Abstract
Plasmids are autonomous, self-replicating, extrachromosomal genetic elements that are typically not essential for growth of their host. They may encode metabolic capabilities, which promote the maintenance of these genetic elements, and may allow adaption to specific ecological niches and consequently enhance survival. Genome sequencing of 16 Lactococcus lactis strains revealed the presence of 83 plasmids, including two megaplasmids. The limitations of Pacific Biosciences SMRT sequencing in detecting the total plasmid complement of lactococcal strains is examined, while a combined Illumina/SMRT sequencing approach is proposed to combat these issues. Comparative genome analysis of these plasmid sequences combined with other publicly available plasmid sequence data allowed the definition of the lactococcal plasmidome, and facilitated an investigation into (bio) technologically important plasmid-encoded traits such as conjugation, bacteriocin production, exopolysaccharide (EPS) production, and (bacterio) phage resistance.
Highlights
Lactococcus lactis is globally applied as a starter culture for dairy-based food fermentations, such as those involved in the production of Cheddar, Colby, Gouda and blue cheeses, and from an economic and biotechnological perspective represents one of the most important bacteria (Ainsworth et al, 2014a)
To ensure complete coverage of the full plasmid complement the complete genomes of all 16 strains were re-sequenced utilizing an Illumina MiSeq approach which resulted in the eludication of a further 14 plasmids that had not been detected based on the original single molecule real time sequencing (SMRT) assemblies
These 14 plasmids ranged in size from 6 to 62 Kbp, indicating that their absence from the SMRT dataset was in the majority of cases not associated with exclusion from the library based on their small size
Summary
Lactococcus lactis is globally applied as a starter culture for dairy-based food fermentations, such as those involved in the production of Cheddar, Colby, Gouda and blue cheeses, and from an economic and (food) biotechnological perspective represents one of the most important bacteria (Ainsworth et al, 2014a). It is widely accepted that L. lactis originated from a plant-associated niche (Price et al, 2012; Wels et al, 2019) and, whilst the majority of sequenced lactococcal representatives are isolated from the dairy environment, this is not representative of the presumed diversity of the taxon It is evident from genome analyses of L. lactis strains isolated from the dairy niche that genome decay (due to functional redundancy) (Makarova et al, 2006; Goh et al, 2011; Ainsworth et al, 2013; Kelleher et al, 2015, 2017), in parallel with the acquisition of novel plasmidencoded traits played a significant role in their adaptation to the nutrient-rich environment of milk. The plasmid-encoded extracellular cell wall proteinase (lactocepin) has been shown to be directly associated with the bitter flavor defect in Cheddar cheese varieties, involving starters which produce lactocepin of the so-called a, e, or h groups, and its characterization is of particular importance when selecting novel starter cultures (Broadbent et al, 2002)
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