Redesigning Microbiomes for Healthy and Sustainable Food Fermentations:
Fermented foods and beverages are a nutritionally and culturally significant component of human diets globally, as well as a primary source of microorganisms and microbial metabolites that shape both food quality and human health. This includes improvements in food nutrition and safety, via the production of microbial metabolites, altering food chemical composition, affecting nutrient absorption or fibre fermentability, and reducing anti-nutrient and toxin levels. Given the role of fermented foods in the human diet, we:
- must preserve the existing biodiversity of fermented foods and characterize their functional roles for the improvement of existing and novel foods (e.g., sustainable plant-based foods); and
- develop technologies for rapid characterization of microbial and chemical profiles of these foods that integrate multiple omics techniques and interpretable machine learning.
We are seeking highly motivated individuals who are passionate about fermented foods/beverages and microbial ecology to join our team. Multiple cross-linked collaborative doctoral projects are available.
- Project 1: Your goal will be to launch a “citizen science” project to catalogue, characterize, and preserve the microbial biodiversity of fermented foods and beverages from Swiss, European, and global sources. You will employ both omics and computational/bioinformatics methods to study the composition and ecological interactions of fermented food microbiomes, metabolomes, their contributions to food quality, and potential applications for rational re-design of microbiomes for fermented foods and beverages.
- Project 2: Your goal will be to integrate multiple metabolomics and microbiome metagenomics technologies with advanced tools and techniques for data analysis to develop a toolbox for rapid fingerprinting and early prediction of food quality and health outcomes from fermented foods, strains, and consortia. This will drive a “culturomics” approach for targeted isolation and characterization of unique strains and consortia for further characterization.
- Project 3: Your goal will be to use food fermentation as a model system for investigating microbial species interactions and genetic traits that direct outcomes for species fitness, community assembly, and food quality. You will use molecular, deep sequencing, and genetic manipulation methods for deep investigation of inter-kingdom interactions in model ecosystems and food matrices, in pursuit of generalizable “rules of life” that transcend these systems.
Projects 1-2 are a collaboration between the Food Systems Biotechnology (FSB) group and the Laboratory of Food Biochemistry in the Department of Health Science and Technology at ETH Zurich. Project 3 will be located in group FSB. The FSB group develops bioinformatics methods and software for microbiome research and applies these tools to study microbial ecosystems at the interfaces of foods, food systems, and human health. The Laboratory of Food Biochemistry conducts fundamental research in the composition of foods using advanced analytical techniques, properties of health-promoting food constituents and their optimization for improved biological effects.
These projects are all inherently multi-disciplinary and will involve collaboration with others in the group, as well as a wider network of collaborators in Switzerland and Europe/globally. The projects will be based on two vibrant, friendly, supportive, and interdisciplinary research groups with a passion for food (fermented and otherwise) that extends beyond our research.
You are a self-motivated scientist with outstanding academic qualifications, superb interpersonal and written communication skills, the ability to independently manage complex projects and datasets, and enthusiasm to engage with a collaborative, interdisciplinary team of scientists. Experience working with at least two of the following three is required: microorganisms/microbiomes, mass spectrometric methods for targeted or non-targeted analyses, and fermented foods or beverages. Experience in metagenomics/microbiome research is an advantage. Doctoral students are expected to disseminate research findings in conference talks and journal articles, and excellent written and spoken English language skills are required.
- Masters-level degree in Food Science, Microbiology, Analytical Chemistry, Viticulture/Enology, Biotechnology, Biology, Bioinformatics, or a related area.
- Excellent knowledge and research experience in relevant areas:
- Project 1: microbiology, microbial ecology, and bioinformatics
- Project 2: mass-spectrometric techniques (ideally LC-MS/MS)
- Project 3: microbiology, molecular biology, and biotechnology (including experimental methods for microbial mutagenesis)
- Passionate and knowledgeable about fermented foods and beverages
- Excellent interpersonal communication, teamwork and organizational skills
- English language proficiency (Level C1 or C2)
- Experience working with microbiome (marker gene, metagenome) or other omics data
- Experience with bioinformatics and/or Python programming
- Evidence of effective scientific communication (publications and/or open-source software projects)
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Curious? So are we.
We look forward to receiving your online application with the following materials:
- A short statement of research interests and motivation (1-2 pages) that describes your suitability for the position, your passion for fermented foods, your vision for your PhD project, and your desired timeline. You should also explicitly mention which project(s) you are applying to.
- An updated curriculum vitae including, education, any relevant experience, and a publication list.
- An academic transcript of your studies.
- Names and contact information of 2-3 professional references.
Please note that we will only accept complete applications that are submitted through our online application portal – applications via email or postal services will not be considered. For additional information, please contact Prof. Nicholas Bokulich (firstname.lastname@example.org) (Projects 1&3), Prof. Laura Nyström (email@example.com) (Project 2).
Review of applications will begin immediately. The position will remain open until a suitable candidate is found. Starting date September 1st, 2022 or on an agreement.
ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.