Complete genome sequence of probiotic Lactobacillus plantarum IDCC3501 isolated from kimchi

Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 438-440 pISSN 0440-2413

DOI https://doi.org/10.7845/kjm.2019.9139 eISSN 2383-9902

Copyright ⓒ 2019, The Microbiological Society of Korea

Complete genome sequence of probiotic

Lactobacillus plantarum IDCC3501 isolated from kimchi

Tae-Yoon Kim, Young-Hoo Kim, Jin Seok Moon* , Hyuk-Sang Kwon, and SungKu Choi Research Laboratories, ILDONG pharmaceutical Co., Ltd., Hwaseong 18449, Republic of Korea

김치에서 분리된 프로바이오틱 Lactobacillus plantarum IDCC3501의 유전체 염기서열 분석

김태윤 ･ 김영후 ･ 문진석* ･ 권혁상 ･ 최성구 일동제약 중앙연구소

(Received November 15, 2019; Revised November 27, 2019; Accepted November 27, 2019)

*For correspondence. E-mail: [email protected];

Tel.: +82-31-371-2896; Fax: +82-31-371-2900

Lactobacillus plantarum IDCC3501 (= KCTC 13586BP) was isolated from kimchi, and it showed a probiotic potential for improving dextran sodium sulfate (DSS)-induced colitis in mice. Here we present the complete genome sequence of L.

plantarum IDCC3501, which consists of a circular 3,242,587 bp chromosome with GC content of 44.52%, 2,976 coding genes (CDS), 84 pseudo genes, and 87 RNA genes. No remarkable virulence-associated and antibiotic resistance genes were detected.

Within the genes involved, probiotic properties were found.

These results will provide a basis for further studies about its molecular genetics.

Keywords: Lactobacillus plantarum, anti-inflammatory, kimchi, probiotics

Lactobacillus plantarum (L. plantarum) is a Gram-positive bacterium that plays a significant role in human nutrition, because of its functional properties (Salvetti et al., 2012). The positive effects of L. plantarum are involved in the enhancement of the epithelial barrier function (Barnett et al., 2018), the maintenance of gut homeostasis (Qiu et al., 2018), and the regulation of immune response (Behera et al., 2018). In our

previous study, L. plantarum IDCC3501 improved the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice (Je et al., 2018). Despite the above biotechnological applications of IDCC3501, the genome sequence of this strain had been unknown. To gain a better insight into the functional properties on intestinal health in humans, the complete genome of L.

plantarum IDCC3501 was sequenced.

Lactobacillus plantarum IDCC3501 was grown in Man, Rogosa and Sharpe (MRS, Difco Laboratory) broth or agar medium at 37°C for 18 h. The culture was maintained in 30%

glycerol solution at -70°C until needed. The genomic DNA of

IDCC3501 was extracted from cells after cultivation in MRS

medium at 37°C using a wizard genomic DNA purification kit

(Promega). DNA concentration and quality were checked using

a spectrophotometer (UV-1601PC, Shimadzu). The complete

genome sequence of strain IDCC3501 was obtained from 1.5

Gb PacBio RS II platform data (Pacific Biosciences) and 1.4

Gb Illumina HiSeq platform data (Illumina) at the Macrogen

Inc. The sequence reads were assembled using a de novo

assembler HGAP3 (The subreads were extracted using the

following parameters: min. subread length: 500 bp; minimum

polymerase read quality: 0.80; minimum read length: 100 bp),

and the contigs were polished by using Pilon (v1.21) (Walker et

Genome sequence of Lb. plantarum IDCC3501∙

439

Korean Journal of Microbiology, Vol. 55, No. 4

Attribute Value

Genome size (bp) 3,242,587

GC content (%) 44.52

No. of contigs 1 (CP031702.1.)

Total genes 3,060

Protein-coding genes 2,976

Pseudogenes 84

rRNAs (5S, 16S, 23S) 16 (6, 5, 5)

tRNAs 66

Other RNAs 4

al., 2014). L. plantrum IDCC4301 genome was annotated by NCBI Prokaryotic Genome Annotation Pipeline with best-placed reference protein set GeneMarkS 2 (v 4.6). Default parameters were used for all software. Virulence factors and antibiotic resistance genes were performed using against the virulence factor database (VFDB) (Chen et al., 2012) and the comprehensive antibiotic resistance database (CARD) (McArthur et al., 2013).

The complete genome of strain IDCC3501 consists of single circular chromosome that is 3,242,587 bp with 44.52% GC- content. A total of 3,464 predicted genes, 2,976 protein coding genes, 67 transfer RNA (tRNA), 16 ribosomal RNA (rRNA), 4 ncRNA, and 84 pseudo genes were annotated (Table 1). No plasmids were present in the genome.

The genome contained oxidative stress response genes such as Na+:H+ antiporter NhaA (D0Y51_01803 and D0Y51_02243), bile salt hydrolase (D0Y51_00034, D0Y51_01906, D0Y51_02089, D0Y51_02223, D0Y51_02781, and D0Y51_02860), thiol peroxidase (D0Y51_00902), glutaredoxin (D0Y51_01437 and D0Y51_01912), and thioredoxin reductase (D0Y51_00902, D0Y51_01370, and D0Y51_02824). Additionally, numerous cell-surface proteins, such as sortase A (D0Y51_01549), and cell-wall-anchored proteins (D0Y51_00045 and D0Y51_01800) were found in the genome. The IDCC3501 genome contained to encode some involved in transcriptional regulation, including the sigma factors (D0Y51_00110, D0Y51_00586, D0Y51_

01152, D0Y51_01348, and D0Y51_01476) and 101 transcrip- tional regulators. Also, L. plantarum IDCC3501 contained stress response genes to prevent aberrant damage to proteins such as the ATP-dependent intracellular proteases ClpP (D0Y51_

00004, D0Y51_00707, and D0Y51_01152). These results

elucidate the adhesive capacity of IDCC3501 to epithelial cells and its survival strategy in the gastrointestinal environment. Also, no remarkable virulence-associated and antibiotic resistance genes were found. The genomic data onto L. plantarum IDCC3501 provides a genetic basis to further elucidate its mechanism of anti-inflammatory activity and will facilitate its application in the functional food industry.

Nucleotide sequence accession number(s)

Lactobacillus plantarum IDCC3501 has been deposited in the korean collection for type cultures (KCTC) under accession number KCTC 13586BP, and its complete genome sequence has been deposited in GenBank under accession number CP031702.1.

적 요

Lactobacillus plantarum는 그람양성, 비운동성이고, 인체 의 다양한 환경에서 서식하고 있다. L. plantarum IDCC3501 은 항염증 효과가 우수한 균주로서, 김치에서 분리되었다.

IDCC3501 균주의 전체 크기는 3,242,587 bp이고 G + C 함량 은 44.52%였으며 2,976개의 단백질 암호화 유전자 및 87개의 RNA 유전자를 보유하고 있었다. 이 결과를 기초로 IDCC3501 균주의 프로바이오틱 및 안전성 관련 유전자를 확인할 수 있 었다.

Acknowledgements

This work was supported by korea institute of planning and evaluation for technology in food, agriculture, forestry and fisheries (IPET) through high value-added food technology development program, funded by, ministry of agriculture, food and rural affairs (MAFRA) (116017032SB010).

References

Barnett AM, Roy NC, Cookson AL, and McNabb WC. 2018.

Metabolism of caprine milk carbohydrates by probiotic bacteria and Caco-2:HT29 MTX epithelial co-cultures and their impact on intestinal barrier integrity. Nutrients 10, 949.

440

미생물학회지 제55권 제4호

Behera SS, Ray RC, and Zdolec N. 2018. Lactobacillus plantarum with functional properties: An approach to increase safety and shelf-life of fermented foods. Biomed. Res. Int. 2018, 9361614.

Chen L, Xiong Z, Sun L, Yang J, and Jin Q. 2012. VFDB 2012 update:

toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 40, 641–645.

Je IG, Lee DG, Jeong DG, Hong D, Yoon JM, Moon JS, and Park S. 2018. The probiotic, ID-JPL934, attenuates dextran sulfate sodium-Induced colitis in mice through inhibition of proin- flammatory cytokines expression. J. Med. Food 21, 858–865.

McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, et al. 2013. The

comprehensive antibiotic resistance database. Antimicrob. Agents Chemother. 57, 3348–3357.

Qiu L, Tao X, Xiong H, Yu J, and Wei H. 2018. Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice. Food Funct. 9, 4299–4309.

Salvetti E, Torriani S, and Felis GE. 2012. The genus Lactobacillus: A taxonomic update. Probiotics Antimicrob. Proteins 4, 217–226.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. 2014. Pilon:

An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963.