A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria

Journal of Microbiological Methods

Volumn 76, Issue 3, 2009, Pages 269-277

  Boesten, Rolf J ^a,b   Schuren, Frank H J ^a   de Vos, Willem M ^b,c  

^a TNO   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Bifidobacterium; DNA DNA hybridization; Genomic comparison; Microarray

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM LONGUM; BIFIDOBACTERIUM PSEUDOLONGUM; DNA DNA HYBRIDIZATION; DNA MICROARRAY; INTESTINE FLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SPECIES IDENTIFICATION; UNINDEXED SEQUENCE;

ANIMALS; BACTERIAL TYPING TECHNIQUES; BIFIDOBACTERIUM; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, BACTERIAL; GENOME, BACTERIAL; GENOMIC LIBRARY; INTESTINES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY;

BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM ANIMALIS SUBSP. ANIMALIS; BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM LONGUM; BIFIDOBACTERIUM PSEUDOLONGUM; MAMMALIA;

EID: 59849103618     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2008.12.006     Document Type: Article

References (49)

1. Akopyants N.S., Clifton S.W., Martin J., Pape D., Wylie T., Li L., Kissinger J.C., Roos D.S., and Beverley S.M. A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Mol. Biochem. Parasitol. 113 (2001) 337-340
2. Baess I. Isolation and purification of deoxyribonucleic acid from mycobacteria. Acta Pathol. Microbiol. Scad. Sect. B. 82 (1974) 780-784
3. Baker G., Smith J., and Cowan D. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55 (2003) 541-555
4. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D., and Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 (2007) 1709-1712
5. Boesten R.J., and De Vos W.M. Interactomics in the human intestine: lactobacilli and bifidobacteria make a difference. J. Clin. Gastroenterol. 42 3 (2008) S163-S167
6. Favier C.F., Vaughan E.E., De Vos W.M., and Akkermans A.D. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68 (2002) 219-226
7. Gibson G.R., McCartney A.L., and Rastall R.A. Prebiotics and resistance to gastrointestinal infections. Br. J. Nutr. 93 (2005) S31-S34
8. Guarner F., and Malagelada J.R. Gut flora in health and disease. Lancet 361 (2003) 512-519
9. Ivanov D., Emonet C., Foata F., Affolter M., Delley M., Fisseha M., Blum-Sperisen S., Kochhar S., and Arigoni F. A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases. J. Biol. Chem. 281 (2006) 17246-17252
10. 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. Evol. Microbiol. 51 (2001) 1633-1638
11. Juntunen M., Kirjavainen P.V., Ouwehand A.C., Salminen S.J., and Isolauri E. Adherence of probiotic bacteria to human intestinal mucus in healthy infants and during rotavirus infection. Clin. Diagn. Lab. Immun. (2001) 293-296
12. Klijn A., Mercenier A., and Arigoni F. Lessons from the genomes of bifidobacteria. FEMS Microbiol. Rev. 29 (2005) 491-509
13. Kunin V., Sorek R., and Hugenholtz P. Evolutionary conservation of sequence and secondary structure in CRISPR repeats. Genome Biol. 8 (2007) R61
14. Kwon H., Yang E., Lee S., Yeon S., Kang B., and Kim T. Rapid identification of potentially probiotic Bifidobacterium species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23S rRNA. FEMS Microbiol. Lett. 250 (2005) 55-62
15. Lauer E., and Kandler O. DNA-DNA homology, murein types and enzyme patterns in the type strains of the genus Bifidobacterium. Syst. Appl. Microbiol. 4 (1983) 42-64
16. Leahy S.C., Higgins D.G., Fitzgerald G.F., and Sinderen D.V. Getting better with bifidobacteria. J. Appl. Microbiol. 98 (2005) 1303-1315
17. Leavis H.L., Willems R.J.L., Wamel W.J.B., Schuren F.H., Caspers M.P.M., and Bonten M.J.M. Insertion sequence-driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium. PLoS Pathog. 3 1 (2007) e7
18. 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. Evol. Microbiol. 46 (1996) 102-111
19. Liu M., van Enckevort F.H.J., and Siezen R.J. Genome update: lactic acid bacteria genome sequencing is booming. Microbiology 151 (2005) 3811-3814
20. LoCascio R.G., Ninonuevo M.R., Freeman S.L., Sela D.A., Grimm R., Lebrilla C.B., Mills D.A., and German J.B. Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation. J. Agric. Food Chem. 55 (2007) 8914-8919
21. Marchesi J., and Shanahan F. The normal intestinal microbiota. Curr. Opin. Infect. Dis. 20 (2007) 508-513
22. Masco L., Ventura M., Zink R., Huys G., and Swings J. Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov. Int. J. Syst. Evol. Microbiol. 54 Pt 4 (2004) 1137-1143
23. Matsuki T., Watanabe K., Fujimoto J., Takada T., and Tanaka R. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl. Environ. Microbiol. 70 (2004) 7220-7228
24. Matsuki T., Watanabe K., Tanaka R., Fukuda M., and Oyaizu H. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 65 (1999) 4506-4512
25. Mattarelli P., Bonaparte C., Pot B., and Biavati B. Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov. Int. J. Syst. Evol. Microbiol. 58 (2008) 767-772
26. Meile L., Ludwig W., Rueger U., Gut C., Kaufmann P., Dasen G., Wenger S., and Teuber M. Bifidobacterium lactis sp. nov., a moderately oxygen tolerant species isolated from fermented milk. Syst. Appl. Microbiol. 20 (1997) 57-64
27. Mohan R., Koebnick C., Schildt J., Schnidt S., Mueller M., Possner M., Radke M., and Blaut M. Effects of Bifidobacterium lactis Bb12 supplementation on intestinal microbiota of preterm infants: a double-blind, placebo-controlled randomized study. J. Clin. Microbiol. (2006) 4025-4031
28. Orla-Jensen S. La classification des bactéries lactiques. Lait 4 (1924) 468-474
29. Oshlack A., Emslie D., Corcoran L.M., and Smyth G.K. Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biol. 8 (2007) R2
30. Parche S., Amon J., Jankovic I., Rezzonico E., Beleut M., Barutçu H., Schendel I., Eddy M.P., Burkovski A., Arigoni F., and Titgemeyer F. Sugar transport systems of Bifidobacterium longum NCC2705. J. Mol. Microbiol. Biotechnol. 12 (2007) 9-19
31. Parvez S., Malik K.A., Kang S.A., and Kim H.-Y. Probiotics and their fermented food products are beneficial for health. J. Appl. Microbiol. (2006) 1171-1185
32. Reuter G. Vergleichende untersuchungen über die Bifidus-Flora im säuglings- und erwachsenenstuhl. Zentrabl. Bakteriol. [Orig. A] 1 (1963) 286-507
33. Ryan S.M., Fitzgerald G.F., and van Sinderen D. Screening for and identification of starch-, amylopectin-, and pullulan-degrading activities in bifidobacterial strains. Appl. Environ. Microbiol. 72 (2006) 5289-5296
34. 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. 52 Pt 6 (2002) 1945-1951
35. Salminen S.J., Gueimonde M., and Isolauri E. Probiotics that modify disease risk. J. Nutr. 135 (2005) 1294-1298
36. Scardovi V., and Crociani F. Bifidobacterium catenulatum, Bifidobacterium dentium, and Bifidobacterium angulatum: three new species and their deoxyribonucleic acid homology relationships. Int. J. Syst. Bacteriol. 24 (1974) 21-28
37. Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., Zwahlen M., Desiere F., Bork P., Delley M., Pridmore D.R., and Arigoni F. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 14422-14427
38. Vaughan E.E., Heilig H.G.H.J., Ben-Amor K., and de Vos W.M. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol. Rev. 29 (2005) 277-490
39. Ventura M., and Zink R. Rapid identification, differentiation, and proposal new taxonomic classification of Bifidobacterium lactis. Appl. Environ. Microbiol. 68 (2002) 6429-6434
40. 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 supple additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl. Environ. Microbiol. 69 (2003) 7517-7522
41. 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. Bacteriol. 56 (2006) 2783-2792
42. Ventura M., Canchaya C., Tauch A., Chandra G., Fitzgerald G.F., Chater K.F., and van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 71 (2007) 495-548
43. Ventura M., O'Connell-Motherway M., Leahy S., Moreno-Munoz J.A., Fitzgerald G.F., and van Sinderen D. From bacterial genome to functionality; case bifidobacteria. Int. J. Food Microbiol. 20 (2007) 13-24
44. Vlaminckx B.J.M., Schuren F.H.J., Montijn R.C., Caspers M.P.M., Fluit A.C., Wannet W.J.B., Schouls L.M., Verhoef J., and Jansen W.T.M. Determination of the relationship between group a streptococcal genome content, m type, and toxic shock syndrome by a mixed genome microarray. Infect. Immun. 75 (2007) 2603-2611
45. Wall R., Hussey S., Ryan C., O'Neill M., Fitzgerald G.F., Stanton C., and Ross R. Presence of two Lactobacillus and Bifidobacterium probiotic strains in the neonatal ileum. ISME J. 2 (2007) 83-91
46. Ward R., Niñonuevo M., Mills D., Lebrilla C., and German J. In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria. Mol. Nutr. Food Res. 51 (2007) 1398-1405
47. Xu J., and Gordon J.I. Honor thy symbionts. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 10452-10459
48. Yaeshima T., Fujisawa T., and Mitsuoka T. Bifidobacterium globosum, subjective synonym of Bifidobacterium pseudolongum, and description of Bifidobacterium pseudolongum subsp. pseudolongum comb. nov. and Bifidobacterium pseudolongum subsp. globosum comb. nov. Syst. Appl. Microbiol. 15 (1992) 280-385
49. Zoetendal E.G., Akkermans A.D., and de Vos W.M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64 (1998) 3854-3859