title: Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.
abstract: The Bifidobacterium genus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particular Bifidobacterium taxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of the Bifidobacterium genus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: GenProbio s.r.l.., Parma, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.affiliation: GenProbio s.r.l.., Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: GenProbio s.r.l.., Parma, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.affiliation: Department of Food Science, University of Liege, Liege, Belgium.
authors.forename: Bernard
authors.initials: B
authors.lastname: Taminiau
authors.affiliation: Department of Food Science, University of Liege, Liege, Belgium.
authors.forename: Véronique
authors.initials: V
authors.lastname: Delcenserie
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy marco.ventura@unipr.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D001644:Bifidobacterium / Q000235:genetics* / Q000502:physiology; D005075:Biological Evolution; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S
chemical_list: D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Int J Syst Evol Microbiol. 2009 Aug;59(Pt 8):2020-4
references.pmid: 19567560
references.citation: Int J Syst Bacteriol. 1992 Jan;42(1):166-70
references.pmid: 1371061
references.citation: Arch Microbiol. 1974 Jul 16;98(3):187-98
references.pmid: 4858764
references.citation: Cell Mol Life Sci. 2014 Jan;71(2):183-203
references.pmid: 23516017
references.citation: J Sci Food Agric. 2014 Jan 30;94(2):163-8
references.pmid: 23963950
references.citation: BMC Bioinformatics. 2003 Jul 10;4:29
references.pmid: 12854978
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72
references.pmid: 15701695
references.citation: Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2945-54
references.pmid: 19060088
references.citation: Int J Syst Evol Microbiol. 2008 Jan;58(Pt 1):144-8
references.pmid: 18175700
references.citation: Genome Res. 2000 Jul;10(7):991-1000
references.pmid: 10899148
references.citation: Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1137-1143
references.pmid: 15280282
references.citation: Bioinformatics. 2012 Feb 1;28(3):416-8
references.pmid: 22130594
references.citation: Int J Syst Evol Microbiol. 2002 May;52(Pt 3):995-999
references.pmid: 12054269
references.citation: Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
references.pmid: 12136088
references.citation: Trends Genet. 2002 Sep;18(9):486
references.pmid: 12175810
references.citation: Int J Syst Evol Microbiol. 2006 Dec;56(Pt 12):2783-2792
references.pmid: 17158978
references.citation: Nucleic Acids Res. 1999 Nov 1;27(21):4218-22
references.pmid: 10518613
references.citation: Genome Announc. 2014 Feb 20;2(1):
references.pmid: 24558236
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: Int J Syst Evol Microbiol. 2000 Jan;50 Pt 1:119-125
references.pmid: 10826794
references.citation: Antonie Van Leeuwenhoek. 1974;40(3):427-40
references.pmid: 4136709
references.citation: Syst Appl Microbiol. 2012 Mar;35(2):92-7
references.pmid: 22225994
references.citation: Int J Syst Evol Microbiol. 2010 Dec;60(Pt 12):2823-2827
references.pmid: 20081020
references.citation: BMC Evol Biol. 2001 Oct 20;1:8
references.pmid: 11734060
references.citation: Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):449-455
references.pmid: 24158945
references.citation: FEMS Microbiol Rev. 2001 Jan;25(1):39-67
references.pmid: 11152940
references.citation: Int J Syst Evol Microbiol. 2013 Nov;63(Pt 11):4350-4353
references.pmid: 24187022
references.citation: Zentralbl Bakteriol Orig. 1963;191:486-507
references.pmid: 14121844
references.citation: Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19514-9
references.pmid: 20974960
references.citation: Microbiol Mol Biol Rev. 2007 Sep;71(3):495-548
references.pmid: 17804669
references.citation: Int J Syst Evol Microbiol. 2002 May;52(Pt 3):1043-1047
references.pmid: 12054223
references.citation: J Mol Evol. 2004 Jan;58(1):1-11
references.pmid: 14743310
references.citation: Biotechniques. 2003 Feb;34(2):374-8
references.pmid: 12613259
references.citation: Z Allg Mikrobiol. 1971;11(5):387-95
references.pmid: 5168878
references.citation: Int J Syst Evol Microbiol. 2004 Mar;54(Pt 2):401-406
references.pmid: 15023951
references.citation: Genome Res. 1999 Jun;9(6):550-7
references.pmid: 10400922
references.citation: Syst Appl Microbiol. 2007 Jul;30(5):381-9
references.pmid: 17321094
references.citation: BMC Evol Biol. 2007 Aug 30;7:154
references.pmid: 17760998
references.citation: Int J Syst Evol Microbiol. 2011 Jun;61(Pt 6):1315-1321
references.pmid: 20656822
references.citation: Int J Syst Evol Microbiol. 2009 Jun;59(Pt 6):1535-40
references.pmid: 19502349
references.citation: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
references.pmid: 17531802
references.citation: Zentralbl Bakteriol Mikrobiol Hyg A. 1988 Jun;268(4):433-4
references.pmid: 3213314
references.citation: Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):373-8
references.pmid: 15630082
references.citation: Int J Syst Bacteriol. 1991 Jan;41(1):163-8
references.pmid: 1995032
references.citation: PLoS Genet. 2009 Dec;5(12):e1000785
references.pmid: 20041198
references.citation: Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81
references.pmid: 17127215
references.citation: Zentralbl Bakteriol Parasitenkd Infektionskr Hyg. 1969;123(1):64-88
references.pmid: 4908741
references.citation: PLoS One. 2012;7(9):e44229
references.pmid: 23028506
references.citation: J Bacteriol. 2009 Jan;191(1):91-9
references.pmid: 18978054
references.citation: Int J Syst Evol Microbiol. 2011 Nov;61(Pt 11):2610-2615
references.pmid: 21148680
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1619-1623
references.pmid: 13130059
references.citation: Antonie Van Leeuwenhoek. 2008 Jun;94(1):35-50
references.pmid: 18338233
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
references.pmid: 19855009
references.citation: Nat Genet. 1999 Jan;21(1):108-10
references.pmid: 9916801
references.citation: Appl Environ Microbiol. 2014 Oct;80(20):6290-302
references.pmid: 25085493
references.citation: PLoS One. 2013 Apr 12;8(4):e60204
references.pmid: 23593174
references.citation: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
references.pmid: 17062412
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Annu Rev Genomics Hum Genet. 2003;4:213-35
references.pmid: 14527302
references.citation: Int J Syst Bacteriol. 1990 Jan;40(1):100-2
references.pmid: 2223594
references.citation: Nat Genet. 2001 Jul;28(3):281-5
references.pmid: 11431701
references.citation: Zentralbl Bakteriol Orig. 1969 May;210(1):52-64
references.pmid: 5361078
references.citation: Bioinformatics. 2004 Sep 1;20(13):2044-9
references.pmid: 15044248
references.citation: Arch Mikrobiol. 1969;68(3):278-94
references.pmid: 5393670
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Genome Res. 2002 Jul;12(7):1080-90
references.pmid: 12097345