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A joined approach to explore seafood microbiomes: from bacterial community structures towards functional insights
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Edité par CCSD -
International audience. Seafood product microbiomes lie at the intersection of bacteria originating from fish and seawater, and from contamination during the food chain processing. During the storage, dynamic of this microbiome is directly related to the product spoilage (i.e off-odor production) and safety. For more than two decades, EM3B Lab has been characterizing bacterial ecosystems of numerous seafood (shrimp, tuna, salmon, sea bass, cuttle fish, blue crab) with classic microbiology, biochemistry and sensory analysis and more recently 16S gene metabarcoding. Today, longitudinal approaches combining both classical technics and multi-omics methods allow to explore more deeply the seafood bacterial microbiome. New challenges consist i) in identifying molecular mechanisms involved in bacterial interactions and thus in population structure (i.e. antimicrobial compound synthesis) and ii) in establishing the relationships between the population structure and functional responses (spoilage, presence of pathogens). For this, two complementary studies focusing on salmon microbiome were conducted in parallel: i) a top-down approach used to decrypt the bacterial communities’ structure and the microbiome functionality of cold smoked salmon samples from 3 different factories using shotgun metagenomics (regional project SALMONICS -2020-2023). ii) a bottom-up approach consisting to understand population structure dynamics from a deep analysis of 100 bacterial strains supposed representative of salmon microbiome (SEABIOMIC project ANR 2021-2024). The combined results of both studies highlight the complexity of seafood microbiome. Taking into consideration these bacterial networks and their metabolic potential will open the way for innovative biocontrol strategies based on microbiome engineering.
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