전체메뉴
검색
Article Search

JMB Journal of Microbiolog and Biotechnology

QR Code QR Code

Research article


References

  1. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. 2014. The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11: 506-514.
    Pubmed CrossRef
  2. Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, et al. 2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ. Microbiol. 12: 758-773.
    Pubmed CrossRef
  3. Pfeiler EA, Klaenhammer TR. 2007. The genomics of lactic acid bacteria. Trends Microbiol. 15: 546-553.
    Pubmed CrossRef
  4. Vastano V, Capri U, Muscariello L, Marasco R, Sacco M. 2010. Lactobacillus plantarum adhesion and colonization: identification of adhesins and effects of intestinal environment on biofilm development. J. Biotechnol. 150: 518-519.
    CrossRef
  5. Arief II, Budiman C, Jenie BS, Andreas E, Yuneni A. 2015. Plantaricin IIA-1A5 from Lactobacillus plantarum IIA-1A5 displays bactericidal activity against Staphylococcus aureus. Benef. Microbes. 6: 603-613.
    Pubmed CrossRef
  6. Bosch M, Méndez M, Pérez M, Farran A, Fuentes MC, Cuñé J. 2012. Lactobacillus plantarum CECT7315 and CECT7316 stimulate immunoglobulin production after influenza vaccination in elderly. Nutr. Hosp. 27: 504-509.
  7. Adesulu-Dahunsi AT, Jeyaram K, Sanni AI, Banwo K. 2018. Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage. PeerJ. 6: e5326.
    Pubmed PMC CrossRef
  8. Hariri M, Salehi R, Feizi A, Mirlohi M, Ghiasvand R, Habibi N. 2015. A randomized, double-blind, placebo-controlled, clinical trial on probiotic soy milk and soy milk: effects on epigenetics and oxidative stress in patients with type II diabetes. Genes Nutr. 10: 52.
    Pubmed PMC CrossRef
  9. Zhang S, Wang T, Zhang D, Wang X, Zhang Z, Lim C, et al. 2022. Probiotic characterization of Lactiplantibacillus plantarum HOM3204 and its restoration effect on antibiotic-induced dysbiosis in mice. Lett. Appl. Microbiol. 74: 949-958.
    Pubmed PMC CrossRef
  10. Garcia-Gonzalez N, Battista N, Prete R, Corsetti A. 2021. Health-promoting role of Lactiplantibacillus plantarum isolated from fermented foods. Microorganisms 9: 349.
    Pubmed PMC CrossRef
  11. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, et al. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 100: 1990-1995.
    Pubmed PMC CrossRef
  12. Jia FF, Zhang LJ, Pang XH, Gu XX, Abdelazez A, Liang Y, et al. 2017. Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells. Genomics 109: 432-437.
    Pubmed CrossRef
  13. Kwak W, Kim K, Lee C, Lee C, Kang J, Cho K, et al. 2016. Comparative analysis of the complete genome of Lactobacillus plantarum GB-LP2 and potential candidate genes for host immune system enhancement. J. Microbiol. Biotechnol. 26: 684-692.
    Pubmed CrossRef
  14. Sinha N, Dabla PK. 2015. Oxidative stress and antioxidants in hypertension-a current review. Curr. Hypertens. Rev. 11: 132-142.
    Pubmed CrossRef
  15. Chandra J, Samali A, Orrenius S. 2000. Triggering and modulation of apoptosis by oxidative stress. Free Radic. Biol. Med. 29: 323-333.
    Pubmed CrossRef
  16. Dasgupta A, Klein K. 2014. Role of oxidative stress in neurodegenerative diseases and other diseases related to aging, pp. 167-184. In: Dasgupta A, Klein K (eds), Antioxidants in Food, Vitamins and Supplements. Ed. Elsevier, San Diego.
  17. Wang Y, Wu Y, Wang Y, Xu H, Mei X, Yu D, et al. 2017. Antioxidant properties of probiotic bacteria. Nutrients 9: 521.
    Pubmed PMC CrossRef
  18. Mishra V, Shah C, Mokashe N, Chavan R, Yadav H, Prajapati J. 2015. Probiotics as potential antioxidants: a systematic review. J. Agric. Food Chem. 63: 3615-3626.
    Pubmed CrossRef
  19. DÜz M, DoĞan YN, DoĞan İ. 2020. Antioxidant activitiy of Lactobacillus plantarum, Lactobacillus sake and Lactobacillus curvatus strains isolated from fermented Turkish Sucuk. An. Acad. Bras. Cienc. 92: e20200105.
    Pubmed CrossRef
  20. Han KJ, Lee JE, Lee NK, Paik HD. 2020. Antioxidant and anti-inflammatory effect of probiotic Lactobacillus plantarum KU15149 derived from Korean homemade diced-radish Kimchi. J. Microbiol. Biotechnol. 30: 591-598.
    Pubmed PMC CrossRef
  21. Zhao J, Tian F, Yan S, Zhai Q, Zhang H, Chen W. 2018. Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in d-galactose-induced aging mice. Food Funct. 9: 917-924.
    Pubmed CrossRef
  22. Ge Q, Yang B, Liu R, Jiang D, Yu H, Wu M, et al. 2021. Antioxidant activity of Lactobacillus plantarum NJAU-01 in an animal model of aging. BMC Microbiol. 21: 182.
    Pubmed PMC CrossRef
  23. Zhang J, Zhao X, Jiang Y, Zhao W, Guo T, Cao Y, et al. 2017. Antioxidant status and gut microbiota change in an aging mouse model as influenced by exopolysaccharide produced by Lactobacillus plantarum YW11 isolated from Tibetan kefir. J. Dairy Sci. 100: 6025-6041.
    Pubmed CrossRef
  24. Zhang Q, Li X, Cui X, Zuo P. 2005. D-galactose injured neurogenesis in the hippocampus of adult mice. Neurol. Res. 27: 552-556.
    Pubmed CrossRef
  25. Li F, Huang G, Tan F, Yi R, Zhou X, Mu J, et al. 2020. Lactobacillus plantarum KSFY06 on d-galactose-induced oxidation and aging in Kunming mice. Food Sci. Nutr. 8: 379-389.
    Pubmed PMC CrossRef
  26. Del Rio D, Stewart AJ, Pellegrini N. 2005. A review of recent studies on malondialdehyde as toxic molecule and biological marker of oxidative stress. Nutr. Metab. Cardiovasc. Dis. 15: 316-328.
    Pubmed CrossRef
  27. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
    Pubmed CrossRef
  28. Rhoads A, Au KF. 2015. PacBio sequencing and its applications. Genom Proteom. Bioinf. 13: 278-289.
    Pubmed PMC CrossRef
  29. Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, et al. 2016. Phased diploid genome assembly with singlemolecule real-time sequencing. Nat. Methods 13: 1050-1054.
    Pubmed PMC CrossRef
  30. Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, et al. 2014. Performance comparison of second- and thirdgeneration sequencers using a bacterial genome with two chromosomes. BMC Genomics 15: 699.
    Pubmed PMC CrossRef
  31. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16: 294.
    Pubmed PMC CrossRef
  32. Wang L, Wu Y, Xu J, Huang Q, Zhao Y, Dong S, et al. 2022. Colicins of Escherichia coli lead to resistance against the diarrhea-causing pathogen enterotoxigenic E. coli in pigs. Microbiol. Spectr. 10: e0139622.
    Pubmed PMC CrossRef
  33. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
    Pubmed PMC CrossRef
  34. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12: 59-60.
    Pubmed CrossRef
  35. Akhter S, Aziz RK, Edwards RA. 2012. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 40: e126.
    Pubmed PMC CrossRef
  36. Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 34: D459-464.
    Pubmed PMC CrossRef
  37. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. 2017. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45: D566-D573.
    Pubmed PMC CrossRef
  38. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-238.
    Pubmed PMC CrossRef
  39. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
    Pubmed PMC CrossRef
  40. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35: 3100-3108.
    Pubmed PMC CrossRef
  41. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: an RNA family database. Nucleic Acids Res. 31: 439-441.
    Pubmed PMC CrossRef
  42. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
    Pubmed PMC CrossRef
  43. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, et al. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43: 6761-6771.
    Pubmed PMC CrossRef
  44. Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, et al. 2012. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem. Biophys. Res. Commun. 419: 779-781.
    Pubmed CrossRef
  45. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
    Pubmed PMC CrossRef
  46. Lin MY, Chang FJ. 2000. Antioxidative effect of intestinal bacteria Bifidobacterium longum ATCC 15708 and Lactobacillus acidophilus ATCC 4356. Dig. Dis. Sci. 45: 1617-1622.
  47. Mahfouz N, Ferreira I, Beisken S, von Haeseler A, Posch AE. 2020. Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. J. Antimicrob. Chemother. 75: 3099-3108.
    Pubmed PMC CrossRef
  48. Cooper AL, Low AJ, Koziol AG, Thomas MC, Leclair D, Tamber S, et al. 2020. Systematic evaluation of whole genome sequencebased predictions of Salmonella serotype and antimicrobial resistance. Front. Microbiol. 11: 549.
    Pubmed PMC CrossRef
  49. van den Nieuwboer M, van Hemert S, Claassen E, de Vos WM. 2016. Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome. Microb. Biotechnol. 9: 452-465.
    Pubmed PMC CrossRef
  50. Ivanovic N, Minic R, Djuricic I, Radojevic Skodric S, Zivkovic I, Sobajic S, et al. 2016. Active Lactobacillus rhamnosus LA68 or Lactobacillus plantarum WCFS1 administration positively influences liver fatty acid composition in mice on a HFD regime. Food Funct. 7: 2840-2848.
    Pubmed CrossRef
  51. Kullisaar T, Songisepp E, Aunapuu M, Kilk K, Arend A, Mikelsaar M, et al. 2010. Complete glutathione system in probiotic Lactobacillus fermentum ME-3. Prikl. Biokhim. Mikrobiol. 46: 527-531.
    CrossRef
  52. Valencia E, Marin A, Hardy G. 2001. Glutathione-nutritional and pharmacologic viewpoints: Part IV. Nutrition 17: 783-784.
    Pubmed CrossRef

Related articles in JMB

More Related Articles

Article

Research article

J. Microbiol. Biotechnol. 2023; 33(8): 1030-1038

Published online August 28, 2023 https://doi.org/10.4014/jmb.2209.09021

Copyright © The Korean Society for Microbiology and Biotechnology.

Whole Genome Sequence of Lactiplantibacillus plantarum HOM3204 and Its Antioxidant Effect on D-Galactose-Induced Aging in Mice

Di Zhang1, Heesung Shin2, Tingting Wang1, Yaxin Zhao3, Suwon Lee1,2, Chongyoon Lim1,2, and Shiqi Zhang1*

1Coree Beijing Co., Ltd., No. A-7 Tianzhu West Rd., Tianzhu Airport Industrial Zone A, Shunyi District, Beijing 101312, P.R. China
2Dx&Vx Co., Ltd., Seoul 13201, Republic of Korea
3Health Food Function Testing Center, College of Applied Arts and Science, Beijing Union University, Beijing 100101, P.R. China

Correspondence to:Shiqi Zhang,       zsqkevin@163.com

Received: September 14, 2022; Revised: April 3, 2023; Accepted: May 24, 2023

Abstract

Lactiplantibacillus plantarum, previously named Lactobacillus plantarum, is a facultative, homofermentative lactic acid bacterium widely distributed in nature. Several Lpb. plantarum strains have been demonstrated to possess good probiotic properties, and Lpb. plantarum HOM3204 is a potential probiotic strain isolated from homemade pickled cabbage plants. In this study, whole-genome sequencing was performed to acquire genetic information and predict the function of HOM3204, which has a circular chromosome of 3,232,697 bp and two plasmids of 48,573 and 17,060 bp, respectively. Moreover, various oxidative stress-related genes were identified in the strain, and its antioxidant activity was evaluated in vitro and in vivo. Compared to reference strains, the intracellular cell-free extracts of Lpb. plantarum HOM3204 at a dose of 1010 colony-forming units (CFU)/ml in vitro exhibited stronger antioxidant properties, such as total antioxidant activity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate, superoxide dismutase activity, and glutathione (GSH) content. Daily administration of 109 CFU Lpb. plantarum HOM3204 for 45 days significantly improved the antioxidant function by increasing the glutathione peroxidase activity in the whole blood and GSH concentration in the livers of D-galactose-induced aging mice. These results suggest that Lpb. plantarum HOM3204 can potentially be used as a food ingredient with good antioxidant properties.

Keywords: Lactiplantibacillus plantarum, whole genome sequence, antioxidant activity, D-galactose-induced aging, oxidative stress

Introduction

Probiotics are live microorganisms that confer health benefits to the host when administered in adequate amounts [1]. Lactiplantibacillus plantarum is one of the main research topics in the field of probiotics. It is a facultative, homofermentative lactic acid bacterium that is widely distributed in fermented foods and various ecological niches, including plants, animals, and the human gut [2, 3]. According to the Food and Agriculture Organization of the United Nations/World Health Organization, probiotics should have outstanding gastrointestinal tolerance, intestinal epithelial cell adhesion ability, and safety [4]. Lpb. plantarum strains exhibit good acid and bile salt tolerance and have various beneficial effects on the host, such as the regulation of intestinal flora [5] and immune response [6], increase in antioxidant activity [7], and reduction of cholesterol and glucose levels [8]. In a previous study, we isolated a Lpb. plantarum strain, HOM3204, from homemade pickled cabbage [9]. In vitro, Lpb. plantarum HOM3204 showed strong tolerance to simulated gastric and intestinal juice, high adhesion to Caco-2 cells, and good antimicrobial activity [9]. It significantly recovered the intestinal flora in ampicillin-induced dysbiotic mice by decreasing the abundance of Enterococci, while increasing the abundance of Lactobacilli and Bifidobacterium. The strain also enhanced the antioxidant capacity by increasing the levels of glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) in the serum [9].

The requirement of whole-genome sequencing (WGS) analysis of probiotic candidates to assess their food safety was proposed by the European Food Safety Authority in 2019 [10]. Accordingly, genes encoding antimicrobial resistance, virulence, and toxigenicity were subjected to extensive assessments [10]. Whole genome sequences of many Lpb. plantarum strains were sequenced and deposited in the GenBank sequence database to better understand and explore their probiotic functions (https://www.ncbi.nlm.nih.gov/genome). Lpb. plantarum WCFS1 is the first Lpb. plantarum strain that was completely genome sequenced [11]. Jia et al. demonstrated the whole genome sequence of Lpb. plantarum KLDS1.0391 and its good adhesion performance in their study [12]. Kwak et al. reported the whole genome sequence of Lpb. plantarum GB-LP2 and its enhanced immune properties [13].

Reactive oxygen species (ROS), including hydroxyl radicals, superoxide anions, and hydrogen peroxide, are produced via oxygen metabolism and balanced by the rate of oxidant formation and elimination [14, 15]. Oxidative stress, caused by an imbalance between the generation of ROS and antioxidant defense systems, is associated with the natural aging process and pathogenesis of many diseases [16]. Accumulating evidence demonstrates that probiotics are effective against oxidative stress via enzymatic antioxidant defenses, including SOD, GSH-Px, and glutathione reductase (GR), and antioxidant metabolites, such as GSH, butyrate, and folate [17, 18]. Several Lpb. plantarum strains have been proven to possess good antioxidant properties [19, 20].

The D-galactose-induced aging mouse model, which mimics natural aging, is one of the most commonly used models for oxidative stress studies [21]. Researchers often employ this model to determine the anti-aging activities and antioxidant effects of probiotics [21-23]. D-Galactose injection increases oxidative stress by increasing the malonaldehyde (MDA) levels and decreasing the activity of antioxidant enzymes in mice [24, 25]. MDA is the principal and most studied product of polyunsaturated fatty acid peroxidation [26]. Some studies have assessed MDA to quantify the level of oxidative stress in vitro and in vivo [26].

In the present study, we conducted WGS analysis of Lpb. plantarum HOM3204 and determined its antioxidant activity in vitro. The D-galactose-induced aging mouse model was selected to preliminarily evaluate the ability of Lpb. plantarum HOM3204 to cope with oxidative stress via enzymatic and non-enzymatic defenses in mice.

Materials and Methods

Genomic DNA Extraction, Genome Sequencing, Assembly, and Annotation

The whole genome of Lpb. plantarum HOM3204 was sequenced by OE Biotech (China) using the shotgun strategy. Genomic DNA was extracted using a Bacterial DNA Kit D3350 (Omega, USA). DNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA) and Qubit (Thermo Fisher Scientific) and subjected to agarose gel electrophoresis.

The genome was sequenced using the PacBio Sequel (Pacific Biosciences, USA)  and Illumina HiSeq platforms (Illumina Inc., USA) [27]. Low-quality reads were filtered out using the single-molecule, real-time sequencing technology (SMRT, v2.3.0) and the high-quality filtered reads were assembled to generate one contig without any gaps [28]. The paired-end strategy was used in the Illumina sequencing platform. Falcon (v0.3.0) was used for sub-read self-correction and three-generation sequence assembly [29]. Sub-reads were then processed to generate consensus sequences using Quiver (v2.2.2) [28]. A single-pass read accuracy improver (Sprai, v0.9.9.23) was used to correct the sequencing errors in single-pass reads [30]. Contigs were circularized using Circlator [31]. The assembled genome was annotated to identify the protein-coding and RNA genes using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline [32].

Gene prediction of the assembled genome was conducted using Prodigal (v2.6.3) [33]. Functions of the predicted protein-coding genes were annotated using the Clusters of Orthologous Groups (COG) database annotations based on protein alignment using the Diamond software (e-value < 1e-5) [34]. Prophages were predicted using PhiSpy (v2.3) [35]. Pathogen–host interactions and the Comprehensive Antibiotic Resistance Database (CARD) were used for pathogenicity and drug resistance analyses, respectively [36, 37]. Carbohydrate-Active Enzymes (CAZy) analysis was performed using the CAZy database [38]. tRNA and rRNA genes were predicted using tRNAscan-SE (v1.3.1) [39] and rRNAmmer (v1.2) [40], respectively. Finally, sRNAs were predicted using BLAST against the Rfam database [41], and the circular genome graph was created using Circos (v0.69) [42].

Comparative Analysis

Ten reference Lpb. plantarum complete genomes were downloaded from the NCBI and European Nucleotide Archive databases. The accession numbers were CP021997.1 (LPL-1), CP004082.1 (ZJ316), CP005942.2 (P-8), CP006033.1 (16), CP019348.1 (KLDS1.0391), GCA_001888735 (299v), CP002222.1 (ST-III), CP033616.1 (J26), CP017066.1 (LP3), and AL935263.2 (WCFS1). The average nucleotide identity (ANI) tree of 10 Lpb. plantarum strains and the Lpb. plantarum HOM3204 strain was constructed using Pyani software [43]. A phylogenetic tree was used to describe the evolutionary relationships between the strains based on WGS data. ParaAT (v2.0) was used as a parallel tool for constructing multiple protein-coding DNA alignments [44], and a maximum likelihood (ML) phylogenetic tree was constructed using RAxML [45].

Evaluation of Antioxidant Activity of Lpb. plantarum Strains In Vitro

Lpb. plantarum Lp-115 and Lpb. plantarum ST-III were isolated from a solid beverage (Dupont, USA) and a fermented milk drink (Bright Dairy, China), respectively, and are reference strains which are popular on the market. Lpb. plantarum strains (HOM3204, Lp-115, and ST-III) were aerobically cultivated thrice in the de Man, Rogosa and Sharp broth at 37°C for 24 h. Bacterial cells were harvested via centrifugation (11,000 ×g, 10 min), washed thrice with phosphate-buffered saline (PBS), and resuspended in PBS with a viable cell density of 4 × 1010 colony-forming units (CFU)/ml. To obtain intracellular cell-free extracts, the suspension of intact cells was disrupted using a homogenizer (APV1000; SPX, Germany) at 850 bar for 10 min. Debris was removed via centrifugation (11,000 ×g, 10 min).

T-AOC and hydroxyl radical scavenging, SOD, GSH-Px, and GSH activities were determined using A015, A018-1-1, A001-2, A005, and A006-1-1 assay kits, respectively (China). Following this, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity was determined, according to a modified method of Lin and Chang [46]. Briefly, 2 ml of intracellular cell-free extract was mixed with 2 ml of DPPH ethanol solution (0.2 mmol/l). The mixed solution was placed in the dark for 30 min at 25°C and centrifuged at 11,000 ×g for 10 min to obtain the supernatant. The absorbance of the supernatant was measured at 517 nm using a spectrophotometer (UV-1800; Shimadzu, Japan) and marked as Ai. For the blank control, the DPPH ethanol solution was replaced with an equal volume of ethanol and the absorbance was marked as Aj; the sample solution was replaced with an equal volume of distilled water and the absorbance was marked as A0; and a mixture of distilled water and ethanol solution was used to adjust the absorbance to zero. Ascorbic acid (0.5 mg/ml; Sigma-Aldrich, USA) was used as the positive control. DPPH scavenging activity was calculated using the following equation:

DPPH scavenging activity (%) = [1 – (Ai – Aj)/A0] ×100%.

All in vitro assays were performed in triplicates.

Antioxidant Effects of Lpb. plantarum HOM3204 on D-Galactose-Induced Aging in Mice

Freeze-dried Lpb. plantarum HOM3204 bacterial powder was produced according to a previously described method [9]. Thirty specific-pathogen-free (SPF), male KM mice (22–26 g, 8-week-old) were purchased from Beijing HFK Bioscience Co., Ltd. (China). The animal experimental protocol was approved by the Ethics Committee of the Health Food Function Testing Center, College of Applied Arts and Science, Beijing Union University (No. 2020-02). The feeding environment of mice was maintained at 22 ± 2°C and 55 ± 5% humidity. Five mice were raised in a cage and fed a pathogen-free diet and water under a 12/12 h light/dark cycle. All materials were autoclaved before use. After one-week of adaptation, 20 mice were subcutaneously injected with 300 mg of D-galactose/kg of body weight for six weeks to establish the D-galactose oxidative damage model. The residual 10 mice were assigned to the control group and subcutaneously injected with an equal volume of sterile deionized water. Each group had 10 mice. The D-galactose oxidative damage model was successfully established, and the MDA level in this model was significantly increased compared to that in the control group (p < 0.01). Twenty mice belonging to the D-galactose oxidative damage model were randomly divided into the model and Lpb. plantarum HOM3204 groups. The Lpb. plantarum HOM3204 group was orally administered with the Lpb. plantarum HOM3204 powder (1 × 109 CFU, once daily) for 45 days, and the model and control groups were orally administered with sterile deionized water. Meanwhile, the model and Lpb. plantarum HOM3204 groups were injected with the same dose of D-galactose over a 45-day period. The control group was injected with an equal volume of sterile deionized water. Body weights were measured on days 0 and 45. Twenty-four hours after the final gavage, the eyeball blood was collected to determine the GSH-Px levels. The serum of the eyeball was used to measure the MDA and SOD levels. GSH and protein carbonyl levels in the liver were also measured. All indices were determined according to the instructions of the assay kits (China).

Statistical Analysis

Data are presented as the mean ± standard error of the mean. Data analysis was conducted using one-way analysis of variance, followed by Tukey’s multiple comparisons test with the SPSS software (version 25, IBM, Corp., USA). Values were considered statistically significant at p < 0.05.

Results

Genome Features

As shown in Fig. 1 and Table 1, the complete genome of Lpb. plantarum HOM3204 was composed of one circular chromosome (3.23 Mbp) with a GC content of 44.61% and two circular plasmids (plasmid 1 [48,573 bp] with 39.04% GC content and plasmid 2 [17,060 bp] with 40.57% GC content). There were 3,027 genes, 122 RNA genes (16 rRNA, 68 tRNA, and 38 sRNA genes) in the circular chromosome, three RNA genes (0 rRNA, 0 tRNA, and 3 sRNA genes) and one RNA gene (0 rRNA, 0 tRNA, and 1 sRNA gene) in plasmid 1 and plasmid 2, respectively.

Table 1 . Genome features of Lactiplantibacillus plantarum HOM3204..

AttributeChromosomePlasmid 1Plasmid 2
Genome size (bp)3,232,69748,57317,060
DNA GC content (%)44.6139.0440.57
Protein-coding genes2,247357
rRNA genes1600
tRNA genes6800
sRNA genes3831


Figure 1. Circular genome graph of Lactiplantibacillus plantarum HOM3204. Circles, from inside to outside, represent the genome size, GC skew, GC contents, coding sequence (CDS) in the reverse strand, tRNA and rRNA genes in reverse strand, tRNA and rRNA genes in forward strand, and CDS in forward strand. A–Z, respectively, indicate the functional classification of CDS genes on the chromosome and plasmids using the Clusters of Orthologous Groups (COG) database. Circos (v0.69) software was used to create a genomic map with the given information.

One prophage in plasmid 1 was identified using PhiSpy. No drug resistance and virulence genes were found according to the minimum cutoff of 90% nucleotide identity over a minimum coverage length of 60% [47, 48] using CARD and VFDB, respectively.

On the chromosome, 2,247 genes (74.2%) were classified into COG functional categories (Fig. 2). Two hundred and fifty-one genes (11.17%) belonged to amino acid transport and metabolism, 282 genes (12.55%) belonged to carbohydrate transport and metabolism, 266 genes (11.84%) belonged to transcription, and 381 genes (16.96%) belonged to general function prediction only.

Figure 2. Functional categorization of all predicted open reading frames (ORFs) in the Lpb. plantarum HOM3204 genome using the COG database. Diamond (E-value < 1e-5) was used for protein alignment.

Comparison of Lpb. plantarum Strains

To understand the evolutionary relationship between the strains, ML and ANI trees were constructed. The results are shown in Figs. 3 and 4, respectively. According to the analysis of the ML tree, 10 strains, namely ST-III, 299v, WCFS1, ZJ316, LPL-1, J26, 16, KDLS1.0391, P-8, and LP3, were not grouped together with HOM3204, suggesting that Lpb. plantarum HOM3204 differs from these strains and may have unique features and functions. The ANI tree was built using the same genomes as the ML tree. Lpb. plantarum WCFS1 was regarded as the closest neighbor of Lpb. plantarum HOM3204 (99.31% of the ANI value).

Figure 3. ML tree analysis of Lpb. plantarum HOM3204 with 10 available complete genome sequences of Lpb. plantarum. ParaAT (V2.0) was used as a parallel tool for constructing multiple protein-coding DNA alignments. The maximum likelihood (ML) phylogenetic tree was constructed using RAxML. Numbers above the branches indicate the bootstrap supports from 500 replicates. The higher the bootstrap value, the more reliable is the evolution tree.

Figure 4. Average nucleotide identity (ANI) tree analysis of Lpb. plantarum HOM3204 and 10 available genome sequences of Lpb. plantarum strains. ANI tree was constructed using Pyani software.

Genome features of the ten Lpb. plantarum reference strains, with detailed WGS information, are presented in Table 2. Each strain had a circular chromosome and a different number of plasmids. The genome size of the control strains was 2.89 to 3.31 Mbp, and the number of plasmids varied from zero to ten.

Table 2 . Comparison of the chromosomal properties of different Lpb. plantarum strains..

StrainHOM3204WCFS1LP3ST-III299vJ26LPL-116P-8ZJ316KLDS1.0391
Genome size (bp)3,232,6973,308,2733,259,8583,254,3763,302,0553,096,4683,186,8593,044,6783,035,7193,203,9642,886,607
No. of plasmids232104110733
GC content (%)44.6144.4744.5044.5844.4044.8044.6544.7444.8044.6544.80
Annotated genes3,0643,1163,0773,0713,1533,0433.0492,8742,9563,0432,891
tRNA genes7272737057706768716352
rRNA genes161616153161616161513
ANI (%)100%99.31%99.22%99.16%99.14%99.06%99.03%98.98%98.98%98.94%98.93%


Oxidative Stress-Related Proteins

We identified the oxidative stress-related proteins encoded in the genome of Lpb. plantarum HOM3204 in the Gene Ontology and COG databases (Table 3). The proteins consisted of GSH-Px, glutathione-disulfide reductase, proteins for removal of superoxide radicals, proteins for removal of oxygen radicals, catalytic proteins, catalase, flavin reductase (NADH), thioredoxin-disulfide reductase, thioredoxin peroxidase, thioredoxin reductase, and a DNA-binding ferritin-like protein named Spy1531. Therefore, the oxidative stress-related proteins in Lpb. plantarum HOM3204 can potentially cope with oxidative stress.

Table 3 . Oxidative stress-related proteins of Lpb. plantarum HOM3204..

Oxidative stress-related proteinLocus tagDatabase
Glutathione peroxidaseChr-gene 0184GO:0004602/COG0386
Removal of superoxide radicalsChr-gene 0584GO:0019430
Glutathione-disulfide reductaseChr-gene 0323, Chr-gene 0991, Chr-gene 1464, Chr-gene 2697GO:0004362
Response to the oxygen radicalChr-gene 1464, Chr-gene 2697GO:0000305
Catalytic activityChr-gene 0102, Chr-gene 1140, Chr-gene 1357, Chr-gene 1915, Chr-gene 1931, Chr-gene 2678GO:0003824
CatalaseChr-gene 2929GO:0004096
Flavin reductase (NADH)Chr-gene 0045, Chr-gene 1116, Chr-gene 2249, Chr-gene 2250, Chr-gene 2680,GO:0036382
Thioredoxin-disulfide reductaseChr-gene 0584, Chr-gene 1888, Chr-gene 2175, Chr-gene 2817GO:0004791
Thioredoxin peroxidaseChr-gene 1928GO:0008379
Thioredoxin reductaseChr-gene 0584, Chr-gene 2138COG:0492
DNA-binding ferritin-like proteinPlasmid 2-gene 0005COG:0783


In Vitro Antioxidant Activity

In this study, six indices (T-AOC, hydroxyl radical, DPPH radical, SOD, GSH-Px, and GSH) were chosen to evaluate the antioxidant activity of Lpb. plantarum HOM3204 in vitro (Table 4). The intracellular cell-free extracts of Lpb. plantarum HOM3204 exhibited the strongest T-AOC activity (23.84 ± 2.44 U/ml) compared to Lpb. plantarum ST-III (4.13 ± 0.44 U/ml, p < 0.01), Lpb. plantarum Lp-115 (15.48 ± 1.13 U/ml, p < 0.01), and 0.05%vitamin C (16.90 ± 1.42 U/ml, p < 0.01). The DPPH radical scavenging rate of Lpb. plantarum HOM3204 (94.18 ± 0.45%) was higher than that of Lpb. plantarum Lp-115 (91.03 ± 0.53%, p < 0.01) and Lpb. plantarum ST-III (93.00± 0.65%, p > 0.05), but lower than that of 0.05% vitamin C (96.14 ± 0.08%, p < 0.01). Lpb. plantarum HOM3204 exhibited the highest SOD activity (28.89 ± 0.30 U/ml) compared to Lpb. plantarum ST-III (27.34 ± 0.52 U/ml, p < 0.05) and Lpb. plantarum Lp-115 (24.63 ± 2.11 U/ml, p < 0.05) strains. The GSH content of Lpb. plantarum HOM3204 (37.56 ± 2.81 U/ml) was significantly higher than that of Lpb. plantarum ST-III (23.72 ± 3.98 U/ml, p < 0.01) and lower than that of Lpb. plantarum Lp-115 (59.85 ± 5.57 U/ml, p < 0.01). The hydroxyl radical-scavenging abilities and GSH-Px activities of the three strains were similar.

Table 4 . Antioxidant activities of different Lpb. plantarum strains in vitro..

StrainT-AOC (U/ml)·OH scavenging (%)DPPH scavenging (%)SOD (U/ml)GSH-Px (U/ml)GSH (mg/l)
HOM320423.84 ± 2.4476.84 ± 0.3694.18 ± 0.4528.89 ± 0.3020.57 ± 2.7337.56 ± 2.81
ST-Ⅲ4.13 ± 0.44**76.57 ± 0.3693.00 ± 0.6527.34 ± 0.52*24.29 ± 3.1823.72 ± 3.98**
Lp-11515.48 ± 1.13**77.16 ± 0.6091.03 ± 0.53**24.63 ± 2.11*15.60 ± 2.0659.85 ± 5.57**
Vitamin C16.90 ± 1.42**36.70 ± 1.33**96.14 ± 0.08**34.32 ± 0.36**NDND

Comparison of the Lpb. plantarum HOM3204 strain with other strains: *p < 0.05, **p < 0.01. ·OH, hydroxyl radical scavenging..

ND, not determined..



Antioxidant Effect of Lpb. plantarum HOM3204 on D-Galactose-Induced Aging in Mice

D-Galactose-induced aging mice showed a significant increase in the level of MDA compared to the control group (D-galactose vs. control, 6.31 ± 0.85 vs. 7.77 ± 1.11 nmol/ml, p < 0.01), indicating the successful construction of the oxidative damage model. After 45 days of oral administration of Lpb. plantarum HOM3204 powder or sterilized water, there was no significant difference in the body weight between the model and control groups (p > 0.05), or between the Lpb. plantarum HOM3204 and model groups (p > 0.05) (data not shown). The probiotic sample had no adverse effects on the body weight of mice.

The effects of Lpb. plantarum HOM3204 in D-galactose-induced aging mice is shown in Table 5. There was no significant difference between the Lpb. plantarum HOM3204 group and the model group in MDA, protein carbonyl, and SOD. GSH-Px activity in the whole blood of the Lpb. plantarum HOM3204 group was significantly higher than that of the model group (469 ± 68 U/ml vs. 390 ± 83 U/ml, p < 0.05). GSH content in the liver tissues of the Lpb. plantarum HOM3204 group was significantly higher than that in the liver tissues of the model group (7.35± 1.47 U/ml vs. 6.17 ± 0.79 U/ml, p < 0.05). These results demonstrated that the administration of 1 × 109 CFU Lpb. plantarum HOM3204 for 45 days alleviated oxidative stress in D-galactose-induced aging mice.

Table 5 . Effects of Lpb. plantarum HOM3204 on malonaldehyde (MDA), protein carbonyl, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glutathione (GSH) levels in the D-galactoseinduced oxidative injury mouse model..

GroupMDA (nmol/ml)Protein carbonyl (nmol/mgprot)SOD (U/ml)GSH-Px (U/ml)GSH (mgGSH/gprot)
Model group7.81 ± 1.437.02 ± 1.36213 ± 38390 ± 836.17 ± 0.79
HOM32047.59 ± 1.196.49 ± 1.98230 ± 48469 ± 68*7.35 ± 1.47*

Comparison of the Lpb. plantarum HOM3204 group with the model group: *p < 0.05..


Discussion

WGS is generally used to study the information and potential functions of genes. Functional genomics research helps to better understand the molecular mechanisms of action of probiotics. [49]. Currently, 682 genome datasets of Lpb. plantarum strains are available on the NCBI genome database.

We used the ML and ANI trees for the comparative analysis of Lpb. plantarum HOM3204 and 10 reference Lpb. plantarum strains. The ML tree showed Lpb. plantarum HOM3204 to be a unique strain that differs from the other 10 Lpb. plantarum strains. In addition, our ANI tree results revealed Lpb. plantarum WCFS1 was the closest neighbor of Lpb. plantarum HOM3204 (99.31% of the ANI value), indicating that the two strains share the highest similarity. Originally isolated from human saliva, Lpb. plantarum WCFS1 is one of the best-explored model strains and has many good characteristics, such as lowering triglyceride and low-density lipoprotein levels in high-fat diet-induced hypercholesterolemia and hepatic steatosis in mice [11, 50].

Hydroxyl radical, DPPH radical, T-AOC, SOD, GSH-Px, and GSH have been widely used as evaluation indices for ROS-related antioxidant activity [19, 20]. Strains with strong antioxidant activity can cope with oxidative stress. In this study, Lpb. plantarum HOM3204 exhibited strong antioxidant activity, as verified by the in vitro and animal experiments. In vitro, the intracellular cell-free extracts of Lpb. plantarum HOM3204 exhibited stronger antioxidant properties (e.g., T-AOC and DPPH radical scavenging, SOD) and GSH activities than the reference strain. Oral administration of 1 × 109 CFU Lpb. plantarum HOM3204 powder decreased the MDA levels and increased the SOD, GSH-Px, and GSH levels in the serum or liver tissue samples of model mice.

Oxidative stress-related proteins, particularly SOD and GSH-Px, were identified in the genome of Lpb. plantarum HOM3204. SOD is an antioxidant enzyme that plays a major role in catalyzing the highly reactive superoxide anion to O2 and the less reactive species, hydrogen peroxide (H2O2) [48]. GSH is an important cellular non-enzymatic antioxidant that is used for reducing lipid peroxides and H2O2 and catalyzes the conversion of GSH into glutathione disulfide (GSSG) [51]. GSSG is transformed into GSH through the cooperation of GR and NADPH to maintain the GSH redox ratio (GSSG/GSH) [51]. A complete glutathione system comprises the basic components of GSH, GSH-Px, GR, and GSSG [52]. Kullisaar et al. showed that L. fermentum ME-3 possesses a complete glutathione system and can transport GSH from the environment to synthesize GSH [51]. The capacity of Lpb. plantarum HOM3204 to alleviate oxidative stress may be attributed to its participation in the GSH system. A previous study reported that Lpb. plantarum CCFM10 alleviated oxidative stress and restored gut microbiota in D-galactose-induced aging mice. Besides, CCFM10 restored the relative abundance of Lactiplantibacillus and suppressed the increase in the abundance of Clostridiales. The protective effect on microbiota could be one of the mechanisms of resistance to oxidative stress in vivo [21].

In this study, we proved that Lpb. plantarum HOM3204 possesses strong antioxidant activity in terms of T-AOC and SOD, GSH, and DPPH radical scavenging activities in vitro. Moreover, oral administration of Lpb. plantarum HOM3204 alleviated oxidative stress in D-galactose-induced aging mice. Our results suggest Lpb. plantarum HOM3204 as an effective probiotic with strong antioxidant properties. However, its specific action mechanism needs to be investigated further in future studies.

Data Availability

The complete nucleotide sequence of Lactiplantibacillus plantarum HOM3204 was deposited in GenBank under the accession number CP098327.

Authors Contributions

D.Z., S.Z. contributed to the experiment design and interpreted all the results. D.Z. performed probiotic characterization in vitro tests. T.W. prepared the probiotics powders. Y.Z. performed animal related experiments. D.Z. performed statistical analysis and wrote the manuscript. S.Z., S.L. and C.L. edited the manuscript. All authors read and approved the final manuscript.

Conflict of Interest

The authors have no financial conflicts of interest to declare.

Fig 1.

Figure 1.Circular genome graph of Lactiplantibacillus plantarum HOM3204. Circles, from inside to outside, represent the genome size, GC skew, GC contents, coding sequence (CDS) in the reverse strand, tRNA and rRNA genes in reverse strand, tRNA and rRNA genes in forward strand, and CDS in forward strand. A–Z, respectively, indicate the functional classification of CDS genes on the chromosome and plasmids using the Clusters of Orthologous Groups (COG) database. Circos (v0.69) software was used to create a genomic map with the given information.
Journal of Microbiology and Biotechnology 2023; 33: 1030-1038https://doi.org/10.4014/jmb.2209.09021

Fig 2.

Figure 2.Functional categorization of all predicted open reading frames (ORFs) in the Lpb. plantarum HOM3204 genome using the COG database. Diamond (E-value < 1e-5) was used for protein alignment.
Journal of Microbiology and Biotechnology 2023; 33: 1030-1038https://doi.org/10.4014/jmb.2209.09021

Fig 3.

Figure 3.ML tree analysis of Lpb. plantarum HOM3204 with 10 available complete genome sequences of Lpb. plantarum. ParaAT (V2.0) was used as a parallel tool for constructing multiple protein-coding DNA alignments. The maximum likelihood (ML) phylogenetic tree was constructed using RAxML. Numbers above the branches indicate the bootstrap supports from 500 replicates. The higher the bootstrap value, the more reliable is the evolution tree.
Journal of Microbiology and Biotechnology 2023; 33: 1030-1038https://doi.org/10.4014/jmb.2209.09021

Fig 4.

Figure 4.Average nucleotide identity (ANI) tree analysis of Lpb. plantarum HOM3204 and 10 available genome sequences of Lpb. plantarum strains. ANI tree was constructed using Pyani software.
Journal of Microbiology and Biotechnology 2023; 33: 1030-1038https://doi.org/10.4014/jmb.2209.09021

Table 1 . Genome features of Lactiplantibacillus plantarum HOM3204..

AttributeChromosomePlasmid 1Plasmid 2
Genome size (bp)3,232,69748,57317,060
DNA GC content (%)44.6139.0440.57
Protein-coding genes2,247357
rRNA genes1600
tRNA genes6800
sRNA genes3831

Table 2 . Comparison of the chromosomal properties of different Lpb. plantarum strains..

StrainHOM3204WCFS1LP3ST-III299vJ26LPL-116P-8ZJ316KLDS1.0391
Genome size (bp)3,232,6973,308,2733,259,8583,254,3763,302,0553,096,4683,186,8593,044,6783,035,7193,203,9642,886,607
No. of plasmids232104110733
GC content (%)44.6144.4744.5044.5844.4044.8044.6544.7444.8044.6544.80
Annotated genes3,0643,1163,0773,0713,1533,0433.0492,8742,9563,0432,891
tRNA genes7272737057706768716352
rRNA genes161616153161616161513
ANI (%)100%99.31%99.22%99.16%99.14%99.06%99.03%98.98%98.98%98.94%98.93%

Table 3 . Oxidative stress-related proteins of Lpb. plantarum HOM3204..

Oxidative stress-related proteinLocus tagDatabase
Glutathione peroxidaseChr-gene 0184GO:0004602/COG0386
Removal of superoxide radicalsChr-gene 0584GO:0019430
Glutathione-disulfide reductaseChr-gene 0323, Chr-gene 0991, Chr-gene 1464, Chr-gene 2697GO:0004362
Response to the oxygen radicalChr-gene 1464, Chr-gene 2697GO:0000305
Catalytic activityChr-gene 0102, Chr-gene 1140, Chr-gene 1357, Chr-gene 1915, Chr-gene 1931, Chr-gene 2678GO:0003824
CatalaseChr-gene 2929GO:0004096
Flavin reductase (NADH)Chr-gene 0045, Chr-gene 1116, Chr-gene 2249, Chr-gene 2250, Chr-gene 2680,GO:0036382
Thioredoxin-disulfide reductaseChr-gene 0584, Chr-gene 1888, Chr-gene 2175, Chr-gene 2817GO:0004791
Thioredoxin peroxidaseChr-gene 1928GO:0008379
Thioredoxin reductaseChr-gene 0584, Chr-gene 2138COG:0492
DNA-binding ferritin-like proteinPlasmid 2-gene 0005COG:0783

Table 4 . Antioxidant activities of different Lpb. plantarum strains in vitro..

StrainT-AOC (U/ml)·OH scavenging (%)DPPH scavenging (%)SOD (U/ml)GSH-Px (U/ml)GSH (mg/l)
HOM320423.84 ± 2.4476.84 ± 0.3694.18 ± 0.4528.89 ± 0.3020.57 ± 2.7337.56 ± 2.81
ST-Ⅲ4.13 ± 0.44**76.57 ± 0.3693.00 ± 0.6527.34 ± 0.52*24.29 ± 3.1823.72 ± 3.98**
Lp-11515.48 ± 1.13**77.16 ± 0.6091.03 ± 0.53**24.63 ± 2.11*15.60 ± 2.0659.85 ± 5.57**
Vitamin C16.90 ± 1.42**36.70 ± 1.33**96.14 ± 0.08**34.32 ± 0.36**NDND

Comparison of the Lpb. plantarum HOM3204 strain with other strains: *p < 0.05, **p < 0.01. ·OH, hydroxyl radical scavenging..

ND, not determined..


Table 5 . Effects of Lpb. plantarum HOM3204 on malonaldehyde (MDA), protein carbonyl, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glutathione (GSH) levels in the D-galactoseinduced oxidative injury mouse model..

GroupMDA (nmol/ml)Protein carbonyl (nmol/mgprot)SOD (U/ml)GSH-Px (U/ml)GSH (mgGSH/gprot)
Model group7.81 ± 1.437.02 ± 1.36213 ± 38390 ± 836.17 ± 0.79
HOM32047.59 ± 1.196.49 ± 1.98230 ± 48469 ± 68*7.35 ± 1.47*

Comparison of the Lpb. plantarum HOM3204 group with the model group: *p < 0.05..


References

  1. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. 2014. The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11: 506-514.
    Pubmed CrossRef
  2. Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, et al. 2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ. Microbiol. 12: 758-773.
    Pubmed CrossRef
  3. Pfeiler EA, Klaenhammer TR. 2007. The genomics of lactic acid bacteria. Trends Microbiol. 15: 546-553.
    Pubmed CrossRef
  4. Vastano V, Capri U, Muscariello L, Marasco R, Sacco M. 2010. Lactobacillus plantarum adhesion and colonization: identification of adhesins and effects of intestinal environment on biofilm development. J. Biotechnol. 150: 518-519.
    CrossRef
  5. Arief II, Budiman C, Jenie BS, Andreas E, Yuneni A. 2015. Plantaricin IIA-1A5 from Lactobacillus plantarum IIA-1A5 displays bactericidal activity against Staphylococcus aureus. Benef. Microbes. 6: 603-613.
    Pubmed CrossRef
  6. Bosch M, Méndez M, Pérez M, Farran A, Fuentes MC, Cuñé J. 2012. Lactobacillus plantarum CECT7315 and CECT7316 stimulate immunoglobulin production after influenza vaccination in elderly. Nutr. Hosp. 27: 504-509.
  7. Adesulu-Dahunsi AT, Jeyaram K, Sanni AI, Banwo K. 2018. Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage. PeerJ. 6: e5326.
    Pubmed KoreaMed CrossRef
  8. Hariri M, Salehi R, Feizi A, Mirlohi M, Ghiasvand R, Habibi N. 2015. A randomized, double-blind, placebo-controlled, clinical trial on probiotic soy milk and soy milk: effects on epigenetics and oxidative stress in patients with type II diabetes. Genes Nutr. 10: 52.
    Pubmed KoreaMed CrossRef
  9. Zhang S, Wang T, Zhang D, Wang X, Zhang Z, Lim C, et al. 2022. Probiotic characterization of Lactiplantibacillus plantarum HOM3204 and its restoration effect on antibiotic-induced dysbiosis in mice. Lett. Appl. Microbiol. 74: 949-958.
    Pubmed KoreaMed CrossRef
  10. Garcia-Gonzalez N, Battista N, Prete R, Corsetti A. 2021. Health-promoting role of Lactiplantibacillus plantarum isolated from fermented foods. Microorganisms 9: 349.
    Pubmed KoreaMed CrossRef
  11. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, et al. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 100: 1990-1995.
    Pubmed KoreaMed CrossRef
  12. Jia FF, Zhang LJ, Pang XH, Gu XX, Abdelazez A, Liang Y, et al. 2017. Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells. Genomics 109: 432-437.
    Pubmed CrossRef
  13. Kwak W, Kim K, Lee C, Lee C, Kang J, Cho K, et al. 2016. Comparative analysis of the complete genome of Lactobacillus plantarum GB-LP2 and potential candidate genes for host immune system enhancement. J. Microbiol. Biotechnol. 26: 684-692.
    Pubmed CrossRef
  14. Sinha N, Dabla PK. 2015. Oxidative stress and antioxidants in hypertension-a current review. Curr. Hypertens. Rev. 11: 132-142.
    Pubmed CrossRef
  15. Chandra J, Samali A, Orrenius S. 2000. Triggering and modulation of apoptosis by oxidative stress. Free Radic. Biol. Med. 29: 323-333.
    Pubmed CrossRef
  16. Dasgupta A, Klein K. 2014. Role of oxidative stress in neurodegenerative diseases and other diseases related to aging, pp. 167-184. In: Dasgupta A, Klein K (eds), Antioxidants in Food, Vitamins and Supplements. Ed. Elsevier, San Diego.
  17. Wang Y, Wu Y, Wang Y, Xu H, Mei X, Yu D, et al. 2017. Antioxidant properties of probiotic bacteria. Nutrients 9: 521.
    Pubmed KoreaMed CrossRef
  18. Mishra V, Shah C, Mokashe N, Chavan R, Yadav H, Prajapati J. 2015. Probiotics as potential antioxidants: a systematic review. J. Agric. Food Chem. 63: 3615-3626.
    Pubmed CrossRef
  19. DÜz M, DoĞan YN, DoĞan İ. 2020. Antioxidant activitiy of Lactobacillus plantarum, Lactobacillus sake and Lactobacillus curvatus strains isolated from fermented Turkish Sucuk. An. Acad. Bras. Cienc. 92: e20200105.
    Pubmed CrossRef
  20. Han KJ, Lee JE, Lee NK, Paik HD. 2020. Antioxidant and anti-inflammatory effect of probiotic Lactobacillus plantarum KU15149 derived from Korean homemade diced-radish Kimchi. J. Microbiol. Biotechnol. 30: 591-598.
    Pubmed KoreaMed CrossRef
  21. Zhao J, Tian F, Yan S, Zhai Q, Zhang H, Chen W. 2018. Lactobacillus plantarum CCFM10 alleviating oxidative stress and restoring the gut microbiota in d-galactose-induced aging mice. Food Funct. 9: 917-924.
    Pubmed CrossRef
  22. Ge Q, Yang B, Liu R, Jiang D, Yu H, Wu M, et al. 2021. Antioxidant activity of Lactobacillus plantarum NJAU-01 in an animal model of aging. BMC Microbiol. 21: 182.
    Pubmed KoreaMed CrossRef
  23. Zhang J, Zhao X, Jiang Y, Zhao W, Guo T, Cao Y, et al. 2017. Antioxidant status and gut microbiota change in an aging mouse model as influenced by exopolysaccharide produced by Lactobacillus plantarum YW11 isolated from Tibetan kefir. J. Dairy Sci. 100: 6025-6041.
    Pubmed CrossRef
  24. Zhang Q, Li X, Cui X, Zuo P. 2005. D-galactose injured neurogenesis in the hippocampus of adult mice. Neurol. Res. 27: 552-556.
    Pubmed CrossRef
  25. Li F, Huang G, Tan F, Yi R, Zhou X, Mu J, et al. 2020. Lactobacillus plantarum KSFY06 on d-galactose-induced oxidation and aging in Kunming mice. Food Sci. Nutr. 8: 379-389.
    Pubmed KoreaMed CrossRef
  26. Del Rio D, Stewart AJ, Pellegrini N. 2005. A review of recent studies on malondialdehyde as toxic molecule and biological marker of oxidative stress. Nutr. Metab. Cardiovasc. Dis. 15: 316-328.
    Pubmed CrossRef
  27. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
    Pubmed CrossRef
  28. Rhoads A, Au KF. 2015. PacBio sequencing and its applications. Genom Proteom. Bioinf. 13: 278-289.
    Pubmed KoreaMed CrossRef
  29. Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, et al. 2016. Phased diploid genome assembly with singlemolecule real-time sequencing. Nat. Methods 13: 1050-1054.
    Pubmed KoreaMed CrossRef
  30. Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, et al. 2014. Performance comparison of second- and thirdgeneration sequencers using a bacterial genome with two chromosomes. BMC Genomics 15: 699.
    Pubmed KoreaMed CrossRef
  31. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16: 294.
    Pubmed KoreaMed CrossRef
  32. Wang L, Wu Y, Xu J, Huang Q, Zhao Y, Dong S, et al. 2022. Colicins of Escherichia coli lead to resistance against the diarrhea-causing pathogen enterotoxigenic E. coli in pigs. Microbiol. Spectr. 10: e0139622.
    Pubmed KoreaMed CrossRef
  33. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
    Pubmed KoreaMed CrossRef
  34. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12: 59-60.
    Pubmed CrossRef
  35. Akhter S, Aziz RK, Edwards RA. 2012. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 40: e126.
    Pubmed KoreaMed CrossRef
  36. Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 34: D459-464.
    Pubmed KoreaMed CrossRef
  37. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. 2017. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45: D566-D573.
    Pubmed KoreaMed CrossRef
  38. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-238.
    Pubmed KoreaMed CrossRef
  39. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
    Pubmed KoreaMed CrossRef
  40. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35: 3100-3108.
    Pubmed KoreaMed CrossRef
  41. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: an RNA family database. Nucleic Acids Res. 31: 439-441.
    Pubmed KoreaMed CrossRef
  42. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
    Pubmed KoreaMed CrossRef
  43. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, et al. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43: 6761-6771.
    Pubmed KoreaMed CrossRef
  44. Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, et al. 2012. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem. Biophys. Res. Commun. 419: 779-781.
    Pubmed CrossRef
  45. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
    Pubmed KoreaMed CrossRef
  46. Lin MY, Chang FJ. 2000. Antioxidative effect of intestinal bacteria Bifidobacterium longum ATCC 15708 and Lactobacillus acidophilus ATCC 4356. Dig. Dis. Sci. 45: 1617-1622.
  47. Mahfouz N, Ferreira I, Beisken S, von Haeseler A, Posch AE. 2020. Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. J. Antimicrob. Chemother. 75: 3099-3108.
    Pubmed KoreaMed CrossRef
  48. Cooper AL, Low AJ, Koziol AG, Thomas MC, Leclair D, Tamber S, et al. 2020. Systematic evaluation of whole genome sequencebased predictions of Salmonella serotype and antimicrobial resistance. Front. Microbiol. 11: 549.
    Pubmed KoreaMed CrossRef
  49. van den Nieuwboer M, van Hemert S, Claassen E, de Vos WM. 2016. Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome. Microb. Biotechnol. 9: 452-465.
    Pubmed KoreaMed CrossRef
  50. Ivanovic N, Minic R, Djuricic I, Radojevic Skodric S, Zivkovic I, Sobajic S, et al. 2016. Active Lactobacillus rhamnosus LA68 or Lactobacillus plantarum WCFS1 administration positively influences liver fatty acid composition in mice on a HFD regime. Food Funct. 7: 2840-2848.
    Pubmed CrossRef
  51. Kullisaar T, Songisepp E, Aunapuu M, Kilk K, Arend A, Mikelsaar M, et al. 2010. Complete glutathione system in probiotic Lactobacillus fermentum ME-3. Prikl. Biokhim. Mikrobiol. 46: 527-531.
    CrossRef
  52. Valencia E, Marin A, Hardy G. 2001. Glutathione-nutritional and pharmacologic viewpoints: Part IV. Nutrition 17: 783-784.
    Pubmed CrossRef