Researcher in ancient metagenomics - Hiring in process/Finished, not possible to apply

A position as a researcher in ancient metagenomics is available at the Department of Ecology and Genetics, Animal Ecology.

The Department of Ecology and Genetics is an international environment with staff and students from all over the world. Our research spans from evolutionary ecology and genetics to studies of ecosystems. For more information, see www.ieg.uu.se.

Project description: We aim to understand the effect of human activities on host-associated microbiomes of wild mammalian populations. More specifically, the project focuses on identifying antimicrobial resistance factors from ancient metacommunities derived from host-associated oral microbiome. Within only few decades after the advent of the antibiotics mass production in 1940s, antimicrobial resistance has become a major global health threat and combatting it now ranks on the top of the agendas of UN and WHO. Yet, we have very little understanding about the effects of antimicrobial resistance in wild animal populations and their potential to act as reservoirs for antimicrobial resistance genes. To provide a baseline, we characterize pristine, naïve bacterial communities from time periods that predate the mass production of antibiotics. In the next step, we evaluate in how far human-produced antibiotics have changed the composition, functional profiles and particularly antimicrobial potential of host-associated microbiomes using Scandinavian brown bears as model system.

Duties: The appointed candidate will contribute to production and carry out the analyses of shotgun sequences from dental calculus specimens of Scandinavian brown bears. The duties includes extraction of DNA using aDNA techniques from museum-preserved specimens, preparation of next-generation sequencing libraries with specific protocols adapted to the needs of the project, bioinformatics analyses of metagenomic data for taxonomic and functional characterization of the mammalian oral microbiome and specific identification and characterization of antibiotic resistance factors. It will also be necessary to construct metagenomic assembled genomes from the challenging ancient DNA samples and track the evolution of antimicrobial resistance in certain microbial linages. In cooperation with the group of Dan Andersson at IMBIM, the candidate will carry out functional analyses on the predicted antimicrobial variants. The candidate will prepare the results for publication in peer-reviewed journals and present the project at (inter)national conferences.

Qualifications required: A doctoral degree, or a foreign degree equivalent to a doctoral degree, in Medical Microbiology or a related field. The candidate is expected to have ample laboratory experience with ancient DNA, in particular with metagenomics samples, which should include library preparation skills. Experience of bioinformatics metagenomics analyses from ancient DNA samples is a must.  The candidate has to demonstrate proficiency working on the UPPMAX system, knowledge of Kraken, MALT and SPARSE bioinformatics tools, familiarity with AMR databases, and experience of analyses of host-associated non-model (non-human) metagenomics datasets.

Candidates must be able to express themselves fluently in spoken as well as written English. In ranking eligible candidates special importance will be given to scientific skills. In the assessment of scientific merits, especially, ancient DNA skills and analytical experience with host-associated non-human metagenomic data will be highly valued.

Qualifications desired: We are looking for a highly independent and proficient person to drive forward the project. The ideal candidate will be a team player and have demonstrated experience supervising and mentoring MSc and BSc students in the lab and for bioinformatics analyses.

Application: The application should include 1) a letter of intent describing yourself, your research interests and why you want this position, 2) your CV, 3) a copy of your doctoral degree, 4) publications produced. The application should be written in English.

Uppsala University strives to be an inclusive workplace that promotes equal opportunities and attracts qualified candidates who can contribute to the University’s excellence and diversity. We welcome applications from all sections of the community and from people of all backgrounds.

Salary: Individual salaries are applied.

Starting date: 2020-01-01.

Type of employment: The position is a temporary position for the duration of 6 months.

Scope of employment: 50%. 

For further information about the position please contact: Assistant Professor Katerina Guschanski, Katerina.guschanski@ebc.uu.se, +46 18 471 26 73.

You are welcome to submit your application no later than 2 December 2019, UFV-PA 2019/3932.

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