terms (a total of 6 years), starting each autumn and spring semester. More information about the programme can be found on the faculty’s web page for doctoral studies (Doctoral Studies at the Faculty of Medicine - Handbook (umu.se)).

Eligibility and Qualifications

You must have at least 240 higher education credits (hc), of which at least 60 hc are at an advanced level, in natural sciences, life sciences, or engineering
Applicants must be skilled in both oral and written communication in English, able to work independently as well as in collaboration with others, and be highly motivated.

Meritorious

A degree in bioinformatics, computational biology, (bio)statistics, (applied) mathematics, computer science, or a related field; candidates from other fields with strong programming/coding skills (see below) are also encouraged to apply.
Proficient in at least one programming language, preferably Python or R.
Experience in any of the following areas: large scale sequence analysis, microbial genomics, human gut microbiota research (shotgun metagenomics), Metagenome assembled genome construction, gut microbial genome, and gene database development.
Comfortable working in a diverse, inclusive, interdisciplinary, and highly collaborative environment.
Ability to navigate UNIX filesystems from the command line, working in conda environment, installation and implementation of packages from github, batch job submissions in clusters
Previous coursework or research experience in the biological sciences, microbiology, bacteria isolation and culturing, DNA extraction and library preparation for short and long read sequencing.

Further details

The position is funded (salary) via the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS; https://www.scilifelab.se/data-driven/), a 12-year initiative aimed at recruiting and training the next generation of data-driven life scientists. In addition to being affiliated with the Department of Clinical Microbiology at Umeå University (https://www.umu.se/en/department-of-clinical-microbiology/), you will be affiliated with the national DDLS program, through which you will have access to computing resources, the national DDLS research school, and other training and networking opportunities throughout Sweden.

You will be further affiliated with the Laboratory for Molecular Infection Medicine Sweden (MIMS; https://www.mims.umu.se/); MIMS is a member of the Nordic EMBL Partnership for Molecular Medicine, which is dedicated to the growing field of life sciences that investigates the molecular basis of disease and explores molecularly and genetically based treatments. There will be opportunities to collaborate with experts throughout Europe and beyond. Locally the research group is affiliated to the Umeå center for microbial research (UCMR; https://www.umu.se/ucmr/om-ucmr/) UCMR is an interdisciplinary research centre established by a consortium of scientists representing medical & molecular microbiology, molecular & structural biology, chemistry & physics, and is devoted to top quality research and novel applications in the fields of microbial pathogenesis.

How to apply

Doctoral position 4 years, starting according to agreement. The application is made electronically (via the system Varbi).

The application must contain:

A cover letter (one A4 page), highlighting your specific qualifications and motivation for the position. [eg: how your background aligns to the research area]
A curriculum vitae (CV), including a full list of publications. [preprints accepted]
Certified copies of diplomas, certificates, and grades.
Names and contact details of at least 2 reference persons.

For more details on the research area, contact

Chinmay Dwibedi [dwibedilab.org] chinmay.dwibedi@umu.se

We welcome your application!