About us

The HolobiomicsLab 🌟

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 🌍 🌱.

Experimental Metabolomics 🔬🧫🧪
The HolobiomicsLab has developed flexible and semi-automated methods for high-throughput metabolite extraction and metabolomics analysis using state-of-the-art high-resolution mass spectrometers. We routinely analyze thousands of samples from various microorganisms, plants, hosts, and tissues. Depending on the scientific objectives and assisted by artificial intelligence, we select and optimize the extraction procedures, pre-enrichment, chromatographic, and mass spectrometric conditions 🌿 🦠.

Artificial Intelligence 🤖 🧠
Integrating AI into metabolomics, we design intelligent systems that streamline data interrogation and enhance discovery. Our contributions in artificial intelligence not only facilitate the exploration of complex omics data but also drive novel applications across biology and medicine. By harnessing advanced machine learning and natural language processing techniques, we develop frameworks that leverage prior knowledge from literature, public data repositories, and large-scale experimental datasets to generate actionable insights.

Computational Metabolomics 💻 🧠
Our lab has extensive experience in computational mass spectrometry, which we leverage to design novel methods and AI-powered pipelines for large-scale mass spectrometry data processing and annotation. Using open-source software, the HolobiomicsLab can transform fragmentation spectra into structural insights, facilitating the discovery of novel molecules and illuminating biological processes 🧬🔍.

Open Sciences and Informatics 🌍 🔗
The HolobiomicsLab is committed to advancing open science and informatics to foster collaboration and accelerate discovery. We embrace open science principles by sharing our methods, data, and tools with the global scientific community. Our informatics platforms are designed to be both modular and user-oriented, enabling researchers worldwide to leverage our resources for their own investigations. By promoting open science, we aim to enhance reproducibility, transparency, and innovation in omics sciences and applied artificial intelligence research.

Integrative Omics 🧬 🧪 🔬
Integrative omics at HolobiomicsLab harnesses the power of multiple molecular layers—(meta)genomics, transcriptomics, proteomics, and metabolomics—to build a comprehensive picture of biological systems. By bridging together these diverse datasets, we capture the dynamic interplay that governs cellular processes and environmental responses. This holistic approach enables robust hypothesis generation and deeper insights into the underlying molecular mechanisms.

Integrative Experimental & Computational Metabolomics 🧪 🧠 💻
Untargeted metabolomics captures a wide diversity of metabolites, but collecting high-quality spectra for annotation can be challenging. To address this, we are designing an AI-powered framework that leverages prior knowledge, multi-omics information, and machine learning models. This framework enhances sensitivity and specificity by adapting mass spectrometry analysis to the scientific and spectral context, improving our ability to translate spectra into chemical information that generates actionable insights and drives discovery.

About us

Location, Facilities, and Equipment 🌴🏫🔬

Location 🌴🏫

The HolobiomicsLab 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. We are part of the D2MS team (Diversité Moléculaire Metabolomics et Synthèse), coordinated by Prof. Mohamed Mehiri, and value their expertise, support, and friendship.

Our lab spaces are located on the 5th floor of the Institut de Chimie de Nice (ICN), which was partially renovated in 2023. We frequently hold meetings outdoors near the Castle or while strolling among the trees and fountains. Additionally, our computational team members are graciously hosted by the WiMMICS team at I3S, INRIA, Université Côte d'Azur, on the Sophia-Antipolis campus near Valbonne.

Facilities and Instrumentation 🔬🧪

The ICN facilities offer comprehensive capabilities to support analytical and organic chemistry research. For mass spectrometry-based metabolomics analysis, the HolobiomicsLab operates two Orbitrap mass spectrometers. Our robust workhorse is a Q-Exactive Focus (installed in 2018), and we use the IQ-X Tribrid Orbitrap (installed in May 2025) for challenging and advanced studies. Two Vanquish UHPLC chromatographic systems, with multiple binary pumps, are deployed, capable of performing dual/tandem chromatography for maximum productivity. We use a microflow-nanoflow multi-nozzle emitter ion source (MnESI, Newomics) for enhanced sensitivity.

Similarly, for compound identification, the HolobiomicsLab has access to state-of-the-art Nuclear Magnetic Resonance (NMR) instruments, including a Bruker Avance Neo 600 MHz equipped with a cryoprobe, installed in 2024.

Semi-Automated Sample Preparation 🤖🧫

The HolobiomicsLab has an entire semi-automated pipeline for 96-well plate-based protocols, including an automated miller (MM-200 Retsch) and a fully customizable liquid handler robot (Opentrons OT-2). We frequently handle batches of a few thousand samples.

Computational Resources 💻🔍

We perform our heavy computations on the Azzura high-performance cluster at Université Côte d'Azur, which features 35 x 32 CPU cores and GPU resources including 1 x A100 and 4 x H100 GPUs (more info). Additionally, we utilize the Jean-Zay national supercomputer, the largest computer in France with 126 petaflops of computing power (more info).

Compound Isolation and Identification 🧪🔬

We work closely with Prof. Mohamed Mehiri (D2MS team) and have access to a range of chromatographic apparatus for fractionation and compound isolation, including analytical, semi-preparative, and preparative HPLC systems (Waters) coupled to a single-quadrupole mass spectrometer for mass-targeted isolation procedures. The D2MS and the PFTC have the instrumentation and expertise to perform de novo structural elucidation of isolated metabolites.

Microbial Culture 🦠🔬

For microbiology, the lab has a laminar flow cultivation hood and can cultivate microorganisms under various conditions. We also operate a single-cell dispenser (Cytena) for automated microbial isolation.

About us

Diversity Statement and Vision 🌍 🌟 🌼 🧠

Synergy of Diversity and Neurodiversity 🌼 🧠
At HolobiomicsLab, we understand that the future of scientific discovery and education is intricately tied to the dynamic synergy between diverse human intellects and technologies. Our commitment to fostering a diverse environment—encompassing identity, gender, culture, and cognitive perspectives—is not just a pillar of our approach; it is the engine that drives our innovation. Diversity, in all its forms, is not merely about inclusion; it is a critical driver of the depth and breadth of our research and educational initiatives.
Embracing Neurodiversity: Unlocking Unique Strengths and Potential 🧠 🌟
At HolobiomicsLab, we celebrate neurodiversity and recognize that individuals with neurological differences, such as autism, ADHD, and dyslexia, bring unique strengths that inspire innovative thinking and challenge conventional methods and perspectives. Rather than viewing these differences as challenges, we see them as variations in cognitive function that offer distinct advantages, especially when combined collaboratively. For example, individuals with autism often display exceptional attention to detail and systematizing skills, while those with ADHD frequently excel in creativity and spontaneous problem-solving. By embracing these diverse perspectives, we create a richer and more dynamic academic environment, where varied cognitive approaches lead to novel insights and discoveries. Our inclusive mindset empowers all team members to fully engage with and contribute to our research, fostering a collaborative spirit that enhances the collective potential of our lab.
Inclusive and Empowering Academic Environment 🌍 🌼 🧠
At HolobiomicsLab, we are dedicated to creating an inclusive environment where all individuals—regardless of their cognitive or neurological profiles, physical abilities, identities, genders, or cultural backgrounds—can thrive. Our commitment to inclusion goes beyond mere accommodation; it is about fostering a space where everyone is empowered to express their unique strengths and contribute to our collective success. We believe that diverse perspectives, shaped by a variety of lived experiences, enhance the depth and scope of our scientific inquiry. By embracing these differences, we cultivate a research culture that celebrates cognitive diversity and promotes innovative thinking. For welcoming international researchers, and for the training of our lab members, English is our primary work language.
AI-Enhanced Learning and Research 🤖 🧠
At HolobiomicsLab, we are not just integrating AI into our research and learning processes; we are pioneering a co-evolutionary adaptation with AI that is reshaping the future of scientific discovery and education. By viewing AI as a co-creative partner, we harness its potential to augment self-learning, human creativity, analytical capabilities, and technical craftiness, allowing us to explore new frontiers and challenge established paradigms across disciplines. This approach creates interdisciplinary opportunities that enable all lab members, trained in various disciplines, to engage deeply with complex scientific questions and computational methods, even without prior formal training in chemistry and computational sciences. Through this co-evolution, we aim to democratize access to advanced AI tools, empowering everyone to contribute to scientific innovation.
Bridging Disciplines through AI Co-Evolution 🧬 🔬 💻
Interdisciplinarity is at the heart of our approach at HolobiomicsLab. We recognize that the most significant scientific advancements occur when knowledge from different fields converges to address complex challenges. AI plays a pivotal role in facilitating this convergence by bridging gaps between disciplines and enabling seamless collaboration. Our lab fosters an environment where biologists, chemists, data scientists, and other specialists can work together, leveraging AI to cross traditional boundaries. This interdisciplinary focus not only enhances the depth and breadth of our research but also fosters a culture of continuous learning and innovation. By integrating diverse expertise with AI, we are pioneering new methodologies and solutions that push the boundaries of what is possible.
AI as a Tool to Enhance Scientific Active-Learning 🤖 ⚙️ 🧠
We believe that artificial intelligence plays a crucial role in enhancing scientific active-learning and supporting neurodiverse individuals within research and academic settings. AI can help design personalized learning experiences that promote efficient self-learning, removing language barriers in acquiring new concepts and skills. This marks a new era for knowledge acquisition and diffusion. Importantly, AI can address some of the unique challenges faced by neurodiverse researchers by providing tailored support that aligns with their cognitive strengths. For instance, AI-driven tools can automate routine tasks, offer structure, and create personalized learning paths, enabling neurodiverse individuals to focus on their strengths, such as creative problem-solving or detailed analysis. Furthermore, AI enhances accessibility by creating environments that reduce sensory overload—a common challenge for many neurodiverse individuals—thus enabling them to thrive in academic settings. Our AI-assisted learning initiatives are specifically designed to bridge gaps between disciplines while accommodating diverse cognitive needs. AI provides personalized and adaptive learning experiences, helping students from diverse backgrounds grasp complex computational concepts and tools with greater ease. This enables them to interact with real data and algorithms at their fingertips or through voice commands. This interdisciplinary and inclusive methodological approach ensures that all students, regardless of their academic background or neurodiversity, can fully participate in and contribute to cutting-edge research, fostering a more collaborative and supportive academic environment. Through our pioneering efforts, we aim to lead the co-evolution of AI in research and education, setting new standards for how technology and human ingenuity can thrive together.

About us

Affiliations, Funding, Acknowledgements

Centre National de la Recherche Scientifique

The Centre National de la Recherche Scientifique (CNRS) is France's leading public research organization and one of the largest in Europe. For more than 80 years, the CNRS supports cutting-edge research across all fields of knowledge, from fundamental sciences to applied technologies. With over 1,000 laboratories and a global network of researchers, the CNRS plays a pivotal role in advancing scientific discovery and innovation.

The CNRS is the primary contributor to the HolobiomicsLab, supporting the lab with two permanent researchers (Louis-Félix Nothias and Tao Jiang), one PhD fellowship (MITI CNRS), and starting funds. The lab also benefits from the CNRS's extensive local and national ecosystem, which includes access to cutting-edge research instrumentation, administrative and grant management support.

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Université Côte d'Azur

Université Côte d'Azur (UniCA) hosts/supports the HolobiomicsLab and plays a crucial role in its success. The lab is located at the Institut de Chimie de Nice (ICN) on the Valrose campus, which offers state-of-the-art analytical chemistry instrumentation. The HolobiomicsLab is associated to the D2MM team (headed by the Prof. Mohamed Mehiri) at the ICN. Additionally, the lab has a access to the Azzura supercomputer for advanced computational research. As a research-intensive institution, Université Côte d'Azur supports the lab through its academic ecosystem, offering administrative assistance, collaborative opportunities, and interdisciplinary educational programs.

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Interdisciplinary Institute for Artificial Intelligence Côte d'Azur

The Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d’Azur, one of the four "Interdisciplinary Institutes for Artificial Intelligence" established in France in 2019, plays a crucial role in supporting the HolobiomicsLab. Through the Affiliated Chair (Louis-Félix Nothias) and co-funded research projects such as that of Madina Bekbegernova, we are deeply integrated into the 3iA Côte d'Azur ecosystem. This integration allows us to tap into the expertise of 3iA’s extensive network, including collaborations with academic leaders at the INRIA Sophia Antipolis and various start-up/industrial partners. Our partnership with 3iA enhances our ability to develop and apply cutting-edge artificial intelligence techniques, creating new translational opportunities for our research methods and tools.

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Our research is supported by the following institutions/programs

The CNRS

This lab is supported by the Centre National de la Recherche Scientifique (CNRS) and the Mission Interdisciplinaire pour les Initiatives Transversales (MITI CNRS).

Initiative d'Excellence

This lab is supported by the French government, through the University Côte d'Azur IDEX (UCA J.E.D.I) Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-15-IDEX-01.

ANR

The Institut de Chimie de Nice (ICN) is supported by the National Research Agency (ANR) with the reference ANR-22-CPJ2-0048-01 & ANR-24-CE44-1190-03.

Region Sud

The HolobiomicsLab and the Institut de Chimie de Nice are benefiting from the Contrat de plan Etat-région (CPER) "Metabolome" co-funded by the Région Sud, the French Governement and the CNRS, and coordinated by Prof. Mohamed Mehiri (UniCA) providing state-of-art instrumentation for mass spectrometry and nuclear magnetic resonance.

FNR Luxembourg

The lab is supported by AFR FNR Luxembourg (project 17994255) that funds the research project of Lucas Pradi aiming at enhancing metabolite detection and annotation by improving MS2 spectral quality and coverage.

We submit every year ambitious interdisciplinary projects to Horizon Europe calls

European Innovation Council (EIC)

Two proposals submitted to the EIC Pathfinder Open call (2023 & 2024). Both were evaluated as "Very good" but below the funding threshold (approx. 5% success rate).

European Research Council

One ERC Starting Grant proposal (2023) that was evaluated up to the interview stage, but not funded.