Postdoc in single cell DNA sequencing of complex microbial communities

Friday 28 Oct 22

Apply for this job

Apply no later than 30 November 2022
Apply for the job at DTU Food by completing the following form.

Apply online (Note: Positions posted after 4-11 must be applied through the link in the job posting.)

Complex microbial communities (e.g., microbiomes) harbour an enormous amount of diverse and rich species, with equally rich gene reservoir for various functions. Our current species and gene identification methods, while advanced, still lack accurate traceability potentials. Horizontal gene transfer (HGT) and antimicrobial resistance (AMR) make up a hotspot for gene plasticity and dynamics, where, for example, plasmid-derived AMR can transfer within a complex community between different bacterial host. Which makes linking AMR gene to their respective plasmid or bacterial carrier problematic. Employing single cell sequencing will allow not only uncover a variety of taxa that have never been sequenced before, without culturing, but also enables linking AMR genes to the mobile genetic elements (e.g., plasmids) and bacterial hosts. It will also allow for a more detailed phylogenetic analyses for bacterial relatedness with higher resolutions. Which could help elucidate hidden dynamics and variation in strain dominance of congeneric species that might have never been described before. Particularly in complex microbial communities such as animal microbiomes. We are seeking a candidate for a vacant postdoc position in microbiology with a focus on investigating the dissemination and dynamics of microbial communities, and their gene reservoirs, within animal microbiomes using single cell sequencing approach.

The postdoc will be affiliated with the Genomic Epidemiology Research Group, which primary task is to conduct targeted research with the aim of predicting and preventing infectious diseases in humans and animals, and supporting global detection, surveillance and control. The research group combines expertise in conventional and molecular microbiology with epidemiology and bioinformatics and act as EU and WHO reference centre for antimicrobial resistance.

The Genomic Epidemiology Research Group is together with several partners worldwide and funded by the Novo Nordisk Foundation establishing a global surveillance of infectious diseases and AMR to a large extent based on metagenomic sequencing of urban sewage (www.genomicepidemiology.org, www.globalmicrobialidentifier.org, www.compare-europe.eu)

An important research objective is to disassemble the linkage between AMR genes and their hosts, and resolve the within congeneric species resolution including strain dominance using single cell DNA sequencing. The position will utilise, amongst other sample sets, faecal sample from animals fed with a number of known (and sequenced) bacterial strains to follow their disseminations within such microbiomes. It will also utilise faecal samples from animal that underwent stressor factors (e.g., increased gastrointestinal acidity). 

The Genomic Epidemiology Research Group has initiated single cell DNA sequencing within its facilities, however, the position will also be expected to contribute to optimising the methods to fulfil the required research questions.

Responsibilities and qualifications

  • Your main responsibility will be to help establish and conduct single cell DNA sequencing from faecal samples of husbandry animals.
  • You will be responsible for employing microfluidic systems for cell sorting and cell encapsulation as part of cell sequence preparation.
  • With assistant from other group members, carry out the library preparation for next generation sequencing.
  • With assistant from other group members, analyse the output, draw conclusions and present the outputs.
  • You will communicate research results by presenting data at project meetings and international conferences, and write reports and manuscripts for publication.
  • You will engage in the general work carried out by the research group, including discussions and planning of strategies and projects, drafting research grant proposals, etc.
  • If your interest lies here and time allows, you will also supervise students and contribute to the group’s teaching activities.
  • Daily work will be in close collaboration with other researchers in the Genomic Epidemiology group and national and international partners associated with the global sewage project. Collaboration includes active participation in national and international meetings and conferences, sharing of data and results, and contribution to joint publications.

Skills:

  • Proficiency in DNA and molecular microbiology techniques. 
  • Proficiency in next generation sequencing, particularly Illumina sequencing platforms.
  • Proficiency in analysis of single cell datasets: microfluidics, single cell DNA-seq, single cell ATAC-seq, and single cell multi-omics analysis of taxa and gene compositions.

Essential:

  • Should be fluent in BASH (unix command line) and possess strong python coding as well as visualization skills.
  • Should be familiar with HPC environments.
  • Familiarity with metagenomic workflows (read mapping, genomic assemblies, genome assessment, phylogeny).

Desirable:

  • Familiarity with SQL databases and how to query them.
  • Deep knowledge of publicly available microbial/genomic databases (ncbi refseq/ENA/JGI/marker gene databases) and able to query the latter.
  • Acquainted with single cell metagenomics.

As a formal qualification, you must hold a PhD degree (or equivalent).

The ideal candidate:

  • Holds a PhD degree within one of the following areas: microbiology, biochemistry, computational biology or similar.
  • Has documented experience with molecular microbiology, next generation sequencing and microbiomes.
  • Preferably, has experience with antimicrobial resistance and bacterial pathogens and is familiar with bioinformatics and genetic epidemiology.
  • Is able to work independently and able to plan and carry out complex tasks, while having the ability to engage constructively in a large, international and cross-disciplinary research group.
  • Has good English communication skills, oral and written.
  • Is ambitious and has a strong drive for obtaining high-quality results

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and terms of employment
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.

The period of employment is 2 years and starting date is according to mutual agreement.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Head of Research Group, Professor Frank M. Aarestrup, 
fmaa@food.dtu.dk

You can read more about the Genomic Epidemiology Research Group at http://www.food.dtu.dk/english/Research/Genomic-Epidemiology

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark.

Application procedure
Your complete online application must be submitted no later than 30 November 2022 (Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • Application (cover letter)
  • CV
  • Academic Diplomas (MSc/PhD – in English)
  • List of publications

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

The National Food Institute (DTU Food) works within six technical focus areas: Biotechnology, nutrition, food quality, food safety, food technology and environment & human health. Activities cover a wide range of food products throughout the entire food chain from farm to table, comprising both research activities and research-based consulting and teaching. Read more at www.food.dtu.dk

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,400 students and 5,800 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.