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.

Therefore, we will start by characterizing pristine, naive bacterial communities from time periods that predate the mass production of antibiotics. In the next step, we will evaluate in how far human-produced antibiotics have changed the composition, functional profiles and particularly antimicrobial potential of host-associated microbiomes in several wild mammalian species. Finally, we will characterize the effects of country-specific policies in combating global antimicrobial resistance, such as for instance implemented in Sweden through Strama program.

Duties: The appointed candidate will be working on producing and analyzing shotgun sequences from dental calculus specimens of several mammalian species. The duties include collection of dental calculus samples from museum and archaeological specimens, extraction of DNA using aDNA techniques, 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. 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 this novel 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 aims for gender balance and diversity in all activities in order to achieve a higher quality at all levels of the organization. We therefore welcome applicants of any gender and with different birth background, functionality and life experience.

Position: A temporary position from 2019-08-01 until 2019-12-31 on 100%.

Salary: Individual salaries are applied.

Access: August 1, 2019.

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 2019-05-29. UFV-PA 2019/1592.

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