Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences

World Journal of Gastroenterology

Volumn 18, Issue 5, 2012, Pages 479-488

  Wei, Yan Xia ^a   Zhang, Zhuo Yang ^a   Liu, Chang ^a   Malakar, Pradeep K ^b   Guo, Xiao Kui ^a  

^a SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^b NORWICH RESEARCH PARK   (United Kingdom)

Author keywords

Antibiotic resistance; Bifidobacterium longum; Genome; Harmful metabolite; Safety assessment; Virulence factor

Indexed keywords

AMIKACIN; AMOXICILLIN; AMPICILLIN; BACITRACIN; CEFALOTIN; CEFOTAXIME; CHLORAMPHENICOL; CIPROFLOXACIN; COTRIMOXAZOLE; ERYTHROMYCIN; GENTAMICIN; IMIPENEM; RIFAMPICIN; STREPTOMYCIN; VANCOMYCIN; VIRULENCE FACTOR;

ADHESION; AMINO ACID TRANSPORT; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL VIRULENCE; BIFIDOBACTERIUM LONGUM; GENE SEQUENCE; GENETIC DATABASE; NONHUMAN; NUCLEOTIDE SEQUENCE; SAFETY; SUGAR TRANSPORT; TRANSCRIPTION REGULATION;

EID: 84863035964     PISSN: 10079327     EISSN: None     Source Type: Journal    
DOI: 10.3748/wjg.v18.i5.479     Document Type: Article

References (65)

1. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 2007; 71: 495-548
2. Marco ML, Pavan S, Kleerebezem M. Towards understanding molecular modes of probiotic action. Curr Opin Biotechnol 2006; 17: 204-210
3. Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci USA 2002; 99: 14422-14427
4. Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci USA 2008; 105: 18964-18969
5. Borriello SP, Hammes WP, Holzapfel W, Marteau P, Schrezenmeir J, Vaara M, Valtonen V. Safety of probiotics that contain lactobacilli or bifidobacteria. Clin Infect Dis 2003; 36: 775-780
6. O'Brien J, Crittenden R, Arthur C. Ouwehand and Seppo Salminen. Safety evaluation of probiotics. Trends in Food Sci and Technol 1999; 10: 418-424
7. McBain AJ, Macfarlane GT. Investigations of bifidobacterial ecology and oligosaccharide metabolism in a three-stage compound continuous culture system. Scand J Gastroenterol Suppl 1997; 222: 32-40
8. Ruiz-Moyano S, Martín A, Benito MJ, Casquete R, Serradilla MJ, Córdoba MD. Safety and functional aspects of pre-selected lactobacilli for probiotic use in Iberian dry-fermented sausages. Meat Sci 2009; Epub ahead of print
9. Wei YX, Zhang ZY, Liu C, Zhu YZ, Zhu YQ, Zheng H, Zhao GP, Wang S, Guo XK. Complete genome sequence of Bifidobacterium longum JDM301. J Bacteriol 2010; 192: 4076-4077
10. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2008; 36: D25-D30
11. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27: 4636-4641
12. Guo FB, Ou HY, Zhang CT. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res 2003; 31: 1780-1789
13. Bose M, Barber RD. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006; 6: 223-227
14. Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 2007; 8: 172
15. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25: 955-964
16. Ghai R, Hain T, Chakraborty T. GenomeViz: visualizing microbial genomes. BMC Bioinformatics 2004; 5: 198
17. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33: D325-D328
18. Liu B, Pop M. ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Res 2009; 37: D443-D447
19. Ventura M, Turroni F, Zomer A, Foroni E, Giubellini V, Bottacini F, Canchaya C, Claesson MJ, He F, Mantzourani M, Mulas L, Ferrarini A, Gao B, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Gupta RS, Zhang Z, Beighton D, Fitzgerald GF, O'Toole PW, van Sinderen D. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 2009; 5: e1000785
20. Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, Coûté-Monvoisin AC, Leyer G, Rendulic S, Steele JL, Broadbent JR, Oberg T, Dudley EG, Schuster S, Romero DA, Roberts RF. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol 2009; 191: 4144-4151
21. Philippe H, Douady CJ. Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 2003; 6: 498-505
22. Ammor MS, Flórez AB, Mayo B. Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria. Food Microbiol 2007; 24: 559-570
23. Delgado S, Flórez AB, Mayo B. Antibiotic susceptibility of Lactobacillus and Bifidobacterium species from the human gastrointestinal tract. Curr Microbiol 2005; 50: 202-207
24. Moubareck C, Gavini F, Vaugien L, Butel MJ, Doucet-Populaire F. Antimicrobial susceptibility of bifidobacteria. J Antimicrob Chemother 2005; 55: 38-44
25. D'Aimmo MR, Modesto M, Biavati B. Antibiotic resistance of lactic acid bacteria and Bifidobacterium spp. isolated from dairy and pharmaceutical products. Int J Food Microbiol 2007; 115: 35-42
26. Wilson JW, Schurr MJ, LeBlanc CL, Ramamurthy R, Buchanan KL, Nickerson CA. Mechanisms of bacterial pathogenicity. Postgrad Med J 2002; 78: 216-224
27. von Ossowski I, Reunanen J, Satokari R, Vesterlund S, Kankainen M, Huhtinen H, Tynkkynen S, Salminen S, de Vos WM, Palva A. Mucosal adhesion properties of the probiotic Lactobacillus rhamnosus GG SpaCBA and SpaFED pilin subunits. Appl Environ Microbiol 2010; 76: 2049-2057
28. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007; 2: 953-971
29. Ventura M, Lee JH, Canchaya C, Zink R, Leahy S, Moreno-Munoz JA, O'Connell-Motherway M, Higgins D, Fitzgerald GF, O'Sullivan DJ, van Sinderen D. Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis. Appl Environ Microbiol 2005; 71: 8692-8705
30. Brussow H. Phages of dairy bacteria. Annu Rev Microbiol 2001; 55: 283-303
31. Touchon M, Rocha EP. Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 2007; 24: 969-981
32. Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol 2006; 62: 718-729
33. O'Driscoll J, Heiter DF, Wilson GG, Fitzgerald GF, Roberts R, van Sinderen D. A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system. BMC Microbiol 2006; 6: 40
34. FEEDAP. Prepared by the Panel on Additives and Products or Substances used in Animal Feed on the Update of the criteria used in the assessment of bacterial resistance to antibiotics of human or veterinary importance. EFSA 2008; 732: 1-15
35. Masco L, Van Hoorde K, De Brandt E, Swings J, Huys G. Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products. J Antimicrob Chemother 2006; 58: 85-94
36. Scott KP, Melville CM, Barbosa TM, Flint HJ. Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut. Antimicrob Agents Chemother 2000; 44: 775-777
37. Munakata S, Arakawa C, Kohira R, Fujita Y, Fuchigami T, Mugishima H. A case of D-lactic acid encephalopathy associated with use of probiotics. Brain Dev 2010; 32: 691-694
38. Bongaerts G, Bakkeren J, Severijnen R, Sperl W, Willems H, Naber T, Wevers R, van Meurs A, Tolboom J. Lactobacilli and acidosis in children with short small bowel. J Pediatr Gastroenterol Nutr 2000; 30: 288-293
39. Uchida H, Yamamoto H, Kisaki Y, Fujino J, Ishimaru Y, Ikeda H. D-lactic acidosis in short-bowel syndrome managed with antibiotics and probiotics. J Pediatr Surg 2004; 39: 634-636
40. Garai G, Dueñas MT, Irastorza A, Martín-Alvarez PJ, Moreno-Arribas MV. Biogenic amines in natural ciders. J Food Prot 2006; 69: 3006-3012
41. Silla Santos MH. Biogenic amines: their importance in foods. Int J Food Microbiol 1996; 29: 213-231
42. Garai G, Dueñas MT, Irastorza A, Moreno-Arribas MV. Biogenic amine production by lactic acid bacteria isolated from cider. Lett Appl Microbiol 2007; 45: 473-478
43. Benno Y, Mitsuoka T. Impact of Bifidobacterium longum on human fecal microflora. Microbiol Immunol 1992; 36: 683-694
44. Kim Y, Lee D, Kim D, Cho J, Yang J, Chung M, Kim K, Ha N. Inhibition of proliferation in colon cancer cell lines and harmful enzyme activity of colon bacteria by Bifidobacterium adolescentis SPM0212. Arch Pharm Res 2008; 31: 468-473
45. Choi SS, Kang BY, Chung MJ, Kim SD, Park SH, Kim JS, Kang CY, Ha NJ. Safety assessment of potential lactic acid bacteria Bifidobacterium longum SPM1205 isolated from healthy Koreans. J Microbiol 2005; 43: 493-498
46. Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci USA 2008; 105: 13580-13585
47. Tanaka H, Doesburg K, Iwasaki T, Mierau I. Screening of lactic acid bacteria for bile salt hydrolase activity. J Dairy Sci 1999; 82: 2530-2535
48. Vankerckhoven V, Huys G, Vancanneyt M, Vael C, Klare I, Romond MB, Entenza JM, Moreillon P, Wind RD, Knol J, Wiertz E, Pot B, Vaughan EE, Kahlmeter G, Goossens H. Biosafety assessment of probiotics used for human consumption: recommendations from the EU-PROSAFE project. Trends in Food Sci and Technol 2008; 19: 102-114
49. Nagengast FM, Grubben MJ, van Munster IP. Role of bile acids in colorectal carcinogenesis. Eur J Cancer 1995; 31A: 1067-1070
50. Marteau P, Gerhardt MF, Myara A, Bouvier E, Trivin F, Rambaud JC. Metabolism of Bile Salts by Alimentary Bacteria During Transit in the Human Small Intestine. Micro Ecol in Heal and Dis 1995; 8: 151-157
51. Jones ML, Chen H, Ouyang W, Metz T, Prakash S. Microencapsulated Genetically Engineered Lactobacillus plantarum 80 (pCBH1) for Bile Acid Deconjugation and Its Implication in Lowering Cholesterol. J Biomed Biotechnol 2004; 2004: 61-69
52. Knaust A, Weber MV, Hammerschmidt S, Bergmann S, Frosch M, Kurzai O. Cytosolic proteins contribute to surface plasminogen recruitment of Neisseria meningitidis. J Bacteriol 2007; 189: 3246-3255
53. Lähteenmäki K, Kuusela P, Korhonen TK. Bacterial plasminogen activators and receptors. FEMS Microbiol Rev 2001; 25: 531-552
54. Candela M, Miccoli G, Bergmann S, Turroni S, Vitali B, Hammerschmidt S, Brigidi P. Plasminogen-dependent proteolytic activity in Bifidobacterium lactis. Microbiology 2008; 154: 2457-2462
55. Candela M, Bergmann S, Vici M, Vitali B, Turroni S, Eikmanns BJ, Hammerschmidt S, Brigidi P. Binding of human plasminogen to Bifidobacterium. J Bacteriol 2007; 189: 5929-5936
56. Candela M, Centanni M, Fiori J, Biagi E, Turroni S, Orrico C, Bergmann S, Hammerschmidt S, Brigidi P. DnaK from Bifidobacterium animalis subsp. lactis is a surface-exposed human plasminogen receptor upregulated in response to bile salts. Microbiology 2010; 156: 1609-1618
57. Luck SN, Turner SA, Rajakumar K, Sakellaris H, Adler B. Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes. Infect Immun 2001; 69: 6012-6021
58. Satin B, Del Giudice G, Della Bianca V, Dusi S, Laudanna C, Tonello F, Kelleher D, Rappuoli R, Montecucco C, Rossi F. The neutrophil-activating protein (HP-NAP) of Helicobacter pylori is a protective antigen and a major virulence factor. J Exp Med 2000; 191: 1467-1476
59. Verbelen C, Dufrêne YF. Direct measurement of Mycobacterium-fibronectin interactions. Integr Biol (Camb) 2009; 1: 296-300
60. Lee JH, Karamychev VN, Kozyavkin SA, Mills D, Pavlov AR, Pavlova NV, Polouchine NN, Richardson PM, Shakhova VV, Slesarev AI, Weimer B, O'Sullivan DJ. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 2008; 9: 247
61. Gaillot O, Pellegrini E, Bregenholt S, Nair S, Berche P. The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes. Mol Microbiol 2000; 35: 1286-1294
62. Alfaleh K, Anabrees J, Bassler D. Probiotics reduce the risk of necrotizing enterocolitis in preterm infants: a meta-analysis. Neonatology 2010; 97: 93-99
63. McFarland LV. Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease. Am J Gastroenterol 2006; 101: 812-822
64. Mach T. Clinical usefulness of probiotics in inflammatory bowel diseases. J Physiol Pharmacol 2006; 57 Suppl 9: 23-33
65. Parvez S, Malik KA, Ah Kang S, Kim HY. Probiotics and their fermented food products are beneficial for health. J Appl Microbiol 2006; 100: 1171-1185