Welcome to the B3D team! Committed to unravelling the complex world of microbiology in the food chain, our primary focus is on understanding and mitigating the hazards posed by pathogens in the context of spatially organised microbial communities present in biofilms and food matrices. Our comprehensive approach aims to develop innovative strategies – from preventative to curative interventions – by harnessing fundamental biological processes and utilising a spectrum of physical, chemical and microbial treatments. Join us on our collaborative journey, weaving together microbiology, molecular biology and advanced imaging techniques to explore the dynamic landscape of spatially organised microbial communities and drive breakthroughs in food microbiology and beyond.
Each year, unsafe food contributes to 600 million cases of foodborne illness and 420,000 deaths worldwide. Children under the age of 5 account for 30% of these deaths. The World Health Organization (WHO) estimates that the consumption of unsafe food results in the loss of approximately 33 million years of healthy life worldwide each year, although this figure is likely to be an underestimate. Recent scientific reports highlight the emergent properties of microbial pathogens in biofilms and spatially organised communities, challenging conventional mitigation strategies in the food chain. The protective extracellular matrix, phenotypic heterogeneity and specific cell behaviours enable these three-dimensional biological structures to withstand harsh environmental conditions such as exposure to disinfectants, food preservatives or digestive stress after ingestion. To unravel these emergent properties and develop effective countermeasures, the B3D team conducts fundamental research on the structural dynamics, heterogeneity and community functions of biofilms down to the single-cell scale. The team uses the latest knowledge on these structured communities to implement innovative control strategies in academic research programmes and industrial partnerships. These interdisciplinary efforts extend beyond the food industry, making significant contributions to the medical, biotechnology and space fields.
In our quest to unravel the mysteries of microbial architectures, our research delves into the dynamic intricacies of microbial communities. We probe surfaces and food matrices and analyse heterogeneities within spatially organised communities to understand their structural nuances. Using cutting-edge transcriptomic techniques such as RNAseq, CRISPRi pool and fluorescent transcriptional fusions, we decipher gene expression patterns at the single-cell scale and explore their profound impact on the structure and function of microbial communities. We are also unravelling the influence of microbial motility on community dynamics and how it shapes adaptive responses and interactions within these populations. We delve into the intricate network of interspecies interactions and examine their central role in promoting community stability, diversity and overall functionality. Finally, we explore emergent community functions, investigating how the structural organisation and collective behaviour of microbial communities contribute to their resilience and adaptability in spatially organised environments.
Advances in knowledge of spatially organised community structures are being used to develop innovative approaches to control unwanted microorganisms. Using cutting-edge techniques, we are investigating the dynamics of cell death within three-dimensional microbial communities – a key factor in understanding and containing unwanted microorganisms. At the same time, our research explores the synergistic potential of molecule combinations, strategically enhancing their collective efficacy to precisely target and mitigate unwanted microorganisms. Our commitment extends to the development of breakthrough sustainable preservation methods designed to maintain the structural integrity of the microbial environment while inhibiting the growth of unwanted microorganisms. Using microbial-based strategies such as positive biofilms and biopreservation, we aim to harness the beneficial activities of microorganisms by creating competitive environments that exclude and suppress unwanted counterparts. This line of research promises significant advances in the monitoring, prevention and management of unwanted microorganisms in structured microbial environments. These innovative control strategies not only promise to advance all stages of the food sector, from farm to fork, but also open up valuable applications in the fields of medicine and space exploration.
The B3D team is a partner of the ACTIA joint Technological Unit entitled “FASTYPERS”. A Mixed Technology Unit (UMT) is a partnership tool between public research units and technical institutes, established and supported by the Ministry responsible for Food under the coordination of ACTIA. Listeria monocytogenes and Salmonella spp are two major foodborne pathogens. Food contamination can originate from either plant or animal raw materials and the food processing environment. The ability of these pathogens to adapt to stress, grow at low temperatures, form biofilms and then persist in food processing facilities for years has made these two pathogens a major challenge for food safety. Successful control of these bacterial strains in the food chain requires appropriate cleaning and sanitation programs. Biocides play an important role in limiting the spread of bacterial pathogens. However, some strains can resist sanitation processes.
The “FASTYPERS” UMT was created in France to gain a deeper insight into the contamination of the pork and dairy sectors for these two pathogens, in a One Health approach. FASTYPERS is a 5-year project involving the French Agency for Food, Environmental and Occupational Safety (ANSES), the National Institute for Agriculture, Food and the Environment (INRAE), the French Institute for Food Safety and Dairy Products (ACTALIA) and the French Institute for Pig and Pork Products (IFIP). The main objectives are:
These strains will be phenotypically tested for biocide resistance and biofilm formation. Genome-wide association studies (GWAS) will identify key genetic markers that contribute to the adaptation of strains in food crops. These markers will then be used to develop two state-of-the-art molecular tools, GenoListeria1 and GenoSalmo2. In a single analysis, these tools will help us detect resistant strains that may persist in food processing facilities. These tests will help the food industry make food processing decisions to improve food safety.
The INRAE Micalis Institute and Lallemand Animal Nutrition (LAN) are pleased to announce the creation of the LabCom “Biofilm1Health,” a collaborative laboratory focused on unlocking the potential of biofilm properties in beneficial microbes. This cutting-edge partnership between the B3D team from the Micalis Institute (UMR 1319 INRAE, AgroParisTech, Université Paris-Saclay) and LAN, with support from the French National Research Agency (ANR), aims to advance the One Health concept, a holistic approach that integrates human, animal, and environmental health.
The mission of LabCom “Biofilm1Health” is to explore the unique properties of beneficial biofilms—complex microbial communities that offer protection and enhanced functionality. By investigating how these biofilms can reduce harmful microorganisms in livestock, food production, and the environment, the initiative seeks to provide sustainable and effective microbial solutions. A defining aspect of this project is its incorporation of advanced biofilm phenotyping and artificial intelligence to enhance our understanding of these intricate ecosystems.
The ultimate goal is to optimize the application of beneficial biofilms to create next-generation solutions that improve sustainability, reduce the need for chemical interventions, and support animal welfare.
The project is structured around four key research axes:
The B3D team at the Micalis Institute is internationally recognized for its pioneering research on biofilms and spatially organized microbial communities. Their work focuses on understanding the complex relationships between microbial community structures and their emergent properties, particularly in biofilm and food-related environments. By exploring phenotypic heterogeneity and interspecies interactions, the B3D team aims to develop novel preventive and curative strategies that can be applied to industries ranging from food production to healthcare and aerospace.
Lallemand Animal Nutrition has been at the forefront of microbial solutions for animal nutrition since the 1980s, including the introduction of the first registered probiotics in Europe for ruminant and monogastric animal feeds. Today, LAN plays a leading role in animal nutrition and environmental management in sectors such as ruminant, pig, poultry, aquaculture, equine, and pet nutrition. Through strategic collaborations and its Blagnac laboratory, LAN continues to innovate by developing products that harness beneficial microorganisms for both nutrition and livestock management.
The creation of LabCom “Biofilm1Health” signals the dawn of a new chapter in microbial innovation, where the combined expertise of INRAE and Lallemand Animal Nutrition will drive forward solutions that benefit human, animal, and environmental health. By unlocking the potential of biofilms and leveraging cutting-edge digital tools, this collaboration will contribute to sustainable practices across multiple industries. The research carried out at LabCom “Biofilm1Health” promises to not only deepen our understanding of microbial ecosystems but also pave the way for transformative solutions that reduce chemical inputs, enhance animal welfare, and promote a healthier planet.
LabCom “Biofilm1Health” is funded by the French National Research Agency .
