Lactococcus lactis has been used for millennia as a starter organism in the production of many fermented dairy products. This announcement includes the draft genome sequences of four strains of Lactococcus lactis, two of dairy origin and two from nondairy sources.
ABSTRACT
Lactococcus lactis has been used for millennia as a starter organism in the production of many fermented dairy products. This announcement includes the draft genome sequences of four strains of Lactococcus lactis, two of dairy origin and two from nondairy sources.
ANNOUNCEMENT
Lactic acid bacteria (LAB) are widely used as commercial dairy starter cultures. Within this group, Lactococcus lactis is the main species used as an industrial and artisanal starter culture due to its ability to produce acid from lactose in milk and to generate a diverse range of flavors (1). Even though this species is traditionally associated with the milk environment, the ancestor of common L. lactis strains occupied a plant niche (2), and indeed, L. lactis possesses a wide ecological distribution in diverse niches. In this context, L. lactis strains can be classified as “domesticated” (related to dairy and fermented products) or “environmental” (isolated from plants, animals, and raw milk) (3). Recently, nondairy L. lactis strains have gained some attention because of their more diverse metabolic capabilities and flavor-forming capacities not usually found in dairy strains (4, 5).
Whole-genome sequencing was performed for two domesticated strains, Lactococcus lactis subsp. cremoris DPC 140 and Lactococcus lactis subsp. cremoris DPC 169, both isolated from mixed-strain starter cultures, and for two wild, or nondairy, strains, Lactococcus lactis subsp. lactis DPC 6756 (strain P-8 described by Alemayehu et al. [5]), isolated from green peas, and Lactococcus lactis subsp. cremoris DPC 6855 (6), isolated from grass. Dairy strains were grown overnight in M-17 broth (Sigma-Aldrich) at 30°C. Nondairy strains were supplemented with 0.5% (wt/vol) d-glucose (Sigma-Aldrich). DNA was isolated using the UltraClean microbial DNA isolation kit (Mo Bio Laboratories, Cambridge, UK) following the manufacturer’s instructions. Default parameters were used for all software unless otherwise specified. Genomic DNA libraries were prepared using a Nextera XT library prep kit (Illumina, San Diego, USA) following the manufacturer’s protocol with the following modifications: 2 ng of DNA instead of 1 ng was used as input, and the PCR elongation time was increased from 30 s to 1 min. Libraries were sequenced on the Illumina HiSeq platform using a 250-bp paired-end protocol (MicrobesNG, University of Birmingham, UK). Reads were adapter trimmed using Trimmomatic 0.30 with a sliding window quality cutoff value of Q15 (7). SPAdes 3.7 was used to perform de novo assembly on the samples (8). The genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (9). The final draft genomes were estimated using CheckM 1.0.12 (10) to be ≥96% complete with <2.5% contamination.
The sequencing data and statistics of the above-mentioned strains are shown in Table 1. These sequencing data contribute to the pool of available Lactococcus lactis genomes from diverse sources for further analysis of potential phenotypes and genotype-phenotype associations. Metabolic pathways can be explored and compared across niches in order to discover new capabilities of interest in the food industry, such as enzyme production and flavor formation.
TABLE 1.
Genome characteristics of the Lactococcus lactis strains used in this study
| Organism | Draft genome size (bp) | No. of contigs | N50 (bp) | G+C content (%) | Mean coverage (×) | Total no. of reads | SRA accession no. | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|
| L. lactis subsp. cremoris DPC 140 | 2,393,364 | 229 | 17,974 | 35.60 | 109 | 627,757 | SRR9283149 | VERZ00000000 |
| L. lactis subsp. cremoris DPC 169 | 2,480,405 | 130 | 36,700 | 35.64 | 117 | 723,132 | SRR9283148 | VERY00000000 |
| L. lactis subsp. lactis DPC 6756 | 2,482,547 | 13 | 637,420 | 34.96 | 83.3 | 497,681 | SRR9283151 | VERX00000000 |
| L. lactis subsp. cremoris DPC 6855 | 2,694,688 | 101 | 151,720 | 35.37 | 37.9 | 253,524 | SRR9283150 | VERW00000000 |
Data availability.
The draft whole-genome sequencing data were deposited in NCBI GenBank and the Sequence Read Archive (SRA) under BioProject no. PRJNA546489. The accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
This research was funded by Dairy Research Ireland (reference 0402) and the Teagasc Walsh Fellowship Program (reference 2018036).
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Associated Data
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Data Availability Statement
The draft whole-genome sequencing data were deposited in NCBI GenBank and the Sequence Read Archive (SRA) under BioProject no. PRJNA546489. The accession numbers are listed in Table 1.