Postdoctoral position – funded by FIS2 – BADGE project Microbial-Driven Bile Acid Modifications and Their Impact on Gut Ecology
CUP: E53C
1) The Scientific Challenge:
Understanding how microbial communities organize and share metabolic functions is a major challenge in microbiome research. Although we know that bacteria collectively shape many aspects of host physiology, we still lack a clear theory for why specific functions are carried by some strains and not others, how these functions are regulated across conditions, and how they influence community behavior.
This project addresses these questions through the study of bile acids (BAs), key molecules in digestion, metabolism, and host–microbe communication. Produced by the liver and released into the gut, BAs are further transformed by the microbiota, which changes their chemical structure and biological activity. In particular, the project focuses on two important microbial transformations: de‑conjugation and the recently discovered re‑conjugation of BAs with alternative amino acids. Disruption of these processes can alter BA homeostasis and has been associated with liver disease and metabolic disorders.
The project aims to understand why only some bacteria can perform one or both of these transformations, what determines the preference for one activity over the other, and how these processes affect microbial community dynamics. More broadly, it seeks to move from description to explanation by developing a theoretical framework for how metabolic functions are distributed and maintained in microbial ecosystems.
To achieve this, the project combines experimental and theoretical approaches, including microbial physiology in controlled growth conditions, single‑cell measurements using microfluidics and microscopy, metabolomics to quantify BA composition, and quantitative analysis to develop and test theory. The long‑term objective is to identify general principles governing bile acid transformations in microbial communities and to use these principles to guide the design of synthetic communities with defined functional properties.
The Lab: The successful candidates will join the Microbial Ecology Lab at Humanitas Research Hospital in Milan, Italy, working under the supervision of Dr. Gabriele Micali. Established in 2022, our lab brings together a strong interdisciplinary team – currently three physicists and five microbiologists – and fosters a multicultural environment (~55% women; representation from three continents).
Single‑cell microfluidics
Quantitative (image) analysis
Microbiology
Molecular biology
3) What we offer
Postdoctoral contract until
State‑of‑the‑art platforms (microfluidics, mass‑spec metabolomics, anaerobic culture).
Personal conference & exchange budget; Milan is centrally located in Europe and internationally connected.
Friendly, curiosity‑driven interdisciplinary atmosphere that prizes diversity, collaboration, and open science.
Competitive salary based on experience
We welcome every background and will happily arrange adjustments for caregiving duties or disabilities – just tell us what you need.
4) Candidate profile
The successful candidate will join a team of four scientists on the FIS2‑BADGE project. They will design and perform single‑cell microfluidics experiments, culture diverse microbial populations, execute gene‑editing protocols, and conduct DNA, RNA, protein, and metabolite extractions. While primarily focused on experimental biology, they will apply quantitative analysis skills and collaborate directly with theoreticians. They will enrich lab culture by generating innovative research ideas, leading group‑meeting presentations, driving scientific discussions, and representing the team at conferences and outreach events.
PhD (or equivalent) in Life Sciences, Microbiology, Quantitative Biology, Physics, Mathematics, Engineering, or a related field, conferred by the starting date
Ability to articulate and defend ideas using quantitative reasoning
A strong publication record in relevant fields.
Curiosity, critical thinking and enthusiasm for interdisciplinary teamwork.
Comfortable communicating in English (Italian not required).
Willingness to collaborate in an interdisciplinary team and learn mathematical modeling and quantitative analysis
Ability to program in at least one of the following languages: Python, MATLAB, R or C
Evidence of outreach, mentoring or community building.
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