Skip to main content
SpringerLink
Log in

Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

An Erratum to this article was published on 26 June 2007

Abstract

The field of microbiology has in recent years been transformed by the ever increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics and evolutionary development of bacteria. Among the latter group of microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. In this review we will discuss how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  CAS  Google Scholar 

  • Azcarate-Peril MA, Altermann E, Lick S, Russell WM, Klaehammer TR (2005) Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus. Appl Environ Microbiol 71:5794–5804

    Article  PubMed  CAS  Google Scholar 

  • Bartosch S, Fite A, Macfarlane GT, McMurdo ME (2004) Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol 70:3575–3581

    Article  PubMed  CAS  Google Scholar 

  • Biavati B, Mattarelli P (2001) The family Bifidobacteriaceae. In: Dworkin M, et al (eds) The prokaryotes: an evolving electronic resource for the microbiological community

  • Bininda-Emonds ORP (2004) The evolution of supertrees. Trends Ecol Evol 19:315–322

    Article  PubMed  Google Scholar 

  • Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245–254

    Article  PubMed  CAS  Google Scholar 

  • Bron PA, Marco M, Hoffer SM, van Mullekom E, de Vos WM, Kleerebezem M (2004) Genetic characterization of the bile salt response in Lactobacillus plantarum and analysis of responsive promoters in vitro and in situ in the gastrointestinal tract. J Bacteriol 186:7829–7835

    Article  PubMed  CAS  Google Scholar 

  • Brown DP, Idler KB, Katz L (1990) Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea. J Bacteriol 172:1877–1888

    PubMed  CAS  Google Scholar 

  • Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281–285

    Article  PubMed  CAS  Google Scholar 

  • Campbell AM (1992) Chromosomal insertion sites for phages and plasmids. J Bacteriol 174:7495–7499

    PubMed  CAS  Google Scholar 

  • Chang DE, Smalley DJ, Tucker DL, other authors (2004) Carbon nutrition of Escherichia coli in the mouse intestine. Proc Natl Acad Sci USA 101:7427–7432

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Cohan FM (2001) Bacterial species and speciation. Syst Biol 50:513–524

    Article  PubMed  CAS  Google Scholar 

  • Combes P, Till R, Bee S, Smith MC (2002) The streptomyces genome contains multiple pseudo-attB sites for the (phi)C31-encoded site-specific recombination system. J Bacteriol 184:5746–5752

    Article  PubMed  CAS  Google Scholar 

  • Corfield MS, Wagner SA, Clamp JR, Kriaris MS, Hoskins LC (1992) Mucin degradation in the human colon: production of sialidase, sialate O-acetylesterase, N-acetylneuraminate lyase, arylesterase, and glycosulfatase activities by strains of fecal bacteria. Infect Immun 60:3971–3978

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Coutinho PM, Henrissat B (1999) Life with no sugars? J Mol Microbiol Biotechnol 1:307–308

    PubMed  CAS  Google Scholar 

  • Cummings JH, Englyst HN (1987) Fermentation in the human large intestine and the available substrates. Am J Clin Nutr 45:1243–1255

    PubMed  CAS  Google Scholar 

  • Daveran-Mingot ML, Campo N, Ritzenthaler P, Le Bourgeois P (1998) A natural large chromosomal inversion in Lactococcus lactis is mediated by homologous recombination between two insertion sequences. J Bacteriol 180:4834–4842

    PubMed  CAS  Google Scholar 

  • Davey HM, Winson MK (2003) Using flow cytometry to quantify microbial heterogeneity. Curr Issues Mol Biol 5:9–15

    PubMed  Google Scholar 

  • Degnan BA, Macfarlane GT (1993) Transport and metabolism of glucose and arabinose in Bifidobacterium breve. Arch Microbiol 160:144–151

    Article  PubMed  CAS  Google Scholar 

  • Delzenne NM, Williams CM (2002) Prebiotics and lipid metabolism. Curr Opin Lipidol 13:61–67

    Article  PubMed  CAS  Google Scholar 

  • Di Caro S, Tao H, Grillo A, Elia C, Gasbarrini G, Sepulveda AR, Gasbarrini A (2005) Effects of Lactobacillus GG on genes expression pattern in small bowel mucosa. Dig Liver Dis 37:320–329

    Article  PubMed  CAS  Google Scholar 

  • Ehrmann MA, Korakli M, Vogel RF (2003) Identification of the gene for beta-fructofuranosidase of Bifidobacterium lactis DSM10140(T) and characterization of the enzyme expressed in Escherichia coli. Curr Microbiol 46:391–397

    Article  PubMed  CAS  Google Scholar 

  • Eisen JA, Heidelberg JF, White O, Salzberg SL (2000) Evidence for symmetric chromosomal inversions around the replication origin of bacteria. BCM Biol 1:1–11

    Google Scholar 

  • Favier CF, Vaughan EE, De Vos WM, Akkermans AD (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68:219–226

    Article  PubMed  CAS  Google Scholar 

  • Frank AC, Lobry JR (1999) Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:65–77

    Article  PubMed  CAS  Google Scholar 

  • Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW (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

    PubMed  CAS  Google Scholar 

  • Gao B, Gupta RS (2005) Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55:2401–2412

    Article  PubMed  CAS  Google Scholar 

  • Gao B, Gupta RS (2006) Signature proteins that are distinctive characteristics of Actinobacteria and their subgrups. Antonie van Leeuwenhoek 90:69–91

    Article  PubMed  CAS  Google Scholar 

  • Garrity GM, Holt JG (2001) The road map to the manual. In: Boone DR, Castenholz RW (eds) Bergery’s manual of systematic bacteriology. Springer-Verlag, Berlin

    Google Scholar 

  • Gevers D, Vandepoele K, Simillon C, Van de Peer Y (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 12:148–154

    Article  PubMed  CAS  Google Scholar 

  • Gibson GR (1999) Dietary modulation of the human gut microflora using the prebiotics oligofructose and inulin. J Nutr 129:1438S–1441S

    PubMed  CAS  Google Scholar 

  • Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226–2238

    PubMed  CAS  Google Scholar 

  • Grohmann E, Muth G, Espinosa M (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Rev 67:277–301, table of contents

    Google Scholar 

  • Grundy FJ, Henkin TM (1998) The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30:737–749

    Article  PubMed  CAS  Google Scholar 

  • Guarner F, Malagelada JR (2003) Gut flora in health and disease. Lancet 361:512–519

    Article  PubMed  Google Scholar 

  • Gueimonde M, Tolkko S, Korpimaki T, Salminen S (2004) New real-time quantitative PCR procedure for quantification of bifidobacteria in human fecal samples. Appl Environ Microbiol 70:4165–4169

    Article  PubMed  CAS  Google Scholar 

  • Gupta RS (2001) The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol 4:187–202

    Article  PubMed  CAS  Google Scholar 

  • Hartemink R, Rombouts FM (1999) Comparison of media for the detection of bifidobacteria, lactobacilli and total anaerobes from faecal samples. J Microbiol Methods 36:181–192

    Article  PubMed  CAS  Google Scholar 

  • Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc Natl Acad Sci USA 96:2192–2197

    Article  PubMed  CAS  Google Scholar 

  • Hinz SW, Pastink MI, van den Broek LA, Vincken JP, Voragen AG (2005) Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans. Appl Environ Microbiol 71:5501–5510

    Article  PubMed  CAS  Google Scholar 

  • Hooper LV, Midtvedt T, Gordon JI (2002) How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr 22:283–307

    Article  PubMed  CAS  Google Scholar 

  • Hoskins LC, Agustines M, McKee WB, Boulding ET, Kriaris M, Niedermeyer G (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 Invest 75:944–953

    Article  PubMed  CAS  Google Scholar 

  • Imamura L, Hisamitsu K, Kobashi K (1994) Purification and characterization of beta-fructofuranosidase from Bifidobacterium infantis. Biol Pharm Bull 17:596–602

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Janer C, Rohr LM, Pelaez C, Laloi M, Cleusix V, Requena T, Meile L (2004) Hydrolysis of oligofructoses by the recombinant beta-fructofuranosidase from Bifidobacterium lactis. Syst Appl Microbiol 27:279–285

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Katayama T, Sakuma A, Kimura T, Makimura Y, Hiratake J, Sakata K, Yamanoi T, Kumagai H, Yamamoto K (2004) Molecular cloning and characterization of Bifidobacterium bifidum 1,2-alpha-l-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95). J Bacteriol 186:4885–4893

    Article  PubMed  CAS  Google Scholar 

  • Kitaoka M, Tian J, Nishimoto M (2005) Novel putative galactose operon involving lacto-N-biose phosphorylase in Bifidobacterium longum. Appl Environ Microbiol 71:3158–3162

    Article  PubMed  CAS  Google Scholar 

  • Klaenhammer TR, Barrangou R, Buck BL, Azcarate-Peril MA, Altermann E (2005) Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiol Rev 29:393–409

    Article  PubMed  CAS  Google Scholar 

  • Klijn A, Mercenier A, Arigoni F (2005) Lessons from the genomes of bifidobacteria. FEMS Microbiol Rev 29:491–509

    Article  PubMed  CAS  Google Scholar 

  • Korbel JO, Snel B, Huynen MA, Bork P (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet 18:158–162

    Article  PubMed  CAS  Google Scholar 

  • Krinos CM, Coyne MJ, Weinacht KG, Tzianabos AO, Kasper DL, Comstock LE (2001) Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 414:555–558

    Article  PubMed  CAS  Google Scholar 

  • Kullen MJ, Brady LJ, O’Sullivan DJ (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

    Article  PubMed  CAS  Google Scholar 

  • Kullin B, Abratt VR, Reid SJ (2006) A functional analysis of the Bifidobacterium longum cscA and scrP genes in sucrose utilization. Appl Microbiol Biotechnol

  • Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13:1589–1594

    Article  PubMed  CAS  Google Scholar 

  • Kunisawa T (1995) Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis. J Mol Evol 40:585–593

    Article  PubMed  CAS  Google Scholar 

  • Kunz C, Rudloff S, Baier W, Klein N, Strobel S (2000) Oligosaccharides in human milk: structural, functional, and metabolic aspects. Annu Rev Nutr 20:699–722

    Article  PubMed  CAS  Google Scholar 

  • Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, Welling GW (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

    PubMed  CAS  Google Scholar 

  • Lay C, Sutren M, Rochet V, Saunier K, Dore J, Rigottier-Gois L (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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Lee JH, O’Sullivan DJ (2006) Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl Environ Microbiol 72:527–535

    Article  PubMed  CAS  Google Scholar 

  • Lee SK, Kim YB, Ji GE (1997) Note: purification of amylase secreted from Bifidobacterium adolescentis. J Appl Microbiol 83:267–272

    Article  PubMed  CAS  Google Scholar 

  • Liepke C, Adermann K, Raida M, Magert HJ, Forssmann WG, Zucht HD (2002) Human milk provides peptides highly stimulating the growth of bifidobacteria. Eur J Biochem 269:712–718

    Article  PubMed  CAS  Google Scholar 

  • Lievin V, Peiffer I, Hudault S, Rochat F, Brassart D, Neeser JR, Servin AL (2000) Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity. Gut 47:646–652

    Article  PubMed  CAS  Google Scholar 

  • Liu M, van Enckevort FH, Siezen RJ (2005) Genome update: lactic acid bacteria genome sequencing is booming. Microbiology 151:3811–3814

    Article  PubMed  CAS  Google Scholar 

  • MacConaill LE, Fitzgerald GF, Van Sinderen D (2003) Investigation of protein export in Bifidobacterium breve UCC2003. Appl Environ Microbiol 69:6994–7001

    Article  PubMed  CAS  Google Scholar 

  • Martin MC, Alonso JC, Suarez JE, Alvarez MA (2000) Generation of food-grade recombinant lactic acid bacterium strains by site-specific recombination. Appl Environ Microbiol 66:2599–2604

    Article  PubMed  CAS  Google Scholar 

  • Matsuki T, Watanabe K, Tanaka R, Oyaizu H (1998) Rapid identification of human intestinal bifidobacteria by 16S rRNA-targeted species- and group-specific primers. FEMS Microbiol Lett 167:113–121

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Matsuki T, Watanabe K, Fujimoto J, Kado Y, Takada T, Matsumoto K, Tanaka R (2004) Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl Environ Microbiol 70:167–173

    Article  PubMed  CAS  Google Scholar 

  • Matsumura H, Takeuchi A, Kano Y (1997) Construction of Escherichia coli-Bifidobacterium longum shuttle vector transforming B. longum 105-A and 108-A. Biosci Biotechnol Biochem 61:1211–1212

    Article  PubMed  CAS  Google Scholar 

  • Maze A, O’Connel-Motherway M, Fitzgerald GF, van Sinderen D (2006) Identification and characterization of a putative fructose PTS of Bifidobacterium breve UCC2003. FEMS Microbiol Lett (in press)

  • McLean MJ, Wolfe KH, Devine KM (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47:691–696

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Soll D (2002) Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc Natl Acad Sci USA 99:2678–2683

    Article  PubMed  CAS  Google Scholar 

  • Missich R, Sgorbati B, LeBlanc DJ (1994) Transformation of Bifidobacterium longum with pRM2, a constructed Escherichia coli–B. longum shuttle vector. Plasmid 32:208–211

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127–141

    Article  PubMed  CAS  Google Scholar 

  • Nagaoka M, Hashimoto S, Watanabe T, Yokokura T, Mori Y (1994) Anti-ulcer effects of lactic acid bacteria and their cell wall polysaccharides. Biol Pharm Bull 17:1012–1017

    PubMed  CAS  Google Scholar 

  • O’Riordan K, Fitzgerald GF (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

    Article  PubMed  CAS  Google Scholar 

  • Ouwehand A, Isolauri E, Salminen S (2002) The role of the intestinal microflora for the development of the immune system in early childhood. Eur J Nutr 41(1), I32–37

    Google Scholar 

  • Park MS, Lee KH, Ji GE (1997) Isolation and characterization of two plasmids from Bifidobacterium longum. Lett Appl Microbiol 25:5–7

    Article  PubMed  CAS  Google Scholar 

  • Philippe H, Douady CJ (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6:498–505

    Article  PubMed  CAS  Google Scholar 

  • Requena T, Burton J, Matsuki T, Munro K, Simon MA, Tanaka R, Watanabe K, Tannock GW (2002) Identification, detection, and enumeration of human bifidobacterium species by PCR targeting the transaldolase gene. Appl Environ Microbiol 68:2420–2427

    Article  PubMed  CAS  Google Scholar 

  • Rocha EP (2003) DNA repeats lead to the accelerated loss of gene order in bacteria. Trends Genet 19:600–603

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Rossi M, Altomare L, Gonzalez Vara y Rodriguez A, Brigidi P, Matteuzzi D (2000) Nucleotide sequence, expression and transcriptional analysis of the Bifidobacterium longum MB 219 lacZ gene. Arch Microbiol 174:74–80

    Article  PubMed  CAS  Google Scholar 

  • Roy D (2001) Media for the isolation and enumeration of bifidobacteria in dairy products. Int J Food Microbiol 69:167–182

    Article  PubMed  CAS  Google Scholar 

  • Rohwer F, Edwards R (2002) The phage proteomic tree: a genome based taxonomy for phage. J Bacteriol 184:4529–4535

    Article  PubMed  CAS  Google Scholar 

  • Ruas-Madiedo P, Gueimonde M, de los Reyes-Gavilan CG, Salminen S (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

    Article  PubMed  CAS  Google Scholar 

  • Ryan SM, Fitzgerald GF, van Sinderen D (2005) Transcriptional regulation and characterization of a novel beta-fructofuranosidase-encoding gene from Bifidobacterium breve UCC2003. Appl Environ Microbiol 71:3475–3482

    Article  PubMed  CAS  Google Scholar 

  • Ryan SM, Fitzgerald GF, van Sinderen D (2006) Screening and identification of starch, amylopectin and pullulan-degrading activities in bifidobacterial strains. Appl Environ Microbiol 72:5289–5296

    Article  PubMed  CAS  Google Scholar 

  • Sakamoto M, Hayashi H, Benno Y (2003) Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities. Microbiol Immunol 47:133–142

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Satokari RM, Vaughan EE, Akkermans AD, Saarela M, de Vos WM (2001) Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 67:504–513

    Article  PubMed  CAS  Google Scholar 

  • Scardovi V, Trovatelli LD, Zani G, Crociani F, Matteuzzi D (1971) Deoxyribonucleic acid homology relationships among species of the genus Bifidobacterium. Int J Syst Bacteriol 21:276–294

    Article  Google Scholar 

  • Schell MA, Karmirantzou M, Snel B other authors (2002) The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci USA 99:14422–14427

    Article  PubMed  CAS  Google Scholar 

  • Servin AL (2004) Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens. FEMS Microbiol Rev 28:405–440

    Article  PubMed  CAS  Google Scholar 

  • Sgorbati B, Scardovi V, Leblanc DJ (1982) Plasmids in the genus Bifidobacterium. J Gen Microbiol 128:2121–2131

    PubMed  CAS  Google Scholar 

  • Sinha VR, Kumria R (2001) Polysaccharides in colon-specific drug delivery. Int J Pharm 224:19–38

    Article  PubMed  CAS  Google Scholar 

  • Slovakova L, Duskova D, Marounek M (2002) Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rabbit caecal bacterium Bifidobacterium pseudolongum. Lett Appl Microbiol 35:126–130

    Article  PubMed  CAS  Google Scholar 

  • Snel B, Bork P, Huynen MA (2002) Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res 12:17–25

    Article  PubMed  CAS  Google Scholar 

  • Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, Buhler JD, Gordon JI (2005) Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307:1955–1959

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E, Schumann P (2000) Introduction to the taxonomy of Actinobacteria. In: Dworkin M, et al. (eds) The prokaryotes: an evolving electronic resource for the microbiological community

  • Stackebrandt E, Rainey FA, WardRainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Article  Google Scholar 

  • Suzuki A, Mitsuyama K, Koga H, Tomiyasu N, Masuda J, Takaki K, Tsuruta O, Toyonaga A, Sata M (2006) Bifidogenic growth stimulator for the treatment of ulcerative colitis: a pilot study. Nutrition 22:76–81

    Article  PubMed  CAS  Google Scholar 

  • Tillier ER, Collins RA (2000) Genome rearrangement by replication-directed translocation. Nat Genet 26:195–197

    Article  PubMed  CAS  Google Scholar 

  • Titgemeyer F, Hillen W (2002) Global control of sugar metabolism: a gram-positive solution. Antonie Van Leeuwenhoek 82:59–71

    Article  PubMed  CAS  Google Scholar 

  • Trindade MI, Abratt VR, Reid SJ (2003) Induction of sucrose utilization genes from Bifidobacterium lactis by sucrose and raffinose. Appl Environ Microbiol 69:24–32

    Article  PubMed  CAS  Google Scholar 

  • Van Laere KM, Abee T, Schols HA, Beldman G, Voragen AG (2000) Characterization of a novel beta-galactosidase from Bifidobacterium adolescentis DSM 20083 active towards transgalactooligosaccharides. Appl Environ Microbiol 66:1379–1384

    Article  PubMed  Google Scholar 

  • Van Laere KM, Hartemink R, Bosveld M, Schols HA, Voragen AG (2000) Fermentation of plant cell wall derived polysaccharides and their corresponding oligosaccharides by intestinal bacteria. J Agric Food Chem 48:1644–1652

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Vaughan EE, Heilig HG, Ben-Amor K, de Vos WM (2005) Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol Rev 29:477–490

    Article  PubMed  CAS  Google Scholar 

  • Ventura M, Elli M, Reniero R, Zink R (2001a) Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiol Ecol 36:113–121

    Article  CAS  Google Scholar 

  • Ventura M, Reniero R, Zink R (2001b) Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-PCR approach. Appl Environ Microbiol 67:2760–2765

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ventura M, Canchaya C, Meylan V, Klaenhammer TR, Zink R (2003a) Analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification. Appl Environ Microbiol 69:6908–6922

    Article  CAS  Google Scholar 

  • Ventura M, Meylan V, Zink R (2003b) Identification and tracing of Bifidobacterium species by use of enterobacterial repetitive intergenic consensus sequences. Appl Environ Microbiol 69:4296–4301

    Article  CAS  Google Scholar 

  • Ventura M, Zink R (2003c) 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

    Article  CAS  Google Scholar 

  • Ventura M, Canchaya C, van Sinderen D, Fitzgerald GF, Zink R (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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Ventura M, van Sinderen D, Fitzgerald GF, Zink R (2004c) Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Van Leeuwenhoek 86:205–223

    Article  CAS  Google Scholar 

  • Ventura M, Canchaya C, Bernini V, Del Casale A, Dellaglio F, Neviani E, Fitzgerald GF, van Sinderen D (2005a) Genetic characterization of the Bifidobacterium breve UCC 2003 hrcA locus. Appl Environ Microbiol 71:8998–9007

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • Ventura M, Zhang Z, Cronin M, Canchaya C, Kenny JG, Fitzgerald GF, van Sinderen D (2005c) The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003. J Bacteriol 187:8411–8426

    Article  CAS  Google Scholar 

  • Ventura M, Zink R, Fitzgerald GF, van Sinderen D (2005d) 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

    Article  CAS  Google Scholar 

  • Ventura M, Canchaya C, Zhang Z, Fitzgerald GF, van Sinderen D (2006a) 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

    Article  CAS  Google Scholar 

  • Ventura M, Canchaya C, Del Casale A, Dellaglio F, Neviani E, Fitzgerald GF, van Sinderen D (2006b) Analysis of bifidobacterial evolution using a multilocus approch. Int J Syst Evol Microbiol (in press)

  • Warchol M, Perrin S, Grill JP, Schneider F (2002) Characterization of a purified beta-fructofuranosidase from Bifidobacterium infantis ATCC 15697. Lett Appl Microbiol 35:462–467

    Article  PubMed  CAS  Google Scholar 

  • Ward RE, Ninonuevo M, Mills DA, Lebrilla CB, German JB (2006) In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri. Appl Environ Microbiol 72:4497–4499

    Article  PubMed  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396

    Article  PubMed  CAS  Google Scholar 

  • Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11:356–372

    Article  PubMed  CAS  Google Scholar 

  • Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI (2003) A genomic view of the human Bacteroides thetaiotamicron symbiosis. Science 299:2074–2076

    Article  PubMed  CAS  Google Scholar 

  • Yildirim Z, Winters DK, Johnson MG (1999) Purification, amino acid sequence and mode of action of bifidocin B produced by Bifidobacterium bifidum NCFB 1454. J Appl Microbiol 86:45–54

    Article  PubMed  CAS  Google Scholar 

  • You HJ, Oh DK, Ji GE (2004) Anticancerogenic effect of a novel chiroinositol-containing polysaccharide from Bifidobacterium bifidum BGN4. FEMS Microbiol Lett 240:131–136

    Article  PubMed  CAS  Google Scholar 

  • Zarate G, Chaia AP, Gonzales S, Oliver G (2000) Viability and beta-galactosidase activity of dairy propionibacteria subjected to digestion by artificial gastric and intestinal fluids. J Food Protect 63:1214–1221

    CAS  Google Scholar 

  • Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68:3401–3407

    Article  PubMed  CAS  Google Scholar 

  • Zoetendal EG, Vaughan EE, de Vos WM (2006) A microbial worlds within us. Mol Microbiol 59:1639–1650

    Article  PubMed  CAS  Google Scholar 

  • Zoetendal EG, Collier CT, Koike S, Mackie RI, Gaskins HR (2004) Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 134:465–472

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This work was financially supported by the Italian Award for Outstanding Young Researcher scheme “Incentivazione alla mobilita’ di studiosi stranieri e italiani residenti all’estero” and to the Marie Curie Reintegration Grant (MERG-CT-2005-03080) to MV, by an IRCSET Embark postdoctoral fellowship scheme 2005 to CC, by the Higher Education Authority Programme for Research in Third Level Institutions and by the Science Foundation Ireland Alimentary Pharmabiotic Centre located at University College Cork. The research work from RSG’s lab was supported by a grant from the National Science and Engineering Research Council of Canada.

Author information

Authors and Affiliations

  1. Department of Genetics, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11a, Parma, 43100, Italy

    Marco Ventura

  2. Alimentary Pharmabiotic Centre and Department of Microbiology, BioSciences Institute, National University of Ireland, Cork, Ireland

    Carlos Canchaya, Gerald F. Fitzgerald & Douwe van Sinderen

  3. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada

    Radhey S. Gupta

Authors
  1. Marco Ventura
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carlos Canchaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gerald F. Fitzgerald
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Radhey S. Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Douwe van Sinderen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marco Ventura.

Additional information

An erratum to this article can be found at http://dx.doi.org/10.1007/s10482-007-9182-2

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ventura, M., Canchaya, C., Fitzgerald, G.F. et al. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek 91, 351–372 (2007). https://doi.org/10.1007/s10482-006-9122-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-006-9122-6

Keywords

Search

Navigation