The Complete Genome Sequence of the Lactic Acid Bacterium <i>Lactococcus lactis</i> ssp. <i>lactis</i> IL1403

TLDR

Lactococcus lactis is a nonpathogenic, AT‑rich gram‑positive bacterium closely related to Streptococcus, widely used as a cheese starter and the best‑characterized lactic acid bacterium. The IL1403 genome was sequenced using a novel two‑step strategy that combined diagnostic whole‑genome sequencing with a shotgun polishing step. The IL1403 genome is 2.37 Mb with 2,310 proteins, 293 prophage genes, and 43 IS elements, whose nonrandom distribution suggests recent recombination; it also contains a full set of late competence genes indicating transformability, and reveals new fermentation and aerobic respiration pathways as well as evidence of horizontal gene transfer to Salmonella‑Escherichia group bacteria. The genome sequence has been deposited in GenBank under accession AE005176.

Abstract

Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group. [The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176 .]