Bifidobacteria: the Model Human Gut Commensal

Marco Ventura; Francesca Turroni; Angela Ribbera; Elena Foroni; Douwe van Sinderen

doi:10.1128/9781555815462.ch4

Chapter 4 : Bifidobacteria: the Model Human Gut Commensal

Authors: Marco Ventura¹, Francesca Turroni², Angela Ribbera³, Elena Foroni⁴, Douwe van Sinderen⁵

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Affiliations: 1: Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy; 2: Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy; 3: Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy; 4: Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy; 5: Alimentary, Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland

Content Type: Monograph

Publication Year: 2008

Category: Clinical Microbiology

Book DOI: 10.1128/9781555815462

Chapter DOI: 10.1128/9781555815462.ch4

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Abstract:

This chapter discusses biology of bifidobacteria for probiotic and replacement therapy. Bifidobacteria were originally isolated from a breast-fed infant. Since then several species have been identified in the gastrointestinal tract (GIT) of mammals and insects. The availability of whole-genome sequences from bifidobacteria is extremely informative for the understanding of the processes underlying speciation and evolution in this genus as well as the adaptation to its specific habitat (e.g., the human intestine). Since bifidobacteria encounter a vast array of substrates in the GIT, information regarding their metabolic properties is crucial to formulate an optimal growth medium. Prebiotics are food substances which resist digestion in the proximal GIT and reach intact the distal region of the gut, where, besides their direct physiological effect, they also affect the GIT ecosystem by specifically stimulating the growth and activity of the probiotic components of the GIT microbiota (e.g., bifidobacteria), thereby eliciting a beneficial effect on the host’s health. Prebiotics are typically oligosaccharides that consist of a mixture of hexose oligomers with a variable extent of polymerization. The transmission of novel genes through horizontal gene transfer (HGT) is generally supported by vectors such as bacteriophages or plasmids which may become integrated into the bacterial chromosome. Generally, plasmids are rarely found in bifidobacteria. So far the majority of bifidobacterial plasmids have been identified within different B. longum biotype longum strains. The chapter ends with a discussion on taxonomy of bifidobacteria.

Citation: Ventura M, Turroni F, Ribbera A, Foroni E, Sinderen D. 2008. Bifidobacteria: the Model Human Gut Commensal, p 35-51. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch4

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16s rRNA Sequencing: 0.41716915
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Bifidobacteria: the Model Human Gut Commensal

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Figure 1

Photomicrographs showing representative bifidobacterial cell shapes. (A) B. animalis subsp. lactis; (B) B. longum biotype longum; (C) B. pseudolongum.

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Figure 1

Photomicrographs showing representative bifidobacterial cell shapes. (A) B. animalis subsp. lactis; (B) B. longum biotype longum; (C) B. pseudolongum.

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Figure 2

Phylogenetic tree of the genus Bifidobacterium based on the 16S rRNA gene sequences (left) and from the concatenation of clpC, dnaB, dnaG, dnaJ1, purF, rpoC, and xfp gene sequences (right). The different phylogenetic groups are indicated.

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Figure 2

References

/content/book/10.1128/9781555815462.ch04

1. Alvarez-Martin, P.,, A. B. Florez, and, B. Mayo. 2006. Screening for plasmids among human bifidobacteria species: sequencing and analysis of pBC1 from Bifidobacterium catenulatum L48. Plasmid 57:165–174.

2. Amann,, R. I.,, W. Ludwig, and, K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143–169.

3. Bengmark, S. 2002. Gut microbial ecology in critical illness: is there a role for prebiotics, probiotics, and synbiotics? Curr. Opin. Crit. Care 8:145–151.

4. Biavati, B., and, P. Mattarelli. 2001. The family Bifidobacteriaceae. In M. Dworkin et al. (ed.), The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community. http://www.bacterialphylogeny.info/index.html.

5. Bininda-Emonds,, O. R. P. 2004. The evolution of supertrees. Trends Ecol. Evol. 19:315–322.

6. Blaut, M. 2002. Relationship of prebiotics and food to intestinal microflora. Eur. J. Nutr. 41:I/11–I/16.

7. Bouhnik, Y.,, B. Flourie, and, M. Riottot. 1996. Effect of fructooligosaccharides ingestion on faecal bifidobacteria and selected metabolic index of colon carcinogenesis in healthy humans. Nutr. Cancer 26:21–29.

8. Brown,, D. P.,, K. B. Idler, and, L. Katz. 1990. Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea. J. Bacteriol. 172:1877–1888.

9. Brown,, J. R.,, C. J. Douady,, M. J. Italia,, W. E. Marshall, and, M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281–285.

10. Campbell,, A. M. 1992. Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174:7495–7499.

11. Chan,, K.,, S. Baker,, C. C. Kim,, C. S. Detweiler,, G. Dougan, and, S. Falkow. 2003. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. J. Bacteriol. 185:553–563.

12. Christensen,, B. B.,, T. Atlung, and, F. G. Hansen. 1999. DnaA boxes are important elements in setting the initiation mass of Escherichia coli. J. Bacteriol. 181:2683–2688.

13. Coenye, T.,, D. Gevers,, Y. Van de Peer,, P. Vandamme, and, J. Swings. 2005. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29:147–167.

14. Cohan,, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50:513–524.

15. Conway,, P. L. 2001. Prebiotics and human health: the state-of-the-art and future perspectives. Scand. J. Nutr. 45:13–21.

16. Corneau, N.,, E. Emond, and, G. LaPointe. 2004. Molecular characterization of three plasmids from Bifidobacterium longum. Plasmid 51:87–100.

17. Coutinho,, P. M., and, B. Henrissat. 1999. Life with no sugars? J. Mol. Microbiol. Biotechnol. 1:307–308.

18. Degnan,, B. A., and, G. T. Macfarlane. 1993. Transport and metabolism of glucose and arabinose in Bifidobacterium breve. Arch. Microbiol. 160:144–151.

19. Delzenne,, N. M. 2003. Oligosaccharides: state of the art. Proc. Nutr. Soc. 62:177–182.

20. Dobrindt,, U.,, F. Agerer,, K. Michaelis,, A. Janka,, C. Buchrieser,, M. Samuelson,, C. Svanborg,, G. Gottschalk,, H. Karch, and, J. Hacker. 2003. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J. Bacteriol. 185:1831–1840.

21. Favier,, C. F.,, E. E. Vaughan,, W. M. De Vos, and, A. D. Akkermans. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68:219–226.

22. Fitzgerald,, J. R.,, D. E. Sturdervant,, S. M. Mackie,, S. R. Gill, and, J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strain and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98:8821–8826.

23. Franks,, A. H.,, H. J. Harmsen,, G. C. Raangs,, G. J. Jansen,, F. Schut, and, G. W. Welling. 1998. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:3336–3345.

24. Fuller, R. 1989. Probiotics in man and animals. J. Appl. Bacteriol. 66:365–378.

25. Gao, B., and, R. S. Gupta. 2005. Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int. J. Syst. Evol. Microbiol. 55:2401–2412.

26. Gao, B., and, R. S. Gupta. 2006. Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups. Antonie Leeuwenhoek 90:69–91.

27. Garrity,, G. M., and, J. G. Holt. 2001. The road map to the manual. In D. R. Boone and, R. W. Castenholz (ed.), Bergey’s Manual of Systematic Bacteriology. Springer-Verlag, Berlin, Germany.

28. Garro,, M. S.,, G. F. de Valdez,, G. Oliver, and, G. S. de Giori. 1999. Hydrolysis of soya milk oligosaccharides by Bifidobacterium longum CRL 849. Z. Lebensm. Unters. Forsch. A 208:57–59.

29. Gibbs,, M. J.,, W. Smeianov,, J. L. Steel,, P. Upcroft, and, B. A. Efimov. 2006. Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. Mol. Biol. Evol. 23:1097–1100.

30. Gibson,, G. R. 2004. Prebiotics. Best Pract. Res. Clin. Gastroenterol. 18:287–298.

31. Gibson,, G. R., and, M. B. Roberfroid. 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125:1401–1412.

32. Guarner, F., and, J. R. Malagelada. 2003. Gut flora in health and disease. Lancet 361:512–519.

33. Guglielmetti, S.,, M. Karp,, D. Mora,, I. Tamagnini, and, C. Parini. 2007. Molecular characterization of Bifidobacterium longum biovar longum NAL8 plasmids and construction of a novel replicon screening system. Appl. Microbiol. Biotechnol. 74:1053–1061.

34. Hopkins,, M. J.,, R. Sharp, and, G. T. Macfarlane. 2001. Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48:198–205.

35. Hopkins,, M. J.,, R. Sharp, and, G. T. Macfarlane. 2002. Variation in human intestinal microbiota with age. Dig. Liver Dis. 34:12–18.

36. Hoskins,, L. C.,, M. Agustines,, W. B. McKee,, E. T. Boulding,, M. Kriaris, and, G. Niedermeyer. 1985. Mucin degradation in human colon ecosystems. Isolation and properties of fecal strains that degrade ABH blood group antigens and oligosaccharides from mucin glycoproteins. J. Clin. Investig. 75:944–953.

37. Hung,, M. N.,, Z. Xia,, N. T. Hu, and, B. H. Lee. 2001. Molecular and biochemical analysis of two β-galactosidases from Bifidobacterium infantis HL96. Appl. Environ. Microbiol. 67:4256–4263.

38. Ivanov,, D.,, C. Emonet,, F. Foata,, M. Affolter,, M. Delley,, M. Fisseha,, S. Blum-Sperisen,, S. Kochhar, and, F. Arigoni. 2006. A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases. J. Biol. Chem. 281:17246–17252.

39. Jian, W.,, L. Zhu, and, X. Dong. 2001. New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int. J. Syst. Evol. Microbiol. 51:1633–1638.

40. Johnson,, I. T. 2004. New approaches to the role of diet in the prevention of cancers of the alimentary tract. Mutat. Res. 551:9–28.

41. Klaenhammer,, T. R.,, R. Barrangou,, B. L. Buck,, M. A. Azcarate-Peril, and, E. Altermann. 2005. Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiol. Rev. 29:393–409.

42. Krinos,, C. M.,, M. J. Coyne,, K. G. Weinacht,, A. O. Tzianabos,, D. L. Kasper, and, L. E. Comstock. 2001. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 414:555–558.

43. Kruse,, H. P.,, B. Kleessen, and, M. Blaut. 1999. Effects of inulin on faecal bifidobacteria in human subjects. Br. J. Nutr. 82:375–382.

44. Kullen,, M. J.,, L. J. Brady, and, D. J. O’Sullivan. 1997. Evaluation of using a short region of the recA gene for rapid and sensitive speciation of dominant bifidobacteria in the human large intestine. FEMS Microbiol. Lett. 154:377–383.

45. Langendijk,, P. S.,, F. Shut,, G. J. Jansen,, G. C. Raangs,, G. R. Kamphuis,, M. H., F. Wilkinson, and, G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:3069–3075.

46. Lay,, C.,, M. Sutren,, V. Rochet,, K. Saunier,, J. Dore, and, L. Rigottier-Gois. 2005. Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Environ. Microbiol. 7:933–946.

47. Leahy,, S. C.,, D. G. Higgins,, G. F. Fitzgerald, and, D. van Sinderen. 2005. Getting better with bifidobacteria. J. Appl. Microbiol. 98:1303–1315.

48. Lecuit,, M.,, S. Vandormael-Pournin,, J. Lefort,, M. Huerre,, P. Gounon,, C. Dupuy,, C. Babinet, and, P. Cossart. 2001. A transgenic model for listeriosis: role of internalin in crossing the intestinal barrier. Science 292:1722–1725.

49. Lee,, J. H., and, D. J. O’Sullivan. 2006. Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl. Environ. Microbiol. 72:527–535.

50. Liepke,, C.,, K. Adermann,, M. Raida,, H. J. Magert,, W. G. Forss-mann, and, H. D. Zucht. 2002. Human milk provides peptides highly stimulating the growth of bifidobacteria. Eur. J. Biochem. 269:712–718.

51. Liu, M.,, G. van Enckevort, and, R. J. Siezen. 2005. Genome update: lactic acid bacteria genome sequencing is booming. Microbiology 151:3811–3814.

52. Mahairas,, G. G.,, P. J. Sabo,, M. J. Hickey,, D. C. Singh, and, C. K. Stover. 1996. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J. Bacteriol. 178:1274–1282.

53. Manning,, T. S., and, G. R. Gibson. 2004. Microbial-gut interactions in health and disease. Prebiotics. Best Pract. Res. Clin. Gastroenterol. 18:287–298.

54. Marteau, P. 2001. Prebiotics and probiotics for gastrointestinal health. Clin. Nutr. 20:41–45.

55. Martin,, M. C.,, J. C. Alonso,, J. E. Suarez, and, M. A. Alvarez. 2000. Generation of food-grade recombinant lactic acid bacterium strains by site-specific recombination. Appl. Environ. Microbiol. 66:2599–2604.

56. Masco, L.,, M. Ventura,, R. Zink,, G. Huys, and, J. Swings. 2004. Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis comb. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis comb. nov. Int. J. Syst. Evol. Microbiol. 54:1137–1143.

57. Matsuki, T.,, K. Watanabe,, R. Tanaka,, M. Fukuda, and, H. Oyaizu. 1999. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 65:4506–4512.

58. Mattarelli, P.,, B. Biavati,, A. Alessandrini,, F. Crociani, and, V. Scardovi. 1994. Characterization of the plasmid pVS808 from Bifidobacterium globosum. New Microbiol. 17:327–331.

59. Maze,, A.,, M. O’Connell-Motherway,, G. F. Fitzgerald,, J. Deutscher, and, D. van Sinderen. 2007. Identification and characterization of a fructose phosphotransferase system in Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 73:545–553.

60. McLean,, M. J.,, K. H. Wolfe,, and K. M. Devine. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:691–696.

61. Mengaud, J.,, H. Ohayon,, P. Gounon,, R. M. Mege, and, P. Cossart. 1996. E-cadherin is the receptor for internalin, a surface protein required for entry of L. monocytogenes into epithelial cells. Cell 84:923–932.

62. Moller,, P. L.,, F. Jorgensen,, O. C. Hansen,, S. M. Madsen, and, P. Stougaard. 2001. Intra- and extracellular β-galactosidases from Bifidobacterium bifidum and B. infantis. Molecular cloning, heterologous expression, and comparative characterization. Appl. Environ. Microbiol. 67:2276–2283.

63. Ochman, H.,, J. G. Lawrence, and, E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304.

64. Oku, T. 1996. Oligosaccharides with beneficial health effects: a Japanese perspective. Nutr. Rev. 54(Part 2, Suppl. S): S59–S66.

65. O’Riordan, K., and, G. F. Fitzgerald. 1999. Molecular characterisation of a 5. 75-kb cryptic plasmid from Bifidobacterium breve NCFB 2258 and determination of mode of replication. FEMS Microbiol. Lett. 174:285–294.

66. Osterman, A., and, R. Overbeek. 2003. Missing genes in metabolic pathways: a comparative genomic approach. Curr. Opin. Chem. Biol. 7:238–251.

67. Park,, M. S.,, K. H. Lee, and, G. E. Ji. 1997. Isolation and characterization of two plasmids from Bifidobacterium longum. Lett. Appl. Microbiol. 25:5–7.

68. Peters,, J. E.,, T. E. Thate, and, N. L. Craig. 2003. Definition of the Escherichia coli MC4100 genome by use of a DNA array. J. Bacteriol. 185:2017–2021.

69. Poupard,, J. A.,, I. Husain, and, R. F. Norris. 1973. Biology of the bifidobacteria. Bacteriol. Rev. 37:136–165.

70. Rezzonico,, E.,, S. Lariani,, C. Barretto,, G. Cuanoud,, G. Giliberti,, M. Delley,, F. Arigoni, and, G. Pessi. 2007. Global transcriptome analysis of the heat response of Bifidobacterium longum. FEMS Microbiol. Lett. 271:136–145.

71. Roberfroid, M. 2007. Prebiotics: the concept revisited. J. Nutr. 137:830S–837S.

72. Roberfroid,, M. B. 2005. Introducing inulin-type fructans. Br. J. Nutr. 93(Suppl. 1):S13–S25.

73. Roberfroid,, M. B., and, N. M. Delzenne. 1998. Dietary fructans. Annu. Rev. Nutr. 18:117–143.

74. Rossi, M.,, P. Brigidi, and, D. Matteuzzi. 1998. Improved cloning vectors for Bifidobacterium spp. Lett. Appl. Microbiol. 26:101–104.

75. Ruas-Madiedo, P.,, M. Gueimonde,, C. G. de los Reyes-Gavilan, and, S. Salminen. 2006. Short communication: effect of exopolysaccharide isolated from “viili” on the adhesion of probiotics and pathogens to intestinal mucus. J. Dairy Sci. 89:2355–2358.

76. Ryan,, S. M.,, G. F. Fitzgerald, and, D. van Sinderen. 2006. Screening and identification of starch, amylopectin and pullulan-degrading activities in bifidobacterial strains. Appl. Environ. Microbiol. 72:5289–5296.

77. Sakai, K.,, T. Tachiki,, H. Kumagai, and, T. Tochikura. 1987. Hydrolysis of α-D-galactosyl oligosaccharides in soymilk by α-galactosidase of Bifidobacterium breve. Agric. Biol. Chem. 51:315–322.

78. Sakata,, S.,, M. Kitahara,, M. Sakamoto,, H. Hayashi,, M. Fukuyame, and, Y. Benno. 2002. Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobacterium longum. Int. J. Syst. Evol. Microbiol. 52:1945–1951.

79. Sanchez,, B.,, M. C. Champomier-Verges,, P. Anglade,, F. Baraige,, C. G. de Los Reyes-Gavilan,, A. Margolles, and, M. Zagorec. 2005. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J. Bacteriol. 187:5799–5808.

80. Savijoki,, K.,, A. Suokko,, A. Palva,, L. Valmu,, N. Kalkkinen, and, P. Varmanen. 2005. Effect of heat-shock and bile salts on protein synthesis of Bifidobacterium longum revealed by [35S]methionine labelling and two-dimensional gel electrophoresis. FEMS Microbiol. Lett. 248:207–215.

81. Schell,, M. A.,, M. Karmirantzou,, B. Snel, et al. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99:14422–14427.

82. Simmering, R., and, M. Blaut. 2001. Pro- and prebiotics—the tasty guardian angels? Appl. Microbiol. Biotechnol. 55:19–28.

83. Stackebrandt, E., and, P. Schumann. 2000. Introduction to the taxonomy of Actinobacteria. In M. Dworkin et al. (ed.), The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community. http://www.bacterialphylogeny.info/index.html.

84. Stackebrandt, E.,, F. A. Rainey, and, N. L. WardRainey. 1997. Proposal for a new hierarchic classification system, Actino-bacteria classis nov. Int. J. Syst. Bacteriol. 47:479–491.

85. Swennen, K.,, C. M. Courtin, and, J. A. Delcour. 2006. Non-digestible oligosaccharides with prebiotic properties. Crit. Rev. Food Sci. Nutr. 46:459–471.

86. Tanaka, K.,, K. Samura, and, Y. Kano. 2005. Structural and functional analysis of pTB6 from Bifidobacterium longum. Biosci. Biotechnol. Biochem. 69:422–425.

87. Tissier, H. 1900. Recherches sur la flore intestinale normale et pathologique du nourrisson. Thesis. University of Paris, Paris, France.

88. Vandamme,, P.,, B. Pot,, M. Gillis,, P. de Vos,, K. Kersters, and, J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407–438.

89. van den Broek,, L. A. M.,, S. W. A. Hinz,, G. Beldman, and, C. H. L. Doeswijk-Voragen. 2005. Glycosyl hydrolases from Bifidobacterium adolescentis DSM20083. Lait 85:125–133.

90. Vaughan,, E. E.,, H. G. Heilig,, K. Ben-Amor, and, W. M. de Vos. 2005. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol. Rev. 29:477–490.

91. Ventura, M., and, R. Zink. 2002. Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis. Appl. Environ. Microbiol. 68:6429–6434.

92. Ventura, M., and, R. Zink. 2003. 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. 69:7517–7522.

93. Ventura,, M.,, C. Canchaya,, D. van Sinderen,, G. F. Fitzgerald,, and R. Zink. 2004a. Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl. Environ. Microbiol. 70:3110–3121.

94. Ventura,, M.,, C. Canchaya,, R. Zink,, G. F. Fitzgerald, and, D. van Sinderen. 2004b. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses. Appl. Environ. Microbiol. 70:6197–6209.

95. Ventura,, M.,, C. Canchaya,, A. Del Casale,, F. Dellaglio,, G. F. Fitzgerald, and, D. van Sinderen. 2005a. Genetic characterization of the Bifidobacterium breve UCC 2003 hrcA locus. Appl. Environ. Microbiol. 71:8998–9007.

96. Ventura, M.,, J. H. Lee,, C. Canchaya, et al. 2005b. Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis. Appl. Environ. Microbiol. 71:8692–8705.

97. Ventura, M.,, R. Zink,, G. F. Fitzgerald, and, D. van Sinderen. 2005c. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl. Environ. Microbiol. 71:487–500.

98. Ventura,, M.,, Z. Zhang,, M. Cronin,, C. Canchaya,, J. G. Kenny,, G. F. Fitzgerald, and, D. van Sinderen. 2005d. The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003. J. Bacteriol. 187:8411–8426.

99. Ventura,, M.,, C. Canchaya,, A. Del Casale,, F. Dellaglio,, G. F. Fitzgerald, and, D. van Sinderen. 2006a. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 56:2783–2792.

100. Ventura, M.,, C. Canchaya,, Z. Zhang,, G. F. Fitzgerald, and, D. van Sinderen. 2006b. How high G + C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators. FEMS Microbiol. Rev. 30:734–759.

101. Ventura,, M.,, C. Canchaya,, G. F. Fitzgerald,, R. S. Gupta, and, D. van Sinderen. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie Leeuwenhoek 91:351–372.

102. Yildirim, Z.,, D. K. Winters, and, M. G. Johnson. 1999. Purification, amino acid sequence and mode of action of bifidocin B produced by Bifidobacterium bifidum NCFB 1454. J. Appl. Microbiol. 86:45–54.

103. Yoshioka, H.,, K. Iseki, and, K. Fujita. 1983. Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants. Pediatrics 72:317–321.

104. Ziemer,, C. J., and, G. R. Gibson. 1998. An overview of probiotics, prebiotics and synbiotics in the functional food concept: perspectives and future strategies. Int. Dairy J. 8:473–479.

105. Zoetendal,, E. G.,, C. T. Collier,, S. Koike,, R. I. Mackie, and, H. R. Gaskins. 2004. Molecular ecological analysis of the gastrointestinal microbiota: a review. J. Nutr. 134:465–472.

Tables

Bifidobacteria: the Model Human Gut Commensal

/content/10.1128/9781555815462.ch04.ch04table01

Table 1

Bifidobacterial species and their origin

Table 1

Bifidobacterial species and their origin

/content/10.1128/9781555815462.ch04.ch04table02

Table 2

General features of bifidobacterial genomes

Table 2

General features of bifidobacterial genomes