title: Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
abstract: BACKGROUND
  Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure and composition of vaginal microbial communities; most of the earlier studies focused on predominant vaginal bacteria in the process of BV. In the present study, the diversity and richness of vaginal microbiota in 50 BV positive and 50 healthy women from China were investigated using culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and barcoded 454 pyrosequencing methods, and validated by quantitative PCR.
  
  
  RESULTS
  Our data demonstrated that there was a profound shift in the absolute and relative abundances of bacterial species present in the vagina when comparing populations associated with healthy and diseased conditions. In spite of significant interpersonal variations, the diversity of vaginal microbiota in the two groups could be clearly divided into two clusters. A total of 246,359 high quality pyrosequencing reads was obtained for evaluating bacterial diversity and 24,298 unique sequences represented all phylotypes. The most predominant phyla of bacteria identified in the vagina belonged to Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. The higher number of phylotypes in BV positive women over healthy is consistent with the results of previous studies and a large number of low-abundance taxa which were missed in previous studies were revealed. Although no single bacterium could be identified as a specific marker for healthy over diseased conditions, three phyla - Bacteroidetes, Actinobacteria and Fusobacteria, and eight genera including Gardnerella, Atopobium, Megasphaera, Eggerthella, Aerococcus, Leptotrichia/Sneathia, Prevotella and Papillibacter were strongly associated with BV (p < 0.05). These genera are potentially excellent markers and could be used as targets for clinical BV diagnosis by molecular approaches.
  
  
  CONCLUSIONS
  The data presented here have clearly profiled the overall structure of vaginal communities and clearly demonstrated that BV is associated with a dramatic increase in the taxonomic richness and diversity of vaginal microbiota. The study also provides the most comprehensive picture of the vaginal community structure and the bacterial ecosystem, and significantly contributes to the current understanding of the etiology of BV.
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
authors.forename: Zongxin
authors.initials: Z
authors.lastname: Ling
authors.forename: Jianming
authors.initials: J
authors.lastname: Kong
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.forename: Haibin
authors.initials: H
authors.lastname: Zhu
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Chen
authors.forename: Yuezhu
authors.initials: Y
authors.lastname: Wang
authors.forename: Lanjuan
authors.initials: L
authors.lastname: Li
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.forename: Yaxian
authors.initials: Y
authors.lastname: Xia
authors.forename: Charlie
authors.initials: C
authors.lastname: Xiang
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D005260:Female; D018628:Gene Dosage / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014621:Vagina / Q000382:microbiology*; D016585:Vaginosis, Bacterial / Q000235:genetics* / Q000382:microbiology*; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial
references.citation: Hum Reprod. 2001 Sep;16(9):1809-13
references.pmid: 11527880
references.citation: J Clin Microbiol. 2009 Apr;47(4):1181-9
references.pmid: 19158255
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2117-22
references.pmid: 18252821
references.citation: Arch Gynecol Obstet. 2006 Jan;273(4):195-202
references.pmid: 16208476
references.citation: PLoS One. 2007 Feb 14;2(2):e197
references.pmid: 17299583
references.citation: BMC Microbiol. 2008 Mar 06;8:43
references.pmid: 18325110
references.citation: Cell. 2006 Feb 24;124(4):837-48
references.pmid: 16497592
references.citation: Science. 2006 Aug 25;313(5790):1126-30
references.pmid: 16931762
references.citation: Appl Environ Microbiol. 2004 Aug;70(8):4800-6
references.pmid: 15294817
references.citation: Nature. 2007 Oct 18;449(7164):811-8
references.pmid: 17943117
references.citation: J Infect Dis. 2008 Oct 15;198(8):1131-40
references.pmid: 18717638
references.citation: J Infect Dis. 2005 Apr 1;191(7):1129-39
references.pmid: 15747249
references.citation: Appl Environ Microbiol. 2005 Mar;71(3):1501-6
references.pmid: 15746353
references.citation: Nature. 2006 Dec 21;444(7122):1027-31
references.pmid: 17183312
references.citation: J Infect Dis. 1999 Dec;180(6):1950-6
references.pmid: 10558952
references.citation: Prim Care Update Ob Gyns. 2000 Sep 1;7(5):181-185
references.pmid: 11025268
references.citation: Cochrane Database Syst Rev. 2007 Jan 24;(1):CD000262
references.pmid: 17253447
references.citation: J Med Microbiol. 1996 Aug;45(2):120-6
references.pmid: 8683547
references.citation: Clin Infect Dis. 1995 Jun;20 Suppl 2:S271-5
references.pmid: 7548573
references.citation: Science. 2009 May 29;324(5931):1190-2
references.pmid: 19478181
references.citation: PLoS One. 2009 Jun 29;4(6):e6074
references.pmid: 19562079
references.citation: BMC Infect Dis. 2007 Nov 07;7:128
references.pmid: 17986357
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: J Nutr. 2007 Sep;137(9):2128-33
references.pmid: 17709453
references.citation: Curr Infect Dis Rep. 2002 Dec;4(6):514-519
references.pmid: 12433327
references.citation: Appl Environ Microbiol. 2008 Aug;74(15):4898-909
references.pmid: 18487399
references.citation: ISME J. 2007 Jun;1(2):121-33
references.pmid: 18043622
references.citation: J Clin Microbiol. 2007 Mar;45(3):1016-8
references.pmid: 17202272
references.citation: J Dent Res. 2008 Nov;87(11):1016-20
references.pmid: 18946007
references.citation: J Clin Microbiol. 1991 Feb;29(2):297-301
references.pmid: 1706728
references.citation: Nature. 2006 Dec 21;444(7122):1022-3
references.pmid: 17183309
references.citation: Am J Obstet Gynecol. 2001 Apr;184(5):845-53; discussion 853-5
references.pmid: 11303191
references.citation: BMC Bioinformatics. 2006 Aug 07;7:371
references.pmid: 16893466
references.citation: BMC Genomics. 2006 Mar 20;7:57
references.pmid: 16549033
references.citation: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references.pmid: 17586664
references.citation: Rev Infect Dis. 1990 Sep-Oct;12(5):856-72
references.pmid: 2237129
references.citation: Lancet. 1997 Aug 23;350(9077):546-50
references.pmid: 9284776
references.citation: Sex Transm Dis. 2007 Apr;34(4):197-202
references.pmid: 17179772
references.citation: Am J Obstet Gynecol. 1955 May;69(5):962-76
references.pmid: 14361525
references.citation: Clin Infect Dis. 1993 Jun;16 Suppl 4:S273-81
references.pmid: 8324131
references.citation: Obstet Gynecol. 1986 Feb;67(2):229-37
references.pmid: 3003634
references.citation: Microbiology (Reading). 2004 Aug;150(Pt 8):2565-2573
references.pmid: 15289553
references.citation: Nat Methods. 2008 Mar;5(3):235-7
references.pmid: 18264105
references.citation: J Infect Dis. 2006 Sep 15;194(6):828-36
references.pmid: 16941351
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
references.pmid: 16880384
references.citation: Curr Opin Microbiol. 2008 Oct;11(5):442-6
references.pmid: 18817891
references.citation: Clin Infect Dis. 2003 Aug 1;37(3):319-25
references.pmid: 12884154
references.citation: Obstet Gynecol. 2004 Aug;104(2):267-72
references.pmid: 15291998
references.citation: J Infect Dis. 1983 Nov;148(5):817-22
references.pmid: 6631073
references.citation: Curr Infect Dis Rep. 2007 Nov;9(6):485-500
references.pmid: 17999885
references.citation: J Clin Microbiol. 2007 Sep;45(9):3145
references.pmid: 17652481
references.citation: ISME J. 2010 Jan;4(1):1-16
references.pmid: 19587773
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: Clin Infect Dis. 2003 Mar 1;36(5):663-8
references.pmid: 12594649
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2927-32
references.pmid: 17293459
references.citation: Cell. 2008 Mar 7;132(5):721-3
references.pmid: 18329356
references.citation: Am J Obstet Gynecol. 2005 Sep;193(3 Pt 1):682-92
references.pmid: 16150261
references.citation: J Infect Dis. 1997 Feb;175(2):406-13
references.pmid: 9203662
references.citation: Obstet Gynecol. 2007 Jan;109(1):114-20
references.pmid: 17197596
references.citation: Proc Natl Acad Sci U S A. 2005 May 31;102(22):7952-7
references.pmid: 15911771
references.citation: J Infect Dis. 2007 Dec 1;196(11):1692-7
references.pmid: 18008255
references.citation: Nature. 2007 Oct 18;449(7164):804-10
references.pmid: 17943116
references.citation: Appl Environ Microbiol. 2007 Sep;73(18):5731-41
references.pmid: 17644631
references.citation: Annu Rev Med. 2000;51:349-56
references.pmid: 10774469
references.citation: Appl Environ Microbiol. 1993 Mar;59(3):695-700
references.pmid: 7683183
references.citation: Appl Environ Microbiol. 2009 May;75(9):2889-98
references.pmid: 19270139
references.citation: ISME J. 2010 May;4(5):642-7
references.pmid: 20090784
references.citation: Nucleic Acids Res. 2008 Oct;36(18):e120
references.pmid: 18723574
references.citation: Lancet Infect Dis. 2005 Dec;5(12):786-94
references.pmid: 16310150
references.citation: Curr Infect Dis Rep. 2000 Feb;2(1):14-17
references.pmid: 11095832
references.citation: Am J Obstet Gynecol. 2004 Oct;191(4):1130-2
references.pmid: 15507931
references.citation: Nat Protoc. 2008;3(2):267-78
references.pmid: 18274529
references.citation: N Engl J Med. 1995 Dec 28;333(26):1737-42
references.pmid: 7491137
references.citation: N Engl J Med. 2005 Nov 3;353(18):1899-911
references.pmid: 16267321
references.citation: Obstet Gynecol. 1992 Mar;79(3):369-73
references.pmid: 1738516
references.citation: Clin Infect Dis. 2008 Jul 1;47(1):33-43
references.pmid: 18513147
references.citation: Int J Syst Bacteriol. 1999 Oct;49 Pt 4:1573-6
references.pmid: 10555338
references.citation: Nucleic Acids Res. 2007;35(19):e130
references.pmid: 17932070
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17994-9
references.pmid: 19004758
references.citation: ISME J. 2007 Aug;1(4):283-90
references.pmid: 18043639
references.citation: Am J Med. 1983 Jan;74(1):14-22
references.pmid: 6600371
references.citation: Science. 2005 Jun 10;308(5728):1635-8
references.pmid: 15831718
references.citation: Curr Infect Dis Rep. 2009 Mar;11(2):143-7
references.pmid: 19239805
references.citation: Cell. 2005 Jul 15;122(1):107-18
references.pmid: 16009137
references.citation: Appl Environ Microbiol. 2008 Mar;74(5):1656-9
references.pmid: 18203860
references.citation: Clin Infect Dis. 2004 Oct 1;39(7):990-5
references.pmid: 15472851
references.citation: Science. 2006 Jun 2;312(5778):1355-9
references.pmid: 16741115
references.citation: J Clin Microbiol. 1989 Feb;27(2):251-6
references.pmid: 2915019