Doctoral Student SNSF in Quantitative Microbial Ecology and Metabolic Interactions

Introduction

UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

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Presentation

The Pacheco Lab (pachecolab.com) in the Department of Fundamental Microbiology at the University of Lausanne offers a position as a Doctoral Student SNSF in quantitative microbial ecology and metabolic interactions (interdisciplinary experimental/computational focus).

Job information

Expected start date: flexible, earliest 01 January 2027
Contract length: 1 year, renewable
Activity rate: 100%
Workplace: University of Lausanne, Dorigny Campus

Your responsibilities

The Pacheco Lab has an open PhD position to investigate how environmental conditions shape microbial interactions, community assembly, and metabolic dependencies, with a particular focus on plant-associated microbial communities.
Microorganisms in nature form complex communities whose properties emerge from interactions among their members. While resource availability strongly influences microbial community composition, we still lack a mechanistic and predictive understanding of how environmental conditions reshape microbial competition, cooperation, and metabolic dependencies.
A major challenge in microbial ecology is that interactions between microorganisms are not fixed, but depend strongly on environmental context. Changes in resource availability, temporal dynamics, and spatial structure can fundamentally alter microbial interactions and community succession. Plant-associated environments provide a particularly interesting setting in which to investigate these processes because of their dynamic resource landscapes and effects on their hosts.
Through this project, we aim to uncover how environmental context rewires microbial interaction networks through metabolic mechanisms. The successful candidate will combine experimental microbiology with quantitative and computational approaches to investigate how resource composition, environmental structure, and temporal dynamics influence bacterial interactions and community assembly.
A central goal is to move beyond pairwise interactions and develop a predictive, network-level understanding of microbial communities, linking metabolic traits and environmental conditions to community-level outcomes. Experimental measurements will be integrated with quantitative analyses and modeling to generate and test ecological hypotheses. A major emphasis will be on developing mechanistic and predictive explanations for community dynamics, rather than solely describing compositional changes.
The project will primarily use controlled experimental systems that capture key ecological features of natural microbial environments, including plant-associated habitats. This work will contribute to a predictive framework connecting metabolism, environmental conditions, microbial interactions, and community succession, with longer-term applications in the design of beneficial microbiomes.

Your qualifications

We are looking for a motivated and curious candidate with a strong interest in microbial ecology and quantitative biology. Applicants should have:
•    A Master's degree in microbiology, biology, bioengineering, systems biology, quantitative biology, or a related discipline
•    A strong interest in microbial interactions, metabolism, community ecology, and community dynamics
•    A good foundation in bacterial physiology, metabolism, and cell biology
•    Practical experience with microbial culturing and general microbiological techniques
•    An interest in quantitative reasoning and data analysis
•    Proficiency in English
•    The ability and motivation to work both independently and collaboratively within an interdisciplinary research environment
We are particularly excited to hear from candidates who enjoy thinking quantitatively about biological problems and moving between experiments, data, and theory. The following experience would be advantageous, but is not required:
•    Programming, quantitative data analysis, or computational biology
•    Mathematical, metabolic, or ecological modeling
•    Plant-associated microbiology, soil microbiology, environmental microbiology, or plant-microbe interactions
The successful candidate will be encouraged to develop increasing scientific independence and intellectual ownership of the project throughout the PhD.

What the post offers you

You will join a new and highly motivated interdisciplinary research group focused on understanding and engineering microbial interactions for host health and sustainability applications. Located in the Biophore building overlooking Lake Geneva and the Alps, our lab is embedded within the vibrant and international research environment of the Department of Fundamental Microbiology at the University of Lausanne. Our state-of-the-art biology and computational lab space is supported by UNIL's excellent research infrastructure (e.g., computing cluster and sequencing, metabolomics, and microscopy facilities) and a collaborative network of leading researchers in microbial ecology, computational biology, sustainable agriculture, and medicine (e.g., NCCR Microbiomes, Department of Ecology and Evolution, Swiss Institute of Bioinformatics, EPFL, and CHUV). UNIL is deeply integrated within the broader Lausanne community and region, which offers ample opportunities for professional training and a rich cultural life. Please visit our website for more information on our group, research interests, and publications: https://pachecolab.com

Your application

Only complete applications submitted through this website will be considered. Please upload the following as separate PDF files:
A.    A motivation letter describing your previous research experience, scientific interests, and motivation for the project. In your motivation letter, please also briefly address the following questions, which are intended to help us understand how you think scientifically and what types of questions motivate you:
o    Tell us about a question in microbial ecology or evolution that you find particularly interesting. Why does it interest you, and what quantitative measurements or approaches could help address it?
o    Based on the project described above, what aspect of microbial interactions or community dynamics would you be most interested in exploring, and how might you begin approaching it?
B.    Your CV
C.    Academic transcripts (Bachelor's and Master's level, where applicable)
D.    Contact information for two academic references

Timeline

We anticipate the following timeline:
•    Application deadline: 30 October 2026. Applications will be evaluated after the deadline and reviewed collectively
•    Initial online interviews: November 4-6
•    Virtual research presentations and discussions with the group: November 11-13
•    Finalist visits to Lausanne: early December
•    Final decision: early December
We encourage applicants to keep these dates in mind when applying. Candidates invited to interview will receive further scheduling information, and we will do our best to accommodate individual constraints within the limited interview windows available.

Contact for further information

Prof. Alan Pacheco: E-Mail schreiben.