Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Whole-Genome Sequencing of Three Lactiplantibacillus plantarum Strains Reveals Potential Metabolites for Boosting Host Immunity Safely

  • I-Chen Li (Biotech Research Institute, Grape King Bio Ltd) ;
  • Yueh-Lun Lee (Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University) ;
  • Tsung-Ju Li (Biotech Research Institute, Grape King Bio Ltd) ;
  • You-Shan Tsai (Biotech Research Institute, Grape King Bio Ltd) ;
  • Yen-Lien Chen (Biotech Research Institute, Grape King Bio Ltd) ;
  • Chin-Chu Chen (Biotech Research Institute, Grape King Bio Ltd)
  • Received : 2024.02.08
  • Accepted : 2024.07.24
  • Published : 2024.10.28
Download PDF
⟨ Previous Next ⟩

Abstract

In response to the growing demand for immune-related products, this study evaluated the safety and immune-modulating potential of three newly discovered Lactiplantibacillus plantarum strains (GKM3, GKK1, and GKD7) through toxicity tests and whole-genome sequencing. Safety evaluations, including the analysis of antimicrobial resistance genes, virulence factors, plasmids, and prophages, classified these strains as safe for human consumption. Acute oral toxicity tests further supported their safety. To evaluate their immune-modulating potential, dendritic cells were exposed to these strains, and the secretion of key cytokines (IFN-β and IL-12) was measured. Among the strains, GKK1 exhibited the highest enhancement of IFN-β and IL-12 production, suggesting its potential as an immune-stimulating probiotic. Bioinformatics analysis revealed potential metabolic pathways and secondary metabolites, including predicted bacteriocins, associated with immune modulation. The presence of a nitrate reductase region in the GKK1 strain indicated its ability to produce nitric oxide, a critical molecule involved in immune regulation and host defense. The presence of glucorhamnan-related gene clusters in GKK1 also suggested immune-enhancing effects. Nitrate reductase expression was confirmed using qPCR, with the highest levels detected in GKK1. Moreover, this study is the first to show an anti-inflammatory effect of plantaricin A, linked to its presence in strain GKM3 and its potential therapeutic applications due to sequence similarity to known anti-inflammatory peptides. Overall, these three L. plantarum strains demonstrated a safe profile and GKK1 showed potential as an immunity-enhancing probiotic. However, additional investigation is required to confirm the involvement of specific metabolic pathways, secondary metabolites, and bacteriocins in immune responses.

Keywords

References

  1. Sender R, Fuchs S, Milo R. 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164: 337-340.
  2. Lynch JB, Hsiao EY. 2019. Microbiomes as sources of emergent host phenotypes. Science 365: 1405-1409.
  3. Olvera-Rosales LB, Cruz-Guerrero AE, Ramirez-Moreno E, Quintero-Lira A, Contreras-Lopez E, Jaimez-Ordaz J, et al. 2021. Impact of the gut microbiota balance on the health-disease relationship: The importance of consuming probiotics and prebiotics. Foods 10: 1261.
  4. Hou K, Wu Z-X, Chen X-Y, Wang J-Q, Zhang D, Xiao C, et al. 2022. Microbiota in health and diseases. Signal Transduct. Target. Ther. 7: 135.
  5. Tsai YL, Lin TL, Chang CJ, Wu TR, Lai WF, Lu CC, et al. 2019. Probiotics, prebiotics and amelioration of diseases. J. Biomed. Sci. 26: 3.
  6. Mack DR. 2005. Probiotics-mixed messages. Can. Fam. Physician 51: 1455-1457, 1462-1454.
  7. Kho ZY, Lal SK. 2018. The human gut microbiome - A potential controller of wellness and disease. Front. Microbiol. 9: 1835.
  8. Cortes-Perez NG, de Moreno de LeBlanc A, Gomez-Gutierrez JG, LeBlanc JG, Bermudez-Humaran LG. 2021. Probiotics and trained immunity. Biomolecules 11: 1402.
  9. Netea Mihai G, Quintin J, van der Meer Jos WM. 2011. Trained immunity: A memory for innate host defense. Cell Host Microbe 9: 355-361.
  10. McFarland LV, Evans CT, Goldstein EJC. 2018. Strain-specificity and disease-specificity of probiotic efficacy: a systematic review and meta-analysis. Front. Med. 5: 124.
  11. Wick RR, Judd LM, Holt KE. 2019. Performance of neural network basecalling tools for Oxford nanopore sequencing. Genome Biol. 20: 129.
  12. De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34: 2666-2669.
  13. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37: 540-546.
  14. Vaser R, Sovic I, Nagarajan N, Sikic M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27: 737-746.
  15. Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094-3100.
  16. Ltd. ONT. 2021. Medaka. Available from https://github.com/nanoporetech/medaka. Accessed Nov. 20, 2023.
  17. Huang YT, Liu PY, Shih PW. 2021. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing. Genome Biol. 22: 95.
  18. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075.
  19. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210-3212.
  20. Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J. 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32: 929-931.
  21. Kwon YJ, Chun BH, Jung HS, Chu J, Joung H, Park SY, et al. 2021. Safety assessment of Lactiplantibacillus (formerly Lactobacillus ) plantarum Q180. J. Microbiol. Biotechnol. 31: 1420-1429.
  22. Dereeper A, Summo M, Meyer DF. 2022. PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pangenomes. Bioinformatics 38: 4412-4414.
  23. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28: 416-418.
  24. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31: 3691-3693.
  25. Perrin A, Rocha EPC. 2021. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genom. Bioinform. 3: lqaa106.
  26. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36.
  27. Bai Z, Zhang N, Jin Y, Chen L, Mao Y, Sun L, et al. 2022. Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks. Front. Cell. Infect. Microbiol. 12: 919701.
  28. Liu YY, Hsu CY, Yang YC, Huang CH, Chen CC. 2023. ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains. Bioinform. Adv. 3: vbad153.
  29. Rychen G, Aquilina G, Azimonti G, Bampidis V, Bastos ML, Bories G, et al. 2018. Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J. 16: e05206.
  30. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. 2013. The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother. 57: 3348-3357.
  31. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, et al. 2020. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75: 3491-3500.
  32. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, et al. 2021. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11: 12728.
  33. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33: D325-328.
  34. Malberg Tetzschner AM, Johnson JR, Johnston BD, Lund O, Scheutz F. 2020. In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data. J. Clin. Microbiol. 58: e01269-20.
  35. OECD. 2002. Test No. 423: Acute Oral toxicity - Acute Toxic Class Method, Ed.
  36. Administration UFaD. 2005. Guidance for Industry: Estimating the Maximum Safe Starting Dose in Initial Clinical Trials for Therapeutics in Adult Healthy Volunteers. Available from https://www.fda.gov/media/72309/download. Accessed Nov. 20, 2023.
  37. Lee YL, Hsu LH, Kuo YH, Lee CC. 2019. Caffeic amide derivatives inhibit allergen-induced bone marrow-derived dendritic cell maturation. Pharmacol. Rep. 71: 194-200.
  38. Juan SH, Lee TS, Tseng KW, Liou JY, Shyue SK, Wu KK, et al. 2001. Adenovirus-mediated heme oxygenase-1 gene transfer inhibits the development of atherosclerosis in apolipoprotein E-deficient mice. Circulation 104: 1519-1525.
  39. van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP. 2018. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 46: W278-W281.
  40. Pascal Andreu V, Roel-Touris J, Dodd D, Fischbach Michael A, Medema Marnix H. 2021. The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota. Nucleic Acids Res. 49: W263-W270.
  41. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, et al. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39: W339-346.
  42. Bru D, Sarr A, Philippot L. 2007. Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments. Appl. Environ. Microbiol. 73: 5971-5974.
  43. Wasfi R, Abd El-Rahman OA, Zafer MM, Ashour HM. 2018. Probiotic Lactobacillus sp. inhibit growth, biofilm formation and gene expression of caries-inducing Streptococcus mutans. J. Cell. Mol. Med. 22: 1972-1983.
  44. Ma Y, Zilles JL, Kent AD. 2019. An evaluation of primers for detecting denitrifiers via their functional genes. Environ. Microbiol. 21: 1196-1210.
  45. van Meerloo J, Kaspers GJ, Cloos J. 2011. Cell sensitivity assays: the MTT assay. Methods Mol. Biol. 731: 237-245.
  46. Koh A, De Vadder F, Kovatcheva-Datchary P, Backhed F. 2016. From dietary fiber to host physiology: Short-chain fatty acids as key bacterial metabolites. Cell 165: 1332-1345.
  47. Hamulka J, Jeruszka-Bielak M, Gornicka M, Drywien ME, Zielinska-Pukos MA. 2020. Dietary supplements during COVID-19 outbreak. results of google trends analysis supported by PLifeCOVID-19 online studies. Nutrients 13: 54.
  48. Umair M, Jabbar S, Zhaoxin L, Jianhao Z, Abid M, Khan KR, et al. 2022. Probiotic-based bacteriocin: Immunity supplementation against viruses. An updated review. Front. Microbiol. 13: 876058.
  49. Vera-Santander VE, Hernandez-Figueroa RH, Jimenez-Munguia MT, Mani-Lopez E, Lopez-Malo A. 2023. Health benefits of consuming foods with bacterial probiotics, postbiotics, and their metabolites: A review. Molecules 28: 1230.
  50. Zhang W, Ji H, Zhang D, Liu H, Wang S, Wang J, et al. 2018. Complete genome sequencing of Lactobacillus plantarum ZLP001, a potential probiotic that enhances intestinal epithelial barrier function and defense against pathogens in pigs. Front. Physiol. 9: 1689.
  51. Mao B, Yin R, Li X, Cui S, Zhang H, Zhao J, et al. 2021. Comparative genomic analysis of Lactiplantibacillus plantarum isolated from different niches. Genes 12: 241.
  52. Ma N, Sun J, Li S, Shao M, Ying N, Liu W, et al. 2023. A potential risk comprehensive evaluation model of probiotic species based on complete genome sequences. Food Anal. Methods 16: 961-973.
  53. Mukherjee P, Roy S, Ghosh D, Nandi SK. 2022. Role of animal models in biomedical research: a review. Lab. Anim. Res. 38: 18.
  54. Ali S, Mann-Nuttel R, Schulze A, Richter L, Alferink J, Scheu S. 2019. Sources of type I interferons in infectious immunity: Plasmacytoid dendritic cells not always in the driver's seat. Front. Immunol. 10: 778.
  55. Boxx GM, Cheng G. 2016. The roles of type I interferon in bacterial infection. Cell Host Microbe 19: 760-769.
  56. Tait Wojno ED, Hunter CA, Stumhofer JS. 2019. The immunobiology of the interleukin-12 family: room for discovery. Immunity 50: 851-870.
  57. Tiso M, Schechter AN. 2015. Nitrate reduction to nitrite, nitric oxide and ammonia by gut bacteria under physiological conditions. PLoS One 10: e0119712.
  58. Radi R. 2018. Oxygen radicals, nitric oxide, and peroxynitrite: Redox pathways in molecular medicine. Proc. Natl. Acad. Sci. USA 115: 5839-5848.
  59. Huang FP, Niedbala W, Wei XQ, Xu D, Feng GJ, Robinson JH, et al. 1998. Nitric oxide regulates Th1 cell development through the inhibition of IL-12 synthesis by macrophages. Eur. J. Immunol. 28: 4062-4070.
  60. Niedbala W, Wei XQ, Campbell C, Thomson D, Komai-Koma M, Liew FY. 2002. Nitric oxide preferentially induces type 1 T cell differentiation by selectively up-regulating IL-12 receptor beta 2 expression via cGMP. Proc. Natl. Acad. Sci. USA 99: 16186-16191.
  61. Li CY, Anuraga G, Chang CP, Weng TY, Hsu HP, Ta HDK, et al. 2023. Repurposing nitric oxide donating drugs in cancer therapy through immune modulation. J. Exp. Clin. Cancer Res. 42: 22.
  62. Reshi ZA, Ahmad W, Lukatkin AS, Javed SB. 2023. From nature to lab: A review of secondary metabolite biosynthetic pathways, environmental influences, and in vitro approaches. Metabolites 13: 895.
  63. Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. 2019. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide. Proc. Natl. Acad. Sci. USA 116: 12672-12677.
  64. Belguesmia Y, Bendjeddou K, Kempf I, Boukherroub R, Drider D. 2020. Heterologous biosynthesis of five new class II bacteriocins from Lactobacillus paracasei CNCM I-5369 with antagonistic activity against pathogenic Escherichia coli strains. Front. Microbiol. 11: 1198.
  65. Syaputri Y, Iwahashi H. 2020. Characteristics of heterologous plantaricin from Lactobacillus plantarum and its future in food preservation. Rev. Agric. Sci. 8: 124-137.
  66. Hu CB, Malaphan W, Zendo T, Nakayama J, Sonomoto K. 2010. Enterocin X, a novel two-peptide bacteriocin from Enterococcus faecium KU-B5, has an antibacterial spectrum entirely different from those of its component peptides. Appl. Environ. Microbiol. 76: 4542-4545.
  67. Meijerink M, van Hemert S, Taverne N, Wels M, de Vos P, Bron PA, et al. 2010. Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization. PLoS One 5: e10632.
  68. Yin X, Heeney D, Srisengfa Y, Golomb B, Griffey S, Marco M. 2018. Bacteriocin biosynthesis contributes to the anti-inflammatory capacities of probiotic Lactobacillus plantarum. Benef. Microbes 9: 333-344.
  69. Kristiansen PE, Fimland G, Mantzilas D, Nissen-Meyer J. 2005. Structure and mode of action of the membrane-permeabilizing antimicrobial peptide pheromone plantaricin A. J Biol. Chem. 280: 22945-22950.
  70. Anderssen EL, Diep DB, Nes IF, Eijsink VG, Nissen-Meyer J. 1998. Antagonistic activity of Lactobacillus plantarum C11: two new two-peptide bacteriocins, plantaricins EF and JK, and the induction factor plantaricin A. Appl. Environ. Microbiol. 64: 2269-2272.
  71. Lee HK, Choi SH, Lee CR, Lee SH, Park MR, Kim Y, et al. 2015. Screening and characterization of lactic acid bacteria strains with anti-inflammatory activities through in vitro and caenorhabditis elegans model testing. Korean J. Food Sci. Anim. Resour. 35: 91-100.