PhD - BADGE project Microbial-Driven Bile Acid Modifications and Their Impact on Gut Ecology

Job Title: 3 PhD positions – funded by FIS2 – BADGE project Microbial-Driven Bile Acid Modifications and Their Impact on Gut Ecology

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.

Humanitas Research is made possible every day by more than 500 passionate physicians, biologists, physicists, data scientists and technologists, that 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.

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 regulate 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 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?

Our evnironment:

All three PhD students will join Microbial Ecology Lab at Humanitas Research Hospital (Milan, Italy) and work under the supervision of Dr. Gabriele Micali. The lab established in 2022 is interdisciplinary (currently: 4 physicists + 1 microbiologist) and multicultural (currently: 40% women; three continents represented).

The strengh relies in coupling:

• single-cell microfluidics
• quantitative (image) analysis
• mathematical modelling
• microbiology
• molecular biology

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

You’re the perfect candidate if you have:

• MSc (or equivalent) finished by Nov 2025 in a life-science or quantitative field (microbiology, biotech, physics, maths, comp-sci…).
• Curiosity, critical thinking and enthusiasm for interdisciplinary teamwork.
• Comfortable communicating in English (Italian not required).

Additional qualities we are looking for:

• Hands-on with any of our core tools (microfluidics, mass-spec, modelling, infection assays).
• A first paper, conference talk or poster.
• Evidence of outreach, mentoring or community building..

We are especially keen on mixed-profile candidates – one or two with stronger theory/computation leanings and one or two who love the wet lab.

What we offer

• Three fully funded 3-year PhD contracts (with the possibility of 1 year extension).
• State-of-the-art platforms (microfluidics, mass-spec metabolomics, anaerobic culture).
• Personal conference & exchange budget; Milan’s is centrally locaded in Europe and internationally connected.
• Career development: weekly data clubs, transferable-skills courses, mentorship.
• Friendly, curiosity-driven interdisciplinary atmosphere that prizes diversity, collaboration and open science.. 

Starting date: 01 December 2025

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.