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

The EM3B laboratory has an important collection of more than 2000 bacterial strains isolated from fresh and processed salmon. 100 strains representative of salmon microbiome diversity will be selected to :

1) establish the bacterial interaction network within the salmon microbiome. Miniaturized cross inhibition activities between strains will allow to i) identify the possible interactions between all bacterial species, whether they are protective, pathogen, spoilage or neutral bacteria; and ii) predict collateral effects of the addition of protective culture in the microbiome.

2) determine the antimicrobial substances potentially involved in bacterial competitions. The 100 genomes will be sequenced (Illumina and Nanopore strategies), assembled and annotated to predict the gene clusters encoding biosynthetic pathways of antimicrobials and provide an exhaustive description of the antimicrobial diversity and capacity at the strain, species and microbiome levels.

3) characterize the regulation of the antimicrobial compounds biosynthesis during salmon conservation. It is well known that abiotic changes can have a great impact on bacterial interactions and production of antimicrobial metabolites. The effect of various conditions mimicking the salmon conservation (culturomics) will be assessed i) on the bacterial competitor behaviour by flow cytometry using labelled strains, and ii) on the expression of antimicrobial biosynthetic gene clusters (transcriptomic analyses).

During this first phase of the project, 100 complete genomes were sequenced and assembled using Illumina technology. These genomes have been deposited on the MAGE automatic annotation platform (Genoscope, Evry) and will be made available to the scientific community as soon as possible. The annotation of the antimicrobial biosynthetic clusters (BGCAM) has been carried out for the moment using the Antismash pipeline. Between 0 and 23 BGCAMs could be identified per genome. Half of them concern the synthesis of peptide molecules (unmodified bacteriocins, RiPPs, NRPs). The genomic data were correlated with the antagonistic activities. These analyses made it possible to select 15 model strains for further analyses.

The next step is to develop genetic tools and flow cytometry protocols to compare the inhibition capacities and kinetics of bacterial strains in co-culture, according to multiple growth conditions. These steps will allow the selection of culture conditions to study the regulation of BGCAM in 5 model strains.

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.