PhD Student Position in Microbiome Science
Life-long relationship with microbes, now studying them for a living.
PhD position
Start: October 2025
Deadline: March 21, 2025
Application through phd-recruiting.medunigraz.at.
Project: Designing the niche space of the human gut microbiome
Virtually every surface of our planet is colonized by microbes and the human body is no exception. The 38 trillion microbes living in our gut metabolize a large fraction of the dietary metabolites, pharmaceutical drugs, and xenobiotics we consume and thus provide an important interface between the environment and our blood stream.
Whereas many of the species forming the human gut microbiome have been well-characterized by now, we still know very little about the factors that determine which microbial species can coexist in any given individual. This currently limits our understanding regarding engraftment of pathogens and probiotics and how those will interact with other microbes and host tissues in the human gut.
Metabolic interactions between microbes in complex microbial communities and their host are a complex ballet of metabolic exchanges and the resulting ecology. The research project will aim to chip away at this complexity using a combination of wet lab and computational techniques with the goal to quantify and predict the nutrient uptake patterns of individual microbial strains and species embedded in complex communities and varying environments. By studying uptake fluxes and the resulting species phenotypes in silico, in vitro, ex vivo, and in vivo, we aim to provide a resource map for important microbial species in the human gut to make nutrient uptake and the resulting microbial phenotypes predictable. Those patterns will then be used to match next generation probiotics to individual microbiomes by orthogonal niche engraftment or to design specific synbiotics to enable engraftment in resistant donor microbiomes.
Our research combines a variety of techniques ranging from high throughput wet lab approaches including metagenomics, metabolomics, and single-cell culturing to computational methods such as metabolic modeling, functional association analysis, and machine learning and thus provides a large degree of flexibility for the applicants background and role within the project.
What we offer
We are a new and still fairly small lab at the Medical University of Graz at the Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine. We value diversity, creativity, communication and research integrity. The team spans a wide array of backgrounds and abilities, and lab members are encouraged to share their knowledge and experiences. Our goal is to support all lab members in accomplishing their individual career goals, while also conducting awesome science with a clear path into clinical application. We collaborate with research groups all around the globe and invite you to be a part of this as well. More info about the lab can be found at dienerlab.com.
What about you?
Do you have some experience in working with the microbiome in the human gut or other environments?
Are you curious and excited about projects that combine microbial ecology, systems biology, and clinical samples or data?
Do you have excellent English communication skills and love to discuss your research with your peers?
Then you will fit in perfectly with our lab.
Skills
Additionally, the following general skills synergize great with the research project, and you will be trained in these during the project. Any prior knowledge is, of course, an advantage.
Dry Lab
1. Analysis of sequencing data.
2. Analysis of mass spectroscopy or NMR data.
3. Metabolic modeling (in Python).
4. Statistics (in R).
Wet Lab
1. Isolation and anaerobic culturing of microbial strains from various biofluids.
2. Culturing of microbial consortia.
3. Sample preparation and library prep for high throughput sequencing and/or metabolomics.
References
1. Fan, Y. & Pedersen, O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 19, 55–71 (2021).
2. Diener, C. et al. Genome-microbiome interplay provides insight into the determinants of the human blood metabolome. Nat Metab 4, 1560–1572 (2022).
3. Szajewska, H. et al. Antibiotic-perturbed microbiota and the role of probiotics. Nat Rev Gastroenterol Hepatol (2024) doi:10.1038/s41575-024-01023-x.
4. Quinn-Bohmann, N. et al. Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nat Microbiol 9, 1700–1712 (2024).
5. Diener, C., Gibbons, S. M. & Resendis-Antonio, O. MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota. mSystems 5, (2020).
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