Microbiology and Biotechnology Letters (한국미생물·생명공학회지)

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

DOI QR Code

Genome Profiling for Health Promoting and Disease Preventing Traits Unraveled Probiotic Potential of Bacillus clausii B106

  • Kapse, N.G. (Bioenergy Group, MACS-Agharkar Research Institute) ;
  • Engineer, A.S. (Bioenergy Group, MACS-Agharkar Research Institute) ;
  • Gowdaman, V. (Bioenergy Group, MACS-Agharkar Research Institute) ;
  • Wagh, S. (Hi Tech BioSciences India Ltd., Research & Development Centre) ;
  • Dhakephalkar, P.K. (Bioenergy Group, MACS-Agharkar Research Institute)
  • Received : 2018.04.05
  • Accepted : 2018.09.19
  • Published : 2018.12.28
Download PDF
⟨ Previous Next ⟩

Abstract

Spore-forming Bacillus species are commercially available probiotic formulations for application in humans. They have health benefits and help prevent disease in hosts by combating entero-pathogens and ameliorating antibiotic-associated diarrhea. However, the molecular and cellular mechanisms of these benefits remain unclear. Here, we report the draft genome of a potential probiotic strain of Bacillus clausii B106. We mapped and compared the probiotic profile of B106 with other reference genomes. The draft genome analysis of B106 revealed the presence of ADI pathway genes, indicating its ability to tolerate acidic pH and bile salts. Genes encoding fibronectin binding proteins, enolase, as well as a gene cluster involved in the biosynthesis of exopolysaccharides underscored the potential of B106 to adhere to the intestinal epithelium and colonize the human gut. Genes encoding bacteriocins were also detected, indicating the antimicrobial ability of this isolate. The presence of genes encoding vitamins, including Riboflavin, Folate, and Biotin, also indicated the health-promoting ability of B106. Resistance of B106 to multiple antibiotics was evident from the presence of genes encoding resistance to chloramphenicol, ${\beta}$-lactams, Vancomycin, Tetracycline, fluoroquinolones, and aminoglycosides. The findings indicate the significance of B. clausii B106 administration during antibiotic treatment and its potential value as a probiotic strain to replenish the health-promoting and disease-preventing gut flora following antibiotic treatment.

Keywords

References

  1. Fuller R. 1989. Probiotics in man and animals. J. Appl. Bacteriol. 66: 365-378. https://doi.org/10.1111/j.1365-2672.1989.tb05105.x
  2. Mazza P. 1994. The use of Bacillus subtilis as an antidiarrhoeal microorganism. Boll. Chim. Farm. 133: 3-18.
  3. Hoa TT, Duc LH, Isticato R, Baccigalupi L, Ricca E, Van PH, et al. 2001. Fate and dissemination of Bacillus subtilis spores in a murine model. Appl. Environ. Microbiol. 67: 3819-3823. https://doi.org/10.1128/AEM.67.9.3819-3823.2001
  4. Bader J, Albin A, Stahl U. 2012. Spore-forming bacteria and their utilisation as probiotics. Benef Microbes. 3: 67-75. https://doi.org/10.3920/BM2011.0039
  5. Lefevre M, Racedo SM, Ripert G, Housez B, Cazaubiel M, Maudet C, et al. 2015. Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Immun. Ageing 12: 24. https://doi.org/10.1186/s12979-015-0051-y
  6. Shobharani P, Padmaja RJ, Halami PM. 2015. Diversity in the antibacterial potential of probiotic cultures Bacillus licheniformis MCC2514 and Bacillus licheniformis MCC2512. Res. Microbiol. 166: 546-554. https://doi.org/10.1016/j.resmic.2015.06.003
  7. Ripert G, Racedo SM, Elie AM, Jacquot C, Bressollier P, Urdaci MC. 2016. Secreted compounds of the probiotic bacillus clausii strain O/C inhibit the cytotoxic effects induced by Clostridium difficile and Bacillus cereus toxins. Antimicrob. Agents Chemother. 60: 3445-3454. https://doi.org/10.1128/AAC.02815-15
  8. Pham M, Lemberg DA, Day AS. 2008. Probiotics: sorting the evidence from the myths. Med. J. Aust. 188: 304-308.
  9. Hong HA, Duc le LH, Cutting SM. 2005. The use of bacterial spore formers as probiotics. FEMS Microbiol. Rev. 29: 813-835. https://doi.org/10.1016/j.femsre.2004.12.001
  10. Lakshmi SG, Jayanthi N, Saravanan M, Ratna MS. 2017. Safety assesment of Bacillus clausii UBBC07, a spore forming probiotic. Toxicol. Rep. 4: 62-71. https://doi.org/10.1016/j.toxrep.2016.12.004
  11. Urdaci MC, Bressollier P, Pinchuk I. 2004. Bacillus clausii probiotic strains: antimicrobial and immunomodulatory activities. J. Clinic Gastroenterol. 38: S86-S90. https://doi.org/10.1097/01.mcg.0000128925.06662.69
  12. Upadrasta A, Pitta S, Madempudi RS. 2016. Draft genome sequence of Bacillus clausii UBBC07, a spore-forming probiotic strain. Genome Announc. 4: e00235-16.
  13. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455-477. https://doi.org/10.1089/cmb.2012.0021
  14. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 9: 75. https://doi.org/10.1186/1471-2164-9-75
  15. Auch AF, Jan M, Klenk HP, Goker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic. Sci. 28: 117-134.
  16. Alikhan NF, Petty NK, Zakour NLB, Beatson SA. 2011. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 12: 402. https://doi.org/10.1186/1471-2164-12-402
  17. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, et al. 2015. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43: W237-W243. https://doi.org/10.1093/nar/gkv437
  18. van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic Acids Res. 41: W448-W453. https://doi.org/10.1093/nar/gkt391
  19. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. 2016. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45: D566-D573.
  20. Holzapfel WH, Haberer P, Geisen R, Bjorkroth J, Schillinger U. 2001. Taxonomy and important features of probiotic microorganisms in food and nutrition. Am. J. Clin. Nutr. 73: 365s-373s. https://doi.org/10.1093/ajcn/73.2.365s
  21. Han XY. 2006. Bacterial identification based on 16S ribosomal RNA gene sequence analysis. In: Advanced techniques in diagnostic microbiology, Springer, Boston, MA, pp. 323-332.
  22. Sleator RD, Watson D, Hill C, Gahan CG. 2009. The interaction between Listeria monocytogenes and the host gastrointestinal tract. Microbiology 155: 2463-2475. https://doi.org/10.1099/mic.0.030205-0
  23. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, et al. 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956. https://doi.org/10.1038/nature08080
  24. Ryan S, Hill C, Gahan CG. 2008. Acid stress responses in Listeria monocytogenes. Adv. Appl. Microbiol. 65: 67-91.
  25. Cotter PD, Hill C. 2003. Surviving the acid test: responses of gram-positive bacteria to low pH. Microbiol. Mol. Biol. Rev. 67: 429-453. https://doi.org/10.1128/MMBR.67.3.429-453.2003
  26. Hain T, Hossain H, Chatterjee SS, Machata S, Volk U, Wagner S, et al. 2008. Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e ${\sigma}$ B regulon. BMC Microbiol. 8: 20. https://doi.org/10.1186/1471-2180-8-20
  27. Lehri B, Seddon AM, Karlyshev AV. 2017. Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872. Stand Genomic Sci. 12: 19. https://doi.org/10.1186/s40793-017-0228-4
  28. Khatri I, Sharma S, Ramya TNC, Subramanian S. 2016. Complete genomes of Bacillus coagulans S-lac and Bacillus subtilis TO-A JPC, two phylogenetically distinct probiotics. PLoS One. 11: e0156745. https://doi.org/10.1371/journal.pone.0156745
  29. Begley M, Gahan CG, Hill C. 2005. The interaction between bacteria and bile. FEMS Microbiol. Re. 29: 625-651. https://doi.org/10.1016/j.femsre.2004.09.003
  30. McAuliffe O, Cano RJ, Klaenhammer TR. 2005. Genetic analysis of two bile salt hydrolase activities in Lactobacillus acidophilus NCFM. Appl. Environ. Microbiol. 71: 4925-4929. https://doi.org/10.1128/AEM.71.8.4925-4929.2005
  31. Denou E, Pridmore RD, Berger B, Panoff JM, Arigoni F, Brussow H. 2008. Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. J. Bacteriol. 190: 3161-3168. https://doi.org/10.1128/JB.01637-07
  32. Lim SM. 2014. Antimutagenicity activity of the putative probiotic strain Lactobacillus paracasei subsp. tolerans JG22 isolated from pepper leaves Jangajji. Food Sci. Biotechnol. 23: 141-150. https://doi.org/10.1007/s10068-014-0019-2
  33. Granato D, Bergonzelli GE, Pridmore RD, Marvin L, Rouvet M, Corthesy-Theulaz IE. 2004. Cell surface-associated elongation factor Tu mediates the attachment of Lactobacillus johnsonii NCC533 (La1) to human intestinal cells and mucins. Infect. Immun. 72: 2160-2169. https://doi.org/10.1128/IAI.72.4.2160-2169.2004
  34. Howarth GS, Wang H. 2013. Role of endogenous microbiota, probiotics and their biological products in human health. Nutrients 5: 58-81. https://doi.org/10.3390/nu5010058
  35. Ruas-Madiedo P, Gueimonde M, Margolles A, de los REYESGAVILAN CG, Salminen S. 2006. Exopolysaccharides produced by probiotic strains modify the adhesion of probiotics and enteropathogens to human intestinal mucus. J. Food Prot. 69: 2011-2015. https://doi.org/10.4315/0362-028X-69.8.2011
  36. Kodali VP, Sen R. 2008. Antioxidant and free radical scavenging activities of an exopolysaccharide from a probiotic bacterium. Biotechnol. J. 3: 245-251. https://doi.org/10.1002/biot.200700208
  37. Haiko J, Westerlund-Wikstrom B. 2013. The role of the bacterial flagellum in adhesion and virulence. Biology 2: 1242-1267. https://doi.org/10.3390/biology2041242
  38. Cotter PD, Ross RP, Hill C. 2013. Bacteriocins-a viable alternative to antibiotics?. Nat. Rev. Microbiol. 11: 95-105. https://doi.org/10.1038/nrmicro2937
  39. Lv LX, Li YD, Hu XJ, Shi HY, Li LJ. 2014. Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains. Gut. Pathog. 6: 36. https://doi.org/10.1186/s13099-014-0036-y
  40. Cotter PD, Hill C, Ross RP. 2005. Food microbiology: bacteriocins: developing innate immunity for food. Nat. Rev. Microbiol. 3: 777-788. https://doi.org/10.1038/nrmicro1273
  41. Gonzalez-Martinez BE, Gomez-Trevino, Jimenez-Salas Z. 2003. Bacteriocinas de probioticos. Rev Cub Salud Publica. 4.
  42. Hertzberger R, Arents J, Dekker HL, Pridmore RD, Gysler C, Kleerebezem M, et al. 2014. $H_2O_2$ production in species of the Lactobacillus acidophilus group: a central role for a novel NADHdependent flavin reductase. Appl. Environ. Microbiol. 80: 2229-2239. https://doi.org/10.1128/AEM.04272-13
  43. Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ. 2012. Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ. Microbiol. 14: 2870-2890. https://doi.org/10.1111/j.1462-2920.2012.02841.x
  44. Roberfroid MB. 2002. Prebiotics and probiotics: are they functional foods?. Am. J. Clin. Nutr. 71: 1682S-1687S.
  45. Campbell JM, Fahey Jr GC, Wolf BW. 1997. Selected indigestible oligosaccharides affect large bowel mass, cecal and fecal shortchain fatty acids, pH and microflora in rats. J. Nutr. 127: 130-136. https://doi.org/10.1093/jn/127.1.130
  46. Gibson GR, McCartney AL, Rastall RA. 2005. Prebiotics and resistance to gastrointestinal infections. Br. J. Nutr. 93: S31-S34. https://doi.org/10.1079/BJN20041343
  47. Grootaert C, Van den Abbeele P, Marzorati M, Broekaert WF, Courtin CM, Delcour JA, et al. 2009. Comparison of prebiotic effects of arabinoxylan oligosaccharides and inulin in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol. Ecol. 69: 231-242. https://doi.org/10.1111/j.1574-6941.2009.00712.x
  48. Gueimonde M, Noriega L, Margolles A, Clara G. 2007. Induction of ${\alpha}$-l-arabinofuranosidase activity by monomeric carbohydrates in Bifidobacterium longum and ubiquity of encoding genes. Arch. Microbiol. 187: 145-153. https://doi.org/10.1007/s00203-006-0181-x
  49. Di Pierro F, Bertuccioli A, Marini E, Ivaldi L. 2015. A pilot trial on subjects with lactose and/or oligosaccharides intolerance treated with a fixed mixture of pure and enteric-coated ${\alpha}$-and ${\beta}$-galactosidase. Clin. Exp. Gastroenterol. 8: 95-100.
  50. Parche S, Amon J, Jankovic I, Rezzonico E, Beleut M, Barutcu H, et al. 2007. Sugar transport systems of Bifidobacterium longum NCC2705. J. Mol. Microbiol. Biotechnol. 12: 9-19. https://doi.org/10.1159/000096455
  51. Preidis GA, Hill C, Guerrant RL, Ramakrishna BS, Tannock GW, Versalovic J. 2011. Probiotics, enteric and diarrheal diseases, and global health. Gastroenterology 140: 8-14. https://doi.org/10.1053/j.gastro.2010.11.010
  52. Saulnier DM, Santos F, Roos S, Mistretta TA, Spinler JK, Molenaar D, et al. 2011. Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS One 6: e18783. https://doi.org/10.1371/journal.pone.0018783
  53. Mills S, Stanton C, Fitzgerald GF, Ross R. 2011, December. Enhancing the stress responses of probiotics for a lifestyle from gut to product and back again. Microb. Cell Fact. 10: S19. https://doi.org/10.1186/1475-2859-10-S1-S19
  54. Van Melderen L. 2010. Toxin-antitoxin systems: why so many, what for?. Curr. Opin. Microbiol. 13: 781-785. https://doi.org/10.1016/j.mib.2010.10.006
  55. Yan X, Gurtler JB, Fratamico PM, Hu J, Juneja VK. 2012. Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food. Cell Biosci. 2: 39. https://doi.org/10.1186/2045-3701-2-39
  56. Aizenman E, Engelberg-Kulka H, Glaser G. 1996. An Escherichia coli chromosomal" addiction module" regulated by guanosine [corrected] 3', 5'-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA 93: 6059-6063. https://doi.org/10.1073/pnas.93.12.6059
  57. Ramisetty BCM, Natarajan B, Santhosh RS. 2015. mazEF-mediated programmed cell death in bacteria: "what is this?". Crit. Rev. Microbiol. 41: 89-100. https://doi.org/10.3109/1040841X.2013.804030
  58. Kappes RM, Kempf B, Bremer E. 1996. Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD. J. Bacteriol. 178: 5071-5079. https://doi.org/10.1128/jb.178.17.5071-5079.1996
  59. Gueimonde M, Sanchez B, de los Reyes-Gavilan CG, Margolles A. 2013. Antibiotic resistance in probiotic bacteria. Front Microbiol. 4: 202.
  60. 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. https://doi.org/10.1128/AAC.00419-13
  61. Eggers CT, Murray IA, Delmar VA, Day AG, Craik CS. 2004. The periplasmic serine protease inhibitor ecotin protects bacteria against neutrophil elastase. Biochem. J. 379: 107-118. https://doi.org/10.1042/bj20031790