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. 2020 May 27;20(1):136.
doi: 10.1186/s12866-020-01820-9.

Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses

Min Young Jung  1 , Changsu Lee  1   2 , Myung-Ji Seo  3 , Seong Woon Roh  1 , Se Hee Lee  4
Affiliations

Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses

Min Young Jung et al. BMC Microbiol. .

Abstract

Background: Lactococcus members belonging to lactic acid bacteria are widely used as starter bacteria in the production of fermented dairy products. From kimchi, a Korean food made of fermented vegetables, Lactococcus raffinolactis WiKim0068 was isolated and its genome was analyzed.

Results: The complete genome of the strain WiKim0068 consists of one chromosome and two plasmids that comprises 2,292,235 bp, with a G + C content of 39.7 mol%. Analysis of orthoANI values among Lactococcus genome sequences showed that the strain WiKim0068 has > 67% sequence similarity to other species and subspecies. In addition, it displayed no antibiotic resistance and can metabolize nicotinate and nicotinamide (vitamin B3).

Conclusion: These results augments our understanding of the genus Lactococcus and suggest that this new strain has potential industrial applications.

Keywords: Genome sequence; Kimchi; Lactococcus raffinolactis; Probiotics; Vitamin B3.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Fig. 1
Fig. 1
Phylogenetic tree based on 16S rRNA gene sequences showing the taxonomic position of the strain WiKim0068. Numbers at the nodes represent bootstrap values (> 70%) and were calculated using neighbor-joining/minimum-evolution/maximum likelihood probabilities based on 1000 replicates. Streptococcus pyogenes ATCC 12344T was used as an out-group. Bar, 0.01 accumulated changes per nucleotides
Fig. 2
Fig. 2
OrthoANI values between Lactococcus raffinolactis WiKim0068 and the closely related strains: L. raffinolactis NBRC 100932T (98.73%), L. raffinolactis 4877 (87.02%), L. piscium MKFS47 (76.57%), L. fujiensis JCM 16395 (68.12%), L. lacitis subsp. lactis IL 1403 (69.41%), and L. garvieae ATCC 49156 (68.55%). The orthoANI values represent the similarity between the genomes
Fig. 3
Fig. 3
Circular comparison of the genomes of Lactococcus raffinolactis WiKim0068 and reference strains, L. raffinolactis NBRC 100932T and L. raffinolactis 4877. The degree of similarity between the strains is represented by color intensity
Fig. 4
Fig. 4
Predicted fermentative metabolic pathways of various carbon compounds in Lactococcus raffinolactis WiKim0068 during fermentation. PTS, phosphotransferase systems; UDP, uridine diphosphate
Fig. 5
Fig. 5
Amino acid metabolism-related genes of Lactococcus raffinolactis WiKim0068
Fig. 6
Fig. 6
Nicotinate and nicotinamide metabolism in Lactococcus raffinolactis WiKim0068. Red boxes indicate enzymes in the nicotinate and nicotinamide metabolic pathway present in the strain WiKim0068
See this image and copyright information in PMC

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