Post Doc

Postdoctoral position – funded by FIS2 – BADGE project Microbial-Driven Bile Acid Modifications and Their Impact on Gut Ecology

Codice grant: FIS-2023-03089

CUP: E53C25000390001

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.

2. Our environment:

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).

Our lab’s strength lies in integrating multiple disciplines:

• Single-cell microfluidics
• Quantitative (image) analysis
• Mathematical modelling
• Microbiology
• Molecular biology

We approach science with the view of physics, aiming to identify principles behind complex systems. We collaborate closely with engineers, immunologists, and clinical microbiologists on campus. Within this project, we will further collaborate with the metabolomic facility.

IRCCS Humanitas Research Hospital: is a highly specialised research and university hospital. It is the first Italian hospital certified for its excellence by the Joint Commission International as Academic Hospital and it hosts a research center, as well as the residency programs and clinical training of Humanitas University, an international Medical School that stands out for its real-world simulation-based approach to medical training.

Our research is made possible every day by more than 500 passionate physicians, biologists, physicists, data scientists, and technologists who work in the hospital wards and across 10.000 square meters of high-tech laboratories at the Humanitas University campus. Their common mission is advancing science to make a difference in patients' life.

Humanitas Research is guided by unmet clinical needs and it leverages high-end technologies to dissect the molecular and cellular mechanisms underlying human pathologies in fields ranging from cardiovascular medicine to neuroscience, from immunology to cancer and microbiology, with the final goal of developing new therapies and new diagnostic and prognostic strategies. The institute is recognized worldwide for its contribution to the field of tumor immunology and to the understanding of the inflammation-cancer connection.

3. What we offer

• Postdoctoral contract untill 30.11.2028
• State-of-the-art platforms (microfluidics, mass-spec metabolomics, anaerobic culture).
• Personal conference & exchange budget; Milan is centrally located in Europe and internationally connected.
• Career development: weekly lab meeting, transferable-skills courses, mentorship.
• 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.

Essential qualifications:

• 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).

Desirable skills:

• 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.

5. Required documents for your application:

• Cover letter explaining why you want to join the team
• Update CV
• Contact information of three referees

On the basis of the profiles received and in the terms indicated by this notice, Humanitas will activate the selection process by inviting suitable candidates to participate in selection interviews, after verification of the cv and qualifications, which will be held in person or in telematic mode.

All candidate data collected from the application shall be processed in accordance with applicable law: Dlgs 198/2006 e dei Dlgs 215/2003 e 216/2003;  privacy ex artt. 13 e 14 del Reg. UE 2016/679.