ABSTRACT
The lactic acid bacterium Lactococcus lactis is widely used for the production of fermented dairy products. Here, we present the draft genome sequences of 24 L. lactis strains isolated from different environments and geographic locations.
GENOME ANNOUNCEMENT
Lactococcus lactis is a Gram-positive bacterium that is predominantly found on plant material and in the dairy environment (1, 2). It is extensively used in dairy fermentations (3), which is mainly due to its role in the development of texture and flavor through, e.g., proteolysis and the production of volatile flavor compounds (4). It also contributes to food preservation through the production of organic acids and bacteriocins such as nisin (5). Four L. lactis subspecies have been defined (6): subsp. lactis (7), subsp. cremoris (8), subsp. hordniae (9), and subsp. tructae (10). In this study we report the draft genome sequences of 24 L. lactis strains, of which 23 belong to subspecies lactis and one (LMG8520) is the type strain for the subspecies hordniae (Table 1) (11). However, we found in a detailed phylogenetic and comparative genome analysis that strain LMG8520 has a L. lactis subsp. lactis genotype.
TABLE 1 .
Overview of the 24 L. lactis strains in NCBI BioProject PRJNA294255
| Strain | Original strain name or culture collection no. | Subspecies | Accession no. | Source of isolation | Country of isolation |
|---|---|---|---|---|---|
| ATCC 19435a | OJ | lactis | LKLC00000000 | Milk (dairy starter) (11) | Denmark |
| DRA4 | lactis biovar diacetylactis | LIWD00000000 | Dairy starter (11) | the Netherlands | |
| E34 | lactis | LKLD00000000 | Silage (11) | the Netherlands | |
| K231 | lactis | LKLE00000000 | White kimchi (11) | Japan | |
| K337 | lactis | LKLF00000000 | White kimchi (11) | Japan | |
| KF134 | lactis | LKLJ00000000 | Alfalfa and radish (15) | New Zealand | |
| KF146 | lactis | LKLK00000000 | Alfalfa and radish (15) | New Zealand | |
| KF196 | lactis | LKLL00000000 | Japanese kaiware shoots (15) | New Zealand | |
| KF201 | lactis | LKLM00000000 | Sliced mixed vegetables (15) | New Zealand | |
| KF24 | lactis | LKLH00000000 | Alfalfa sprouts (15) | New Zealand | |
| KF282 | lactis | LKLN00000000 | Mustard and cress (15) | New Zealand | |
| KF67 | lactis | LKLI00000000 | Grapefruit juice (15) | New Zealand | |
| KF7 | lactis | LKLG00000000 | Alfalfa sprouts (15) | New Zealand | |
| Li-1 | lactis | LKLO00000000 | Grass (11) | Belgium | |
| LMG14418 | TM 147 | lactis | LKLT00000000 | Bovine milk (11) | Belgium |
| LMG8520a | HC-1-1 | hordniae | LKLP00000000 | Leaf hopper (11) | United States |
| LMG8526 | B 6113 | lactis | LKLQ00000000 | Chinese radish (11) | United Kingdom |
| LMG9446 | 21L | lactis | LKLR00000000 | Frozen peas (11) | United Kingdom |
| LMG9447b | 31L | lactis | LKLS00000000 | Frozen peas (11) | United Kingdom |
| M20 | lactis biovar diacetylactis | LKLU00000000 | Soil (11) | the Netherlands | |
| ML8 | NCDO1994 | lactis | LKLV00000000 | Dairy starter (11) | United Kingdom |
| N42 | lactis | LKLW00000000 | Soil and grass (11) | the Netherlands | |
| NCDO895 | X62 | lactis | LKLX00000000 | Dairy starter (11) | United Kingdom |
| UC317 | lactis | LKLY00000000 | Dairy starter (11) | Ireland |
The strains were grown overnight in 5 mL LM17 broth at 30°C. After propagation in fresh medium, cells were harvested during midexponential growth and total DNA was isolated as previously described (11) with the following modifications. Cell pellets were resuspended in a buffer [6.7% sucrose, 1 mM EDTA, 50 Mm TrisHCl (pH 8.0)] and incubated with RNase (0.5 mg/mL) and lysozyme (2 mg/mL) at 37°C for 1 h. Subsequently, cells were lysed by treating the samples with SDS (1% wt/vol final concentration) at 37°C for 10 min. The total DNA was extracted with phenol-chloroform, precipitated with isopropanol and sodium acetate (12), and dissolved in sterile water.
Whole-genome sequencing was performed at GATC Biotech (Konstanz, Germany) with 50 bp paired-end libraries on an Illumina HiSeq 2000. Raw sequence reads of each of the genomes were assembled de novo using IDBA (13) with default parameters at a target coverage of 50×. This resulted in draft genomic sequences for 24 L. lactis strains (Table 1). Annotation of the contig sequences was performed by the RAST server (14).
Accession number(s).
The genome sequences of the 24 L. lactis strains have been deposited as whole-genome shotgun projects at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.
Footnotes
Citation Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SAFT, Bachmann H. 2017. Draft genome sequences of 24 Lactococcus lactis strains. Genome Announc 5:e01737-16. https://doi.org/10.1128/genomeA.01737-16.
REFERENCES
- 1.Van Hylckama Vlieg JET, Rademaker JLW, Bachmann H, Molenaar D, Kelly WJ, Siezen RJ. 2006. Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol 17:183–190. doi: 10.1016/j.copbio.2006.02.007. [DOI] [PubMed] [Google Scholar]
- 2.Kelly WJ, Ward LJH, Leahy SC. 2010. Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures. Genome Biol Evol 2:729–744. doi: 10.1093/gbe/evq056. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM. 2005. Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71:8371–8382. doi: 10.1128/AEM.71.12.8371-8382.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Smit G, Smit BA, Engels WJM. 2005. Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products. FEMS Microbiol Rev 29:591–610. doi: 10.1016/j.femsre.2005.04.002. [DOI] [PubMed] [Google Scholar]
- 5.Cotter PD, Hill C, Ross RP. 2005. Bacteriocins: developing innate immunity for food. Nat Rev Microbiol 3:777–788. doi: 10.1038/nrmicro1273. [DOI] [PubMed] [Google Scholar]
- 6.Schleifer KH, Kraus J, Dvorak C, Kilpper-Bälz R, Collins MD, Fischer W. 1985. Transfer of Streptococcus lactis and related streptococci to the genus Lactococcus gen. nov. Syst Appl Microbiol 6:183–195. doi: 10.1016/S0723-2020(85)80052-7. [DOI] [Google Scholar]
- 7.Lister JB. 1873. A further contribution to the natural history of bacteria: and the germ theory of fermentative changes. Q J Microsc Sci 13:380–408. [Google Scholar]
- 8.Orla-Jensen S. 1919. The lactic acid bacteria. Host & Sons, Co., Copenhagen, Denmark. [Google Scholar]
- 9.Latorre-Guzman BA, Kado CI, Kunkee RE. 1977. Lactobacillus hordniae, a new species from the leafhopper (Hordnia circellata). Int J Syst Bacteriol 27:362–370. doi: 10.1099/00207713-27-4-362. [DOI] [Google Scholar]
- 10.Pérez T, Balcázar JL, Peix A, Valverde A, Velázquez E, de Blas I, Ruiz-Zarzuela I. 2011. Lactococcus lactis subsp. tructae subsp. nov. isolated from the intestinal mucus of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 61:1894–1898. doi: 10.1099/ijs.0.023945-0. [DOI] [PubMed] [Google Scholar]
- 11.Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M, Molenaar D, Wels M, van Hijum SAFT, van Hylckama Vlieg JE. 2011. Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol 4:383–402. doi: 10.1111/j.1751-7915.2011.00247.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Sambrook J, Russell DW. 2001. Molecular cloning, Vols. 1, 2, 3 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. [Google Scholar]
- 13.Peng Y, Leung HC, Yiu SM, Chin FY. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–1428. doi: 10.1093/bioinformatics/bts174. [DOI] [PubMed] [Google Scholar]
- 14.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Kelly WJ, Davey GP, Ward LJ. 1998. Characterization of lactococci isolated from minimally processed fresh fruit and vegetables. Int J Food Microbiol 45:85–92. doi: 10.1016/S0168-1605(98)00135-4. [DOI] [PubMed] [Google Scholar]
- 16.Rademaker JLW, Herbet H, Starrenburg MJC, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JET. 2007. Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol 73:7128–7137. doi: 10.1128/AEM.01017-07. [DOI] [PMC free article] [PubMed] [Google Scholar]