Complete Genome Sequence of Lactococcus piscium CNCM I-4031, a Bioprotective Strain for Seafood Products

ABSTRACT Lactococcus piscium CNCM I-4031 is a psychotrophic foodborne lactic acid bacterium showing potential interest for the biopreservation of seafood products due to its inhibition properties toward pathogenic and spoilage bacteria. The analysis of its genome will provide a better understanding of the mechanisms of interaction between these bacteria.

L actococcus piscium is a psychrotrophic species first isolated in 1990 from rainbow trout (1). Studies have reported the presence of this species in a large variety of food products, including meat, seafood, and vegetables (2,3). L. piscium CNCM I-4031 (also named EU2241), isolated from raw salmon packs (4), might present interests for seafood biopreservation: it improves the sensory quality of seafood and limits the growth of spoilage (Brochothrix thermosphacta and Serratia proteamaculans) or pathogenic (Listeria monocytogenes) bacteria (5)(6)(7). Although the mechanisms of growth inhibition have not yet been elucidated, a previous study suggested the requirement for a contact between L. piscium CNCM I-4031 and the target-inhibited strain as well as putative involvement of quorum sensing (8).
The whole-genome sequencing of L. piscium CNCM I-4031 was carried out by Eurofins MWG Operon laboratories (Ebersberg, Germany) using GS FLX/FLXϩ technologies with shotgun and 8-kbp-long paired-end libraries. The genome sequencing coverage is 63ϫ. The assembly realized with Newbler 2.6 (9) showed an N 50 of 144,750 bp for 31 contigs. The final assembly gave two scaffolds with seven contigs and a genome size of 2.26 Mbp, in accordance with results obtained by pulsed-field gel electrophoresis (PFGE) (data not shown). The first scaffold (2.06 Mb), composed of six contigs, is the complete sequence of the chromosome, with a GϩC content of 38.74%. The second scaffold (one contig) formed a 20-kb plasmid with a GϩC content of 34.36%. Automatic annotation and manual curation were performed on the whole genome thanks to the MicroScope platform (10, 11) (Genoscope, Évry, France). The results showed that L. piscium CNCM I-4031 chromosome contains 2,205 predicted coding DNA sequences (CDSs), as observed in Lactococcus lactis genomes (around 2,500).
Thirty-one percent of the predicted CDSs were assigned to proteins of unknown functions, 40% were predicted as enzymes, 6% as transcriptional factors, and 4% as proteins of cell structure. The remaining proteins are involved in diverse cell processes (including carriers, lipoproteins, receptors, and other membrane proteins) or from an extrachromosomal origin. Seventy-five genes (3.4%) were manually curated as carbohydrate-active enzymes (CAZymes) that degrade or modify carbohydrates or create glycosidic bonds.
The plasmid encompasses 26 CDSs, including a complete ribose gene cluster, rbsRKDACB. The rbs genes are involved in ribose utilization but have also been reported to be responsible for internalization of autoinducer II (AI-2) involved in quorum sensing (12,13).
Accession number(s). This whole-genome shotgun project has been deposited in ENA under the accession no. FLZT01000001 to FLZT01000007. The versions described in this paper are the first versions.

ACKNOWLEDGMENTS
The LABGeM (CEA/IG/Genoscope & CNRS UMR 8030) and the France Génomique National infrastructure (funded as part of Investissement d'Avenir Program managed by Agence Nationale pour la Recherche, contract ANR-10-INBS-09) are acknowledged for support within the MicroScope annotation platform. Taous Saraoui was the recipient of a Ph.D. fellowship program from the French Ministry of Higher Education and Research. This study was financially supported by the Région des Pays de la Loire, France within the context of the COM-BACT research program (contract 2014 07957).