Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium

Microbiology

Volumn 77, Issue 3, 2008, Pages 251-260

  Sidarenka, A V ^a   Novik, G I ^a   Akimov, V N ^b  

^a INSTITUTE OF MICROBIOLOGY   (Belarus)

^b SKRYABIN INSTITUTE OF BIOCHEMISTRY AND PHYSIOLOGY OF MICROORGANISMS   (Russian Federation)

Author keywords

Bifidobacteria; Classification; Identification; Molecular methods

Indexed keywords

BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM;

EID: 45749154868     PISSN: 00262617     EISSN: None     Source Type: Journal    
DOI: 10.1134/S0026261708030016     Document Type: Review

References (76)

1. Gomes, A.M. and Malcata, F.X., Bifidobacterium spp. and Lactobacillus acidophilus: Biological, Biochemical, Technological and Therapeutical Properties Relevant for Use as Probiotics, Trends in Food Science & Technology, 1999, no. 10, pp. 139-157.
2. Nebra, Y. and Blanch, A.R., A New Selective Medium for Bifidobacterium spp., Appl. Environ. Microbiol., 1999, vol. 65, no. 11, pp. 5173-5176.
3. Leahy, S.C., Higgins, D.G., Fitzgerald, G.F., and van Sinderen, D., Getting Better with Bifidobacteria, J. Appl. Microbiol., 2005, no. 98, pp. 1303-1315.
4. Ventura, M., van Sinderen, D, Fitzgerald, G.F., and Zink, R., Insights Into the Taxonomy, Genetics and Physiology of Bifidobacteria, Antonie van Leeuwenhoek, 2004, no. 86, pp. 205-223.
5. O'sullivan, D.J. and Kullen, M.J., Tracking of Probiotic Bifidobacteria in the Intestine, Int. Dairy J., 1998, vol. 8, pp. 513-525.
6. Vaughan, E.E., Heilig, H.G.H.J., Zoetendal, E.G., Satokari, R., Collins, J.K., Akkermans, A.D.L., and de Voss, W.M., Molecular Approaches To Study Probiotic Bacteria, Trends in Food Science & Technology, 1999, no. 10, pp. 400-404.
7. O'sullivan, D.J., Methods for Analysis of the Intestinal Microflora, Curr. Iss. Intest. Microbiol., 2000, no. 1, pp. 39-50.
8. Zoetendal, E.G., Collier, C.T., Koike, S., Mackie, R.I., and Gaskins, H.R., Molecular Ecological Analysis of the Gastrointestinal Microbiota: a Review, J. Nutr., 2004, vol. 134, pp. 465-472.
9. Ward, P. and Roy, D., Review of Molecular Methods for Identification, Characterization and Detection of Bifidobacteria, Lait, 2005, vol. 85, pp. 23-32.
10. Tissier, H., Recherches sur la flore intestinale des nourrissons (etat normal et pathologique), Paris Theses, 1900, pp. 1-253.
11. Orla-Jensen, S., La classification des bacteries lactiques, Lait, 1924, no. 4, pp. 468-474.
12. Poupard, J.A., Husain, I., and Norris, R.F., Biology of the Bifidobacteria, Bacteriol. Rev., 1973, vol. 37, no. 2, pp. 136-165.
13. AL, in Bergey's Manual of Systematic Bacteriology, 1st ed., Sneath, P.H.A., Mayr, N.S., Sharpe, M.E., and Holt, J.G., Eds., Baltimore: Williams and Wilkins, 1986, vol. 2, pp. 1418-1434.
14. Arunachalam, K.D., Role of Bifidobacteria in Nutrition, Medicine and Technology, Nutrit. Res., 1999, vol. 19, no. 10, pp. 1559-1597.
15. de Vuyst, L., Application of Functional Starter Cultures, Food Technol. Biotechnol., 2000, no. 38, pp. 105-112.
16. Simpson, P.J., Ross, R.P., Fitzgerald, G.F., and Santon, C., Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., Isolated from Porcine Caecum, Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 401-406.
17. Scardovi, V. and Trovatelli, L.D., The Fructose-6-Phosphate Shunt as a Peculiar Pattern of Hexose Degradation in the Genus Bifidobacterium, Ann. Microbiol. Enzymol., 1965, vol. 15, pp. 19-29.
18. de Vries, W. and Stouthamer, A.H., Pathway of Glucose Fermentation in Relation To the Taxonomy of Bifidobacteria, J. Bacteriol., 1967, vol. 93, pp. 574-576.
19. Gavini, F., van Esbroeck, M., Touzel, J.P., Fourment, A., and Goosens, H., Detection of Fructose-6-Phosphate Phosphoketolase (F6PPK), a Key Enzyme of the Bifid-Shunt, in Gardnerella vaginalis, Anaerobe, 1996, vol. 2, pp. 191-193.
20. Sebald, M., Gasser, F., and Werner, H., Teneru GC% et classification. Application au groupe des bifidobacteries et a quelques genres voising, Ann. Inst. Pasteur, 1965, no. 109, pp. 259-269.
21. Goodfellow, M., Suprageneric Classification of Actinomycetes, in Bergey's Manual of Systematic Bacteriology, 1st ed., Williams, S.A., Sharpe, M.E., and Holt, J.G., Eds., Baltimore: Williams and Wilkins, 1989, vol. 4, pp. 2333-2339.
22. AL, in Bergey's Manual of Systematic Bacteriology, 1st ed., Williams, S.A., Sharpe, M.E., and Holt, J.G., Eds., Baltimore: Williams and Wilkins, 1989, vol. 4, pp. 2379-2382.
23. AL, in Bergey's Manual of Determinative Bacteriology, Buchanan, R.E. and Gibbons, N.E., Eds., Baltimore: Williams and Wilkins, 1974, pp. 669-676.
24. Euzeby, J.P., List of Prokaryotic Names with Standing in Nomenclature-Genus Bifidobacterium, J.P. Uzeby SBSV, 2007, http://www.bacterio. cict.fr.
25. Dehnert, J., Untersuchung uber die grampositive Stuhlflora des Brustmilchkindes, Zentralbl. Bacteriol. Parasitenk. Infektionskr. Hyg. Abt. Orig., 1957, no. 169, pp. 66-79.
26. Reuter, G., Vergleichende Untersuchungen uber die Bifidus-Flora in Sauglings und Erwachsenenstuhl, Zentralbl. Bakteriol. Parasitenk. Hyg. Abt. Orig., 1963, no. 191, pp. 486-507.
27. Mitsuoka, T., Vergleichende Untersuchungen uber die Bifidobakterien aus dem Verdauungstrakt von Menschen und Tieren, Zentralbl. Bakteriol. Parasitenk. Hyg. Abt. Orig., 1969, no. 210, pp. 52-64.
28. Scardovi, V., Trovatelli, L.D., Zani, G., Crociani, F., and Metteuzzi, D., Deoxyribonucleic Acid Homology Relationships Among Species of the Genus Bifidobacterium, Int. J. Syst. Bacteriol., 1971, no. 21, pp. 276-294.
29. Holdeman, L.V. and Moore, W.E.C., Anaerobe laboratory manual., Blacksburg: Virginia Polytechnic Institute and State University, 1972.
30. AL, in Bergey's Manual of Systematic Bacteriology, Sneath, P.E., Mair, N.S., and Sharpe, M.E., Eds., Baltimore: Williams and Wilkins, 1986, vol. 2, pp. 1209-1234.
31. Holzapfel, W.H., Haberer, P., Geisen, R., Bjorkroth, J., and Schillinger, U., Taxonomy and Important Features of Probiotic Microorganisms in Food and Nutrition, Amer. J. Clin. Nutrit, 2001, vol. 73, no. 2, pp. 365-373.
32. Bannikova, L.A., Koroleva, N.S., and Semenikhina, V.F., Mikrobiologicheskie osnovy molochnogo proizvodstva: spravochnik (Microbiological Basics of Diary Industry: a Manual), Kostin, Ya.I., Ed., Moscow: Agropromizdat, 1987.
33. Klein, G., Pack, A., Bonaparte, C., and Reuter, G., Taxonomy and Physiology of Probiotic Lactic Acid Bacteria, Int. J. Food Microbiol., 1998, no. 41, pp. 103-125.
34. Zhu, L., Li, W., and Dong, X., Species Identification of Genus Bifidobacterium Based on Partial HSP60 Gene Sequences and Proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov., Int. J. Syst. Evol. Microbiol., 2003, vol. 53, pp. 1619-1623.
35. Matsuki, T., Watanabe, K., Tanaka, R., and Oyaizu, H., Rapid Identification of Human Intestinal Bifidobacteria by 16S rRNA-Targeted Species-and Group-Specific Primers, FEMS Microbiol. Lett., 1998, vol. 167, pp. 113-121.
36. Yeung, P.S.M., Sanders, M.E., Kitts, C.L., Cano, R., and Tong, P.S., Species-Specific Identification of Commercial Probiotic Strains, J. Dairy Sci., 2002, no. 85, pp. 1039-1051.
37. Biavati, B., Sgorbati, B., and Scardovi, V., The Genus Bifidobacterium, in The Procaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Application, Balows, A., Ed., New York: Springer, 1992, pp. 816-833.
38. Roy, D., Berger, J.L., and Reuter, G., Characterization of Dairy-Related Bifidobacterium spp. Based on Their Beta-Galactosidase Electrophoretic Patterns, Int. J. Food Microbiol., 1994, vol. 23, pp. 55-70.
39. Woese, C.R., Bacterial Evolution, Microbiol. Rev., 1987, vol. 51, pp. 221-271.
40. Stackebrandt, E., Rainey, F.A., and Ward-Rainey, N.L., Proposal for a New Hierarchic Classification System, Actinobacteria classis nov., Int. J. Syst. Bacteriol., 1997, no. 47, pp. 479-491.
41. Leblond-Bourget, N., Philippe, H., Mangin, I., and Decaris, B., 16S rRNA and 16S to 23S Internal Transcribed Spacer Sequence Analyses Reveal Inter-and Intraspecific Bifidobacterium Phylogeny, Int. J. Syst. Bacteriol., 1996, no. 56, pp. 102-111.
42. Jian, W. and Dong, X., Transfer of Bifidobacterium inopinatum and Bifidobacterium denticolens to Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov., Respectively, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 809-812.
43. Schleifer, K.H. and Ludwig, W., Phylogeny of the Genus Lactobacillus and Related Genera, Syst. Appl. Microbiol., 1995, no. 18, pp. 461-467.
44. Schleifer, K.H. and Ludwig, W., Phylogenetic Relationships of Lactic Acid Bacteria, The Genera of Lactic Acid Bacteria, Wood, B.J.B. and Holzapfel W.H, Eds., London: Chapman and Hall, 1995, pp. 7-18.
45. Stackebrandt, E. and Goebel, B.M., Taxonomic Note: a Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology, Int. J. Syst. Bacteriol., 1994, no. 44, pp. 846-849.
46. Lauer, E. and Kandler, O., DNA-DNA Homology, Murein Type and Enzyme Patterns in the Type Strains of the Genus Bifidobacterium, Syst. Appl. Microbiol., 1983, vol. 4, pp. 42-64.
47. Sakata, S., Kitahara, M., Sakamoto, M., Hayashi, H., Fukuyama, M., and Benno, Y., Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobacterium longum, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 1945-1951.
48. International Committee on Systematics of Prokaryotes; Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of meetings, 1-2 April 2005, Stuttgart-Hohenheim, Germany, Int. J. Syst. Evol. Microbiol., 2006, V. 56. P. 2501-2503.
49. Miyake, T., Watanabe, K., Watanabe, T., and Oyaizu, H., Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences, Microbiol. Immunol., 1998, no. 42, pp. 661-667.
50. Jian, W., Zhu, L., and Dong, X., New Approach to Phylogenetic Analysis of the Genus Bifidobacterium Based on Partial HSP60 Gene Sequences, Int. J. Syst. Bacteriol., 1991, vol. 41, pp. 548-557.
51. Ventura, M., Canchaya, C., Meylan, V., Klaenhammer, T.R., and Zink, R., Analysis, Characterization and Loci of the tuf Genes in Lactobacillus and Bifidobacterium Species and Their Direct Application for Species Identification, Appl. Environ. Microbiol., 2003, vol. 69, pp. 7517-7522.
52. Ventura, M., Canchaya, C., Casale, A.D., Dellaglio, F., Neviani, E., Fitzgerald, G.F., and van Sinderen, D., Analysis of Bifidobacterial Evolution Using a Multilocus Approach, Int. J. Syst. Evol. Microbiol, 2006, vol. 56, pp. 2783-2792.
53. McCartney, A.L., Wenzhi, W., and Tannock, G.W., Molecular Analysis of the Composition of the Bifidobacterial and Lactobacillus Microflora of Humans, Appl. Environ. Microbiol., 1996, vol. 62, pp. 4608-4613.
54. Farber, J.M., An Introduction to the Hows and Whys of Molecular Typing, J. Food Prot., 1996, no. 59, pp. 1091-1101.
55. Sakata, S., Ryu, C.S., Kitahara, M., Sakamoto, M., Hayashi, H., Fukuyama, M., and Benno, Y., Characterization of the Genus Bifidobacterium by Automated Ribotyping 16S rRNA Gene Sequences, Microbiol. Immunol., 2006, vol. 50, pp. 1-10.
56. Stach, J.E.M., Maldonado, L.A., Ward, A.C., Goodfellow, M., and Bull, A.T., New Primers for the Class Actinobacteria: Application to Marine and Terrestrial Environments, Environ. Microbiol., 2003, vol. 5, pp. 828-841.
57. Kok, R.G., Waal, A.D., Schut, F., Welling, G.W., Weenk, G., and Helligwerf, K.J., Specific Detection and Analysis of Probiotic Bifidobacterium Strain in Infant Feces, Appl. Environ. Microbiol., 1996, vol. 62, pp. 3668-3672.
58. Kaufmann, P., Pfefferkorn, A., Teuber, M., and Meile, L., Identification and Quantification of Bifidobacterium Species Isolated from Food with Genus-Specific 16S rRNA-Targeted Probes by Colony Hybridization and PCR, Appl. Environ. Microbiol., 1997, vol. 63, pp. 1268-1273.
59. Matsuki, T., Watanabe, K., and Tanaka, R., Genus-and Species-Specific PCR Primers for the Detection and Identification of Bifidobacteria, Curr. Issues Intest. Microbiol., 2003, vol. 4, pp. 61-69.
60. Ventura, M., Reniero, R., and Zink, R., Specific Identification and Targeted Characterization of Bifidobacterium lactis from Different Environmental Isolates by a Combined Multiplex-PCR Approach, Appl. Environ. Microbiol., 2001, vol. 67, pp. 2760-2765.
61. Roy, D. and Sirois, S., Molecular Differentiation of Bifidobacterium Species with Amplified Ribosomal DNA Restriction Analysis and Alignment of Short Regions of the ldh Gene, FEMS Microbiol. Lett., 2000, vol. 191, no. 1, pp. 17-24.
62. Ventura, M., Elli, M., Reniero, R., and Zink, R., Molecular Microbial Analysis of Bifidobacterium Isolates from Different Environments by the Species-Specific Amplified Ribosomal DNA Restriction Analysis (ARDRA), FEMS Microbiol. Ecol., 2001, vol. 36, nos. 2-3, pp. 113-121.
63. Mangin, I., Bourget, N., Bouhnik, Y., Bisetti, N., Simonet, J.M., and Decaris, B., Identification of Bifidobacterium Strains by RRNA Restriction Patterns, Appl. Environ. Microbiol., 1994, vol. 60, pp. 1451-1458.
64. Barry, T., Colleran, G., Glennon, M., Dunican, L.K., and Gannon, F., The 16S/23S Ribosomal Spacer Region as a Target for DNA Probes To Identify Eubacteria, PCR Methods and Applications, 1991, no. 1, pp. 51-56.
65. Ventura, M. and Zink, R., Rapid Identification, Differentiation and Proposed New Taxonomic Classification of Bifidobacterium lactis, Appl. Environ. Microbiol., 2002, vol. 68, pp. 6429-6434.
66. Kullen, M.J., Brady, L.J., and O'sullivan, D.J., Evaluation of Using a Short Region of the recA Gene for the Rapid and Sensitive Speciation of Dominant Bifidobacteria in the Human Large Intestine, FEMS Microbiol. Lett., 1997, vol. 154, pp. 377-383.
67. Ventura, M. and Zink, R., Comparative Sequence Analysis of the tuf and recA Genes and Restriction Fragment Length Polymorphism of the Internal Transcribed Spacer Region Sequences Supply Additional Tools for Discriminating Bifidobacterium lactis from Bifidobacterium animalis, Appl. Environ. Microbiol., 2003, vol. 69, pp. 7517-7522.
68. Requena, T., Burton, J., Matsuki, T., Munro, K., Simon, M.A., Tanaka, R., Watanabe, K., and Tannock, G.W., Identification, Detection, and Enumeration of Human Bifidobacterium Species by PCR Targeting the Transaldolase Gene, Appl. Environ. Microbiol., 2002, vol. 68, pp. 2420-2427.
69. Satokari, R.M., Vaughan, E.E., Smidt, H., Saarela, M., Matto, J., and de Vos, W.M., Molecular Approaches for the Detection and Identification of Bifidobacteria and Lactobacilli in the Human Gastrointestinal Tract, Syst. Appl. Microbiol., 2003, vol. 26, pp. 572-584.
70. Simpson, P.J., Stanton, C., Fitzgerald, G.F., and Ross, R.P., Genomic Diversity and Relatedness of Bifidobacteria Isolated from a Porcine Cecum, J. Bacteriol., 2003, vol. 185, no. 8, pp. 2571-2581.
71. Vincent, D., Roy, D., Mondou, F., and Dery, C., Characterization of Bifidobacteria by Random DNA Amplification, Int. J. Food Microbiol., 1998, no. 43, pp. 185-193.
72. Fanedl, L., Nekrep, F.V., and Avgustin, G., Random Amplified Polymorphic DNA Analysis and Demonstration of Genetic Variability among Bifidobacteria Isolated from Rats Fed with Raw Kidney Beans, Can. J. Microbiol., 1998, vol. 44, pp. 1094-1101.
73. Ventura, M., Meylan, V., and Zink, R., Identification and Tracing of Bifidobacterium Species by Use of Enterobacterial Repetitive Intergenic Consensus Sequences, Appl. Environ. Microbiol., 2003, vol. 69, no. 7, pp. 4296-4301.
74. Masco, L., Huys, G., Gevers, D., Verbugghen, L., and Swings, J., Identification of Bifidobacterium Species Using rep-PCR Fingerprinting, Syst. Appl. Microbiol., 2003, vol. 26, pp. 557-563.
75. Yamamoto, T., Morotomi, M., and Tanaka, R., Species-Specific Oligonucleotide Probes for Five Bifidobacterium Species Detected in Human Intestinal Microflora, Appl. Environ. Microbiol., 1992, vol. 58, pp. 4076-4079.
76. Hayashi, H., Takahashi, R., Nishi, T., Sakamoto, M., and Benno, Y., Molecular Analysis of Jejunal, Ileal, Caecal and Rectosigmoidal Human Colonic Microbiota Using 16S rRNA Gene Libraries and Terminal Restriction Fragment Length Polymorphism, J. Med. Microbiol., 2005, no. 54, pp. 1093-1101.