Understanding of the bacterial interaction network within seafood microbiome towards a sustainable biopreservation – SEABIOMIC

The EM3B laboratory has a large collection of over 2,000 bacterial strains isolated from fresh and processed salmon. 100 strains representative of the diversity of the salmon microbiome were selected to :

1) Establish the network of bacterial competitions within the salmon microbiome. Miniaturized cross-inhibition activities were carried out to identify possible interactions between all bacterial species, whether protective, pathogenic, spoilage or neutral.

2) Explain the mechanisms involved in the observed inhibition activities. The 100 genomes were sequenced (Illumina and Nanopore strategies), assembled and annotated. Genes encoding biosynthetic pathways of antimicrobial compounds were predicted to provide a comprehensive description of antimicrobial diversity and capacity at strain, species and microbiome levels. The expression of these genes was assessed in fish juice under conditions similar to those of smoked salmon storage. In parallel, the involvement of nutritional competition was addressed using high-throughput phenotyping microarrays.

3) Characterize the regulation of antimicrobial biosynthesis during salmon preservation. The effect of different abiotic parameters, including smoked salmon juice, was evaluated on antimicrobial activity and on the expression of biosynthetic genes encoding different types of bacteriocins in Carnobacterium maltaromaticum.

One hundred strains representing the taxonomic and phenotypic diversity of the smoked salmon microbiome were selected. Miniaturized cross-inhibition tests between the 100 strains (10,000 tests in all) revealed 613 inhibitions and, for the first time, a network of bacterial competitions was described. This network makes it possible to assess the impact that bioprotective strains could have in the matrix on species other than Listeria, to identify possible candidates for inhibiting spoilers, and to gain for the first time a global view of the interactions that can take place in this microbiota.

In order to identify bacterial competitions linked to the synthesis of antimicrobial compounds, the 100 genomes were completely sequenced, assembled and annotated. They are now available (ENA, PRJEB60605; Sauvage et al., 2023) and constitute a reference database for this type of microbiota. Around 500 clusters of genes encoding potential antimicrobial agents have been predicted and compared in silico. Between 0 and 17 clusters per genome were identified, half of them encoding peptide molecules (unmodified bacteriocins, RiPPs, NRPs). The expression of these clusters under conditions mimicking those of smoked salmon storage is still under RNA-seq analysis.

The impact of different abiotic parameters on the production of active molecules was studied through the comparison of three Carnobacterium maltaromaticum strains with variable antibacterial profiles and containing between 3 and 7 gene clusters encoding bacteriocins of different categories (lanthipeptides, sactipeptides...). A high-throughput RT-qPCR method was developed to monitor the expression of these clusters under different conditions. The results showed a wide range of responses from different strains.

The SEABIOMIC project has generated numerous -omic data and new strategies for studying the interactions of seafood microbiomes. This enabled us to initiate the study of the seafood microbiota dynamics, and to make further progress in our understanding of bacterial interactions.

This more fundamental approach of seafood biopreservation than those proposed to date should allow to understand how these microbiomes evolve during storage, to better control them and to be able to propose more effective microbiome engineering strategies.

Passerini Delphine, Kolypczuk Laetitia, Mace Sabrina, Pilet Marie-France, Leroi Francoise (2021). Biopréservation des produits de la mer avec des bactéries marines . Techniques de l'Ingénieur , BIO 9 240 (27p.) . doi.org/10.51257/a-v1-bio9240

Biopreservation is a method of food preservation consisting in the inoculation of protective bacteria to prevent the growth of unwanted microorganisms (human pathogens, spoilage bacteria). The recent description of the microbiome of seafood products makes possible to go further in the understanding of bacterial interactions which represent the biopreservation underlying mechanisms. The SEABIOMIC project aims to describe for the first time the bacterial interaction networks of the microbiome of seafood products as a whole. The identification of antimicrobial molecule biosynthesis pathways and their regulation will provide a better understanding of the factors that trigger bacterial competition during product conservation. The knowledge acquired during this project will allow to better predict the evolution of the microbiome during biopreservation process and to develop a more targeted and more efficient biopreservation.