Postdoctoral positions_Experimental Profile

Postdoctoral positions_Experimental 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:

Bile acids (BAs) are central to digestion, cholesterol regulation, and host–microbe communication. Synthesized in the liver and released into the gut, host‐produced BAs undergo a variety of microbial-driven modifications that diversify their chemical structures and biological functions. These alterations are sensed by the host, which in turn regulates BA production. When this cycle is disrupted, BA homeostasis can break down, leading to liver disease and metabolic disorders. Despite extensive research, we lack a full understanding of how and why bacteria collectively modify BAs.

The project focuses on two fundamental and complementary BA modifications: de‐conjugation and the recently discovered re‐conjugation of BAs with different amino acids.

A not exhaustive list of questions we aim to tackle as part of this project are: Why are only some bacteria capable of performing one or both processes? Under which environmental conditions do organisms that can execute both modifications perform one over the other? How do these alterations influence community dynamics, particularly in the context of pathogen invasion?

By combining microbial physiology assays in different growth conditions with microfluidics, which allows us to quantify growth and death of single-cells, metabolomics for the quantification of the BA composition, and quantitative data analysis, we aim to provide a fundamental understanding of how to build synthetic communities able to achieve target BA profiles.

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 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 qualitications:

• PhD (or equivalent) in Life Sciences, Microbiology, Quantitative Biology, or a related field, conferred by November 2025
• 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.

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.

to read the privacy notice ex art. 13 and 14 of EU Reg. 2016/679.