The chemistry of holobionts.
Part of the Institut de Chimie de Nice (ICN, UMR 7272) and the Interdisciplinary Institute for Artificial Intelligence (3iA Côte d'Azur) at Université Côte d'Azur, the HolobiomicsLab is an interdisciplinary group at the intersection of chemistry, biology, and artificial intelligence. Since July 2023, our mission is to build the next-generation toolbox for mass-spectrometry metabolomics — deciphering the metabolic interplay between hosts and their microbiomes, with a focus on the role of the microbiome in holobiont phenotypes.
Since December 2025, the lab is a co-founding member of the eDIAM team — an institutional step that aligns and expands our research effort and vision at the interface of chemistry, metabolomics, and AI. Since June 2026, eDIAM also brings the lab into the Centre Inria de l'Université Côte d'Azur (Sophia-Antipolis).
Experimental metabolomics
Flexible, semi-automated methods for high-throughput metabolite extraction and analysis on state-of-the-art high-resolution mass spectrometers. We routinely process thousands of samples from microorganisms, plants, hosts, and tissues — selecting and optimising extraction, pre-enrichment, chromatography, and MS conditions, assisted by AI.
Computational metabolomics
Extensive experience in computational mass spectrometry, designing novel methods and AI-powered pipelines for large-scale MS data processing and annotation. Using open-source software, we transform fragmentation spectra into structural insights, surfacing novel molecules and illuminating biological processes.
Multi-agent AI systems
A defining focus of the lab: open multi-agent AI systems that operate instruments, query knowledge graphs in natural language, and orchestrate data-driven discovery. Our Mimosa framework generates and iteratively refines task-specific multi-agent workflows — a step toward autonomous scientific research — supported by MetaboT and the Toolomics MCP tooling platform.
Integrative omics
Harnessing multiple molecular layers — (meta)genomics, transcriptomics, proteomics, and metabolomics — to build a comprehensive picture of biological systems, capturing the dynamic interplay that governs cellular processes and environmental responses.
Open science & informatics
We share methods, data, and tools with the global community. Our informatics platforms are modular and user-oriented, enabling researchers worldwide to leverage our resources — advancing reproducibility, transparency, and innovation in omics and applied AI.
Integrative experimental & computational metabolomics
An AI-powered framework that adapts mass spectrometry analysis to the scientific and spectral context — leveraging prior knowledge, multi-omics information, and ML models to improve sensitivity and specificity, translating spectra into chemical information that drives discovery.
A botanical-garden campus in Nice.
Location
Set in the Valrose Parc of Université Côte d'Azur — a botanical-garden campus in the heart of Nice, on the French Riviera between the Mediterranean Sea and the Maritime Alps. Our lab spaces are on the 5th floor of the Institut de Chimie de Nice (ICN). Computational members are also hosted by the Wimmics team at I3S / INRIA on the Sophia-Antipolis campus.
Mass spectrometry
An IQ-X Tribrid Orbitrap (2025) for advanced studies, two Vanquish UHPLC systems capable of dual/tandem chromatography, and a microflow–nanoflow multi-nozzle emitter ion source (MnESI, Newomics) for enhanced sensitivity.
NMR & structural elucidation
Access to a Bruker Avance Neo 600 MHz with a cryoprobe (2024), plus analytical and semi-preparative HPLC for fractionation and compound isolation — supporting de novo structural elucidation of isolated metabolites.
Semi-automated sample prep
An entire semi-automated pipeline for 96-well-plate protocols, including an automated mill (MM-200 Retsch) and a customisable liquid-handling robot (Opentrons OT-2). We routinely handle batches of several thousand samples.
Computational resources
Heavy computation runs on Azzurra, Université Côte d'Azur's HPC cluster (CPU/GPU nodes, large-memory and visualization nodes, fast InfiniBand). We also access national HPC, including the Jean Zay supercomputer (IDRIS/CNRS).
Collaborative biology
For microbiology, host-associated studies, and in vivo work, we operate through a collaborative model — providing advanced metabolomics workflows, analytical-chemistry expertise, and multi-omics integration that connects biological observations to molecular mechanisms.
Diversity is the engine of our research, not a side note.
The future of scientific discovery and education is tied to the synergy between diverse human intellects and technologies. Our commitment to a diverse environment — encompassing identity, gender, culture, and cognitive perspectives — is a critical driver of the depth and breadth of our research and education.
We celebrate neurodiversity and recognise that neurological differences bring unique strengths that inspire innovative thinking. We see them as variations in cognitive function that offer distinct advantages — especially combined collaboratively. For welcoming international researchers and training lab members, English is our primary working language.
We are pioneering a co-evolutionary adaptation with AI that reshapes scientific discovery and education. By viewing AI as a co-creative partner, we augment self-learning, creativity, and analytical capabilities — creating interdisciplinary opportunities for all lab members, even without prior formal training in chemistry or computational sciences.
AI helps design personalised learning experiences, removes language barriers, and provides tailored support aligned with diverse cognitive strengths — democratising access to advanced tools and empowering everyone to contribute to scientific innovation.
Active funding · €1.96 M+
The CNRS is the primary contributor to HolobiomicsLab, supporting two permanent researchers, a PhD fellowship (MITI CNRS), and starting funds. UniCA hosts the lab and provides the ICN's analytical instrumentation; 3iA Côte d'Azur integrates us into its AI ecosystem through an affiliated chair and co-funded projects. The lab is further supported by France 2030, the ANR, the Région Sud CPER "Metabolome", FNR Luxembourg, and a partnership with Generare Bioscience.
| Years | Amount | Source | Reference |
|---|---|---|---|
| 2025–28 | €450k | ANR–SNSF bilateral (MetaboLinkAI) | ANR-24-CE93-0012-01 · SNF 10002786 |
| 2025 | €120k | CNRS MITI — PhD fellowship | marine holobionts |
| 2024–25 | €70k | Académie 1 IdEx UniCA — KG-bot postdoc | ANR-15-IDEX-01 |
| 2025–28 | €191k | ANR — partnership with ANR POPS | ANR-24-CE44-1190 |
| 2024–28 | €200k | FNR Luxembourg — L. Pradi PhD | project 17994255 |
| 2024–27 | €120k | EUR Spectrum / 3iA — international PhD | with Prof. W. Bittremieux (Antwerp) |
| 2023–28 | €805k | CNRS Chaire Prof. Junior + IdEx UniCA | ANR-22-CPJ2-0048-01 · ANR-15-IDEX-01 |
We hire at all levels.
Postdoc, PhD, and staff positions appear regularly. We welcome applications from outstanding Master's students, MSCA postdoctoral candidates, prospective visiting scholars, and researchers preparing CNRS permanent applications.