Postdoctoral positions_Quantitative Profile

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

Codice grant: FIS-2023-03089

CUP: E53C25000390001

The Scientific Challenge:

Microbial ecosystems are complex adaptive systems whose emergent behavior remains poorly understood from first principles. In particular, it is not clear how functional diversity (i.e. the genetic `capabilities’) is distributed and maintained across community members, and how these distributions of functions shape ecosystem-level properties. Answering these questions in a host-associated microbiome has direct relevance for human health.

Bile acids (BAs) offer a powerful, tractable window into these questions. Synthesized in the liver and released into the gut, host-derived BAs undergo multiple transformations. For instance, microbes are responsible for the de-conjugation of glycine or taurine and re-conjugation with alternative amino acids, which reshape their chemical structure and signaling activity. These reactions feedback to host BA synthesis; when this feedback is disrupted, BA homeostasis can break down, contributing to liver disease and metabolic disorders. Yet we do not know why only some gut strains can perform one or both de- and re-conjugation, what determines a cell’s choice between de- versus re-conjugation, and under which specific conditions bacteria preferentially perform one versus the other modification.

By marrying first-principles theory – trade-off analysis, game theory, reaction-diffusion, and consumer-resources models – with single-cell tracking and synthetic community experiments, this project will reveal the design rules by which microbial communities allocate and share metabolic functions. Such insights will not only advance fundamental ecology but also illuminate strategies for steering microbiomes toward host health.

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 two microbiologists—and fosters a multicultural environment (40% 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.

What we offer

• 3-year Postdoctoral contract
• 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.
• The salary will be commensurate with the candidate’s experience and qualifications (CCNL AIOP - National Collective Labour Agreement)
• We welcome every background and will happily arrange adjustments for caregiving duties or disabilities – just tell us what you need.

Candidate profile

The successful candidate will join four scientists on the FIS2-BADGE project, iteratively collaborating to develop predictive mathematical models and refine parameters for single-cell, genomics, and metabolomics data analyses. While primarily focused on computational work, they may elect to acquire hands-on experience with microfluidics or other experimental methods.
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:

• A PhD (or equivalent) in a quantitative discipline (physics, mathematics, quantitative biology or similar) completed by November 2025
• Proficiency in at least one programming language: Python, MATLAB, R or C
• 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 work in an interdisciplinary team and learn the strengths and limitations of experimental techniques
• Eagerness to perform hands-on experiments (prior bench experience a plus).
• Evidence of outreach, mentoring, or community building.

Required documents for your application:

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

Open Position (published): 08/08/2025 

End Published: 30 /09 / 2025

Starting Date: 01 /12 / 2025  

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 presence or in telematic mode.

The selection committee, composed of the Project Manager and the Human Resources Department, will take charge of the overall evaluation of the applications received.

The notice is addressed to candidates in compliance with Dlgs 198/2006 and Dlgs 215/2003 and 216/2003. Interested persons are invited to read the privacy notice ex art. 13 and 14 of EU Reg. 2016/679.