Louis-Félix Nothias, PhD
Junior Group Leader / Professor Chair CNRS @Université Côte d'Azur
Affiliated Chair of Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur
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Junior Group Leader / Professor Chair CNRS @Université Côte d'Azur
Affiliated Chair of Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur
I am a CNRS junior group leader based at the University Côte d'Azur & the Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, France. In 2023, I founded the HolobiomicsLab, where we develop experimental and computational methods for studying host/microbial metabolism in holobionts and their microbiomes.
The lab is pioneering advanced mass spectrometry (MS)-based metabolomics techniques in multi-omics studies using artificial intelligence. Prior to this, I was a postdoctoral researcher at the University of California San Diego with Prof. Pieter Dorrestein (2016-2021), where I contributed to the GNPS ecosystem, and a research associate at the University of Geneva with Prof. Jean-Luc Wolfender (2021-2023).
I have contributed to both experimental and computational methods for MS-based metabolomics annotation (as postdoc with Prof. Dorrestein and in collaboration with the SIRIUS team/Sebastian Boecker lab, see CASMI 2022) and have pioneered integrative multi-omics studies for studying microbiota biosynthetic potential and metabolism in ecosystems, including through the collaborative Earth Microbiome Project.
At HolobiomicsLab, we are dedicated to integrate advanced/computational mass spectrometry and artificial intelligence to decode the intricate metabolic interplay between hosts and their associated microbiota (aka holobionts). Our interdisciplinary approach spans from deep metabolomics to AI-driven data analysis, enabling breakthrough discoveries in environmental science, microbial ecology, and holobiont biology/engineering.
We leverage advanced analytical chemistry and artificial intelligence to observe and decode the intricate metabolic interplay between hosts and their associated microbiota. Our approach enables the systematic spectral annotation of metabolites and the sensitive detection of low-abundance metabolites, including microbially derived metabolites that are inaccessible by conventional methods.
We employ state-of-the-art instrumentation and specialized expertise to conduct high-throughput mass spectrometry metabolomics across thousands of microbial and environmental extracts. Our approach integrates customized analytical pipelines with advanced pre-enrichment techniques and optimized chromatography.
At HolobiomicsLab, we employ cutting-edge omics technologies—including genomics, proteomics, transcriptomics, and metabolomics—paired with advanced computational methods and integrated artificial intelligence to provide a unified, comprehensive view of complex biological systems. Our current research investigates the molecular crosstalk between marine host organisms and their associated microbiomes, with marine holobionts—such as sea anemones and corals—serving as essential models for understanding how host-microbe interactions drive adaptation to environmental stresses and underpin ecosystem resilience.
Our approach centers on developing AI-driven tools that streamline mass spectrometry data acquisition & interpretation in metabolomics, by designing AI systems that autonomously operate our mass spectrometers and assist in data interpretation while I co-coordinate the MetaboLinkAI project—which harnesses open, integrative AI and knowledge graph frameworks to advance metabolomics data analysis by uniting eight leading institutions from France and Switzerland, and applying natural language processing, graph mining, and machine learning to overcome key data challenges and accelerate breakthroughs in biomarker discovery and chemodiversity exploration.
2011 – 2015: PhD in Organic Chemistry (Université de Corse and part-time at the ICSN-CNRS)
2009 – 2011: Master in Phytochemistry, with high honors (Université de Corse)
2007 – 2009: Bachelor's in Chemistry (Université de Corse)
Since 2023/06: Chaire de Prof. Junior, Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Nice , Université Côte d'Azur, Nice, France
Since 2024/01: Affiliated chair Institut Interdisciplinaire d'Intelligence Artificielle (3iA) Côte d'Azur , Sophia-Antipolis, France
2021 – 2023: Research associate in analytical and computational chemistry, with Prof. Jean-Luc Wolfender, Dept. of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
2016 – 2021: Post-doctoral researcher in experimental and computational metabolomics, with Prof. Pieter Dorrestein, Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, Center for Microbiome Innovation, University of California San Diego, USA
2017 – 2018: MSCA Global postdoctoral researcher, Institut de Chimie des Substances Naturels, CNRS, Gif-sur-Yvette, FR
Part of the Institut de Chimie de Nice (ICN) and the Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur at Université Côte d'Azur (UniCA), the HolobiomicsLab is an interdisciplinary laboratory focused on the intersection of chemistry, biology, and artificial intelligence.
Since July 2023, our mission is to create the next-generation toolbox for mass spectrometry-based metabolomics, deciphering the complex metabolic compositions and interactions in environments and living organisms, with a particular focus on the role of the microbiome in holobiont phenotypes.
The HolobiomicsLab specializes in experimental and computational metabolomics, integrating omics and artificial intelligence systems for hypothesis generation and data interpretation. Our tools and methods are modular, open, and applicable to any model organisms and environment, enabling us to accelerate insights in health, ecology, and bio-industries.
The lab is situated in the Valrose Parc of Université Côte d'Azur, nestled in the heart of Nice—France's fifth-largest city—on the French Riviera between the Mediterranean Sea and the Maritime Alps. Our lab is set within a magnificent botanical garden, often regarded as one of the most pleasant campuses in France, providing an inspiring environment for scientific research.
At the core of my research philosophy is a commitment to interdisciplinary collaboration, embracing diversity of thought, background, and expertise. Science thrives on different perspectives, and by integrating AI, mass spectrometry, and systems biology, I aim to contribute to a holistic understanding of complex biological systems. In HolobiomicsLab, we strive to foster inclusivity and equitable access to scientific knowledge, recognizing that open science and collective intelligence are crucial for tackling grand challenges like climate change, biodiversity loss, and human health.
Having spent many years of my life amid libraries and the wilds of nature, I reserve a couple of days each week for 14-hour deep work sessions. I blend scientific rigor with a healthy dose of humor and adventure—a perspective shaped by growing up in bustling, diverse Paris, enjoying blessed Corsican summers in the village, and cherishing thrilling times in California. This outlook is further enriched by my love for discovering other cultures and their diverse perspectives, which continuously inspires collaboration and fresh insights.
We are what we eat, so I like to think my metabolism—powered by tea, coffee, and hearty bowls of rice, beans, lentils, nuts, cabbage, apple, and oats—is a little metabolomics experiment in itself. But beyond just food, we are also what we learn, share, and explore. If you’d like to learn more about the ethos of HolobiomicsLab, our approach to open science, diversity, and interdisciplinary research, visit our Diversity Statement & Vision.
I am not just a researcher dedicated to science; I am a proud father of three incredible, curious, and playful kiddos who keep me on my toes—both in and out of the lab. My passions range from jamming to diverse music, embracing the outdoors (think barefoot runs in the forest, dream snorkeling in the Mediterranean, and relaxing in wild rivers), and I aspire to return to vigorous karate practice. Deeply concerned about global ecocide and pollution—and armed with a soft spot for artificial intelligence—I maintain a global, integrative research perspective rooted in open science, believing it can lead to a better understanding of life and our world.
For more information, check out the HolobiomicsLab website.
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