Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing

Research in Microbiology

Volumn 161, Issue 2, 2010, Pages 82-90

  Delétoile, Alexis ^a   Passet, Virginie ^a   Aires, Julio ^b   Chambaud, Isabelle ^c   Butel, Marie José ^b   Smokvina, Tamara ^c   Brisse, Sylvain ^a  

^a INSTITUT PASTEUR   (France)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c Centre Daniel Carasso   (France)

Author keywords

Bifidobacterium; Identification; Multilocus sequence typing (MLST); Phylogeny; Recombination; Taxonomy

Indexed keywords

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM LONGUM; BIOLOGICAL ACTIVITY; CLONAL VARIATION; CONTROLLED STUDY; GENE CLUSTER; GENE IDENTIFICATION; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SPECIES IDENTIFICATION;

BIFIDOBACTERIUM; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, BACTERIAL; GENETIC VARIATION; GENOTYPE; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

BIFIDOBACTERIUM; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM LONGUM;

EID: 77949917258     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2009.12.006     Document Type: Article

References (55)

1. Aires J., Doucet-Populaire F., Butel M.J. Tetracycline resistance mediated by tet(W), tet(M), and tet(O) genes of Bifidobacterium isolates from humans. Appl. Environ. Microbiol. 2007, 73:2751-2754.
2. Barrangou R., Briczinski E.P., Traeger L.L., Loquasto J.R., Richards M., Horvath P., et al. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J. Bacteriol. 2009, 191:4144-4151.
3. Bishop C.J., Aanensen D.M., Jordan G.E., Kilian M., Hanage W.P., Spratt B.G. Assigning strains to bacterial species via the internet. BMC Biol. 2009, 7:3.
4. Boesten R.J., Schuren F.H., de Vos W.M. A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria. J. Microbiol. Methods 2009, 76:269-277.
5. Briczinski E.P., Roberts R.F. Technical note: a rapid pulsed-field gel electrophoresis method for analysis of bifidobacteria. J. Dairy. Sci. 2006, 89:2424-2427.
6. Brigidi P., Vitali B., Swennen E., Bazzocchi G., Matteuzzi D. Effects of probiotic administration upon the composition and enzymatic activity of human fecal microbiota in patients with irritable bowel syndrome or functional diarrhea. Res. Microbiol. 2001, 152:735-741.
7. Deletoile A., Decre D., Courant S., Passet V., Audo J., Grimont P., et al. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing. J. Clin. Microbiol. 2009, 47:300-310.
8. Dykhuizen D.E., Green L. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 1991, 173:7257-7268.
9. EFSA Panel on Dietetic Products, N.a.A Scientific Opinion on the substantiation of health claims related to non-characterised microorganisms pursuant to Article 13(1) of Regulation (EC) No 1924/2006. ESFA J. 2009, 7:1247.
10. Enright M.C., Day N.P., Davies C.E., Peacock S.J., Spratt B.G. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J. Clin. Microbiol. 2000, 38:1008-1015.
11. Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164:1567-1587.
12. Falush D., Torpdahl M., Didelot X., Conrad D.F., Wilson D.J., Achtman M. Mismatch induced speciation in Salmonella: model and data. Phil. Trans. R. Soc. Lond. B: Biol. Sci. 2006, 361:2045-2053.
13. Fearnhead P., Donnelly P. Estimating recombination rates from population genetic data. Genetics 2001, 159:1299-1318.
14. Feil E.J., Li B.C., Aanensen D.M., Hanage W.P., Spratt B.G. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 2004, 186:1518-1530.
15. Feil E.J., Spratt B.G. Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 2001, 55:561-590.
16. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 2007, 57:81-91.
17. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
18. Guttman D.S., Dykhuizen D.E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 1994, 266:1380-1383.
19. Guttman D.S., Dykhuizen D.E. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 1994, 138:993-1003.
20. Hamilton-Miller J.M., Shah S. Deficiencies in microbiological quality and labelling of probiotic supplements. Int. J. Food Microbiol. 2002, 72:175-176.
21. Hanage W.P., Fraser C., Spratt B.G. Fuzzy species among recombinogenic bacteria. BMC Biol. 2005, 3:6.
22. Hanage W.P., Fraser C., Spratt B.G. Sequences, sequence clusters and bacterial species. Phil. Trans. R. Soc. Lond. B: Biol. Sci. 2006, 361:1917-1927.
23. Hanage W.P., Spratt B.G., Turner K.M., Fraser C. Modelling bacterial speciation. Phil. Trans. R. Soc. Lond. B: Biol. Sci. 2006, 361:2039-2044.
24. Jian W., Zhu L., Dong X. New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int. J. Syst. Evol. Microbiol. 2001, 51:1633-1638.
25. Kohara T., Hayashi S., Hamatsuka J., Nishitani Y., Masuda Y., Osawa R. Intra-specific composition and succession of Bifidobacterium longum in human feces. Syst. Appl. Microbiol. 2007, 30:165-168.
26. Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U S A 2005, 102:2567-2572.
27. Lawrence J.G. Gene transfer in bacteria: speciation without species?. Theor. Popul. Biol. 2002, 61:449-460.
28. Maiden M.C. Multilocus sequence typing of bacteria. Annu. Rev. Microbiol. 2006, 60:561-588.
29. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U S A 1998, 95:3140-3145.
30. Martin D.P., Williamson C., Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262.
31. Masco L., Ventura M., Zink R., Huys G., 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. 2004, 54:1137-1143.
32. Matsuki T., Watanabe K., Tanaka R., Fukuda M., Oyaizu H. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 1999, 65:4506-4512.
33. Matsuki T., Watanabe K., Tanaka R., Oyaizu H. Rapid identification of human intestinal bifidobacteria by 16S rRNA-targeted species- and group-specific primers. FEMS Microbiol. Lett. 1998, 167:113-121.
34. Matsumoto T., Ishikawa H., Tateda K., Yaeshima T., Ishibashi N., Yamaguchi K. Oral administration of Bifidobacterium longum prevents gut-derived Pseudomonas aeruginosa sepsis in mice. J. Appl. Microbiol. 2008, 104:672-680.
35. Mattarelli P., Bonaparte C., Pot B., 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. 2008, 58:767-772.
36. McVean G., Awadalla P., Fearnhead P. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 2002, 160:1231-1241.
37. Mohania D., Nagpal R., Kumar M., Bhardwaj A., Yadav M., Jain S., et al. Molecular approaches for identification and characterization of lactic acid bacteria. J. Dig. Dis. 2008, 9:190-198.
38. Mullie C., Odou M.F., Singer E., Romond M.B., Izard D. Multiplex PCR using 16S rRNA gene-targeted primers for the identification of bifidobacteria from human origin. FEMS Microbiol. Lett. 2003, 222:129-136.
39. Paauw A., Caspers M.P., Schuren F.H., Leverstein-van Hall M.A., Deletoile A., Montijn R.C., et al. Genomic diversity within the Enterobacter cloacae complex. PLoS ONE 2008, 3:e3018.
40. Ragon M., Wirth T., Hollandt F., Lavenir R., Lecuit M., Le Monnier A., et al. A new perspective on Listeria monocytogenes evolution. PLoS Pathog. 2008, 4:e1000146.
41. Retchless A.C., Lawrence J.G. Temporal fragmentation of speciation in bacteria. Science 2007, 317:1093-1096.
42. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
43. Saavedra J.M., Bauman N.A., Oung I., Perman J.A., Yolken R.H. Feeding of Bifidobacterium bifidum and Streptococcus thermophilus to infants in hospital for prevention of diarrhoea and shedding of rotavirus. Lancet 1994, 344:1046-1049.
44. Sakata S., Kitahara M., Sakamoto M., Hayashi H., Fukuyama M., Benno Y. Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobacterium longum. Int. J. Syst. Evol. Microbiol. 2002, 52:1945-1951.
45. Salerno A., Deletoile A., Lefevre M., Ciznar I., Krovacek K., Grimont P., et al. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing. J. Bacteriol. 2007, 189:7808-7818.
46. Santos S.R., Ochman H. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ. Microbiol. 2004, 6:754-759.
47. Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. U S A 2002, 99:14422-14427.
48. Sela D.A., Chapman J., Adeuya A., Kim J.H., Chen F., Whitehead T.R., et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc. Natl. Acad. Sci. U S A 2008, 105:18964-18969.
49. Suau A., Bonnet R., Sutren M., Godon J.J., Gibson G.R., Collins M.D., et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 1999, 65:4799-4807.
50. Turner K.M., Feil E.J. The secret life of the multilocus sequence type. Int. J. Antimicrob. Agents 2007, 29:129-135.
51. Ventura M., Canchaya C., Del Casale A., Dellaglio F., Neviani E., Fitzgerald G.F., et al. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 2006, 56:2783-2792.
52. Ventura M., O'Connell-Motherway M., Leahy S., Moreno-Munoz J.A., Fitzgerald G.F., van Sinderen D. From bacterial genome to functionality; case bifidobacteria. Int. J. Food Microbiol. 2007, 120:2-12.
53. Ventura M., Zink R. Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis. Appl. Environ. Microbiol. 2002, 68:6429-6434.
54. Ventura M., 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, 69:7517-7522.
55. Youn S.Y., Seo J.M., Ji G.E. Evaluation of the PCR method for identification of Bifidobacterium species. Lett. Appl. Microbiol. 2008, 46:7-13.