Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Siddiqui, Huma ^a   Nederbragt, Alexander J ^a   Lagesen, Karin ^a   Jeansson, Stig L ^a   Jakobsen, Kjetill S ^a  

^a UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S; BACTERIAL DNA;

ADULT; AMPLICON; ARTICLE; BACTERIAL VIRULENCE; BACTERIUM CULTURE; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; GARDNERELLA; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN EXPERIMENT; LACTOBACILLUS; NORMAL HUMAN; PREVOTELLA; RNA SEQUENCE; TAXONOMY; URINALYSIS; BACTERIUM; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; METAGENOME; MICROBIOLOGY; NUCLEIC ACID DATABASE; URINE;

ADULT; BACTERIA; DATABASES, NUCLEIC ACID; DNA, BACTERIAL; FEMALE; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; URINE;

MLCS; MLOWN;

EID: 80055117479     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-244     Document Type: Article

References (101)

1. Host-bacterial mutualism in the human intestine. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI, Science (New York, NY) 2005 307 5717 1915 1920 10.1126/science.1104816 (Pubitemid 40404694)
2. A core gut microbiome in obese and lean twins. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al. Nature 2009 457 7228 480 484 10.1038/nature07540 19043404
3. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Hooper LV, Midtvedt T, Gordon JI, Annual review of nutrition 2002 22 283 307 10.1146/annurev.nutr.22.011602.092259 12055347 (Pubitemid 35221463)
4. Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W, Journal of dental research 2008 87 11 1016 1020 10.1177/154405910808701104 18946007
5. Gut microbiota in obesity and metabolic disorders. Sanz Y, Santacruz A, Gauffin P, The Proceedings of the Nutrition Society 2010 1 8
6. Incidental detection of S. pyogenes-DNA in psoriatic skin by PCR. Weisenseel P, Prinz JC, Archives of dermatological research 2005 296 12 573 576 10.1007/s00403-005-0559-7 15856267 (Pubitemid 40869057)
7. Bacteria of dental caries in primary and permanent teeth in children and young adults. Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, Dewhirst FE, Leys EJ, Paster BJ, J Clin Microbiol 2008 46 4 1407 1417 10.1128/JCM.01410-07 18216213 (Pubitemid 351563587)
8. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Oakley BB, Fiedler TL, Marrazzo JM, Fredricks DN, Appl Environ Microbiol 2008 74 15 4898 4909 10.1128/AEM.02884-07 18487399
9. Hidden pathogens uncovered: metagenomic analysis of urinary tract infections. Imirzalioglu C, Hain T, Chakraborty T, Domann E, Andrologia 2008 40 2 66 71 10.1111/j.1439-0272.2007.00830.x 18336452 (Pubitemid 351379675)
10. Urine examination and clinical interpretation. Dukes CE, New York: Oxford Medical Publications 1939
11. Acute Urinary-Tract Infection: A Condition Overdiagnosed in Women? Osborne NG, Journal of Gynecologic Surgery 2008 24 1 51 54 10.1089/gyn.2007. 999993 (Pubitemid 351373479)
12. Absence of bacterial DNA in the bladder of patients with interstitial cystitis. Haarala M, Jalava J, Laato M, Kiilholma P, Nurmi M, Alanen A, J Urol 1996 156 5 1843 1845 10.1016/S0022-5347(01)65549-6 8863628 (Pubitemid 26344066)
13. A prospective study of microorganisms in urine and bladder biopsies from interstitial cystitis patients and controls. Keay S, Schwalbe RS, Trifillis AL, Lovchik JC, Jacobs S, Warren JW, Urology 1995 45 2 223 229 10.1016/0090-4295(95) 80009-3 7855970
14. Polymerase chain reaction amplification of bacterial 16S rRNA genes in interstitial cystitis and control patient bladder biopsies. Keay S, Zhang CO, Baldwin BR, Jacobs SC, Warren JW, J Urol 1998 159 1 280 283 10.1016/S0022- 5347(01)64082-5 9400495 (Pubitemid 27525623)
15. Dormant microbes in interstitial cystitis. Domingue GJ, Ghoniem GM, Bost KL, Fermin C, Human LG, J Urol 1995 153 4 1321 1326 10.1016/S0022-5347(01)67594- 3 7869536
16. Urinary tract infection: an overview. Barnett BJ, Stephens DS, Am J Med Sci 1997 314 4 245 249 10.1097/00000441-199710000-00007 9332263 (Pubitemid 27435451)
17. Manual of Clinical Microbiology. Murray PR, Baron EJ, Jorgensen JH, Landry ML, Pfaller MA, ASM Press 9 2007 1
18. A molecular view of microbial diversity and the biosphere. Pace NR, Science (New York, NY) 1997 276 5313 734 740 10.1126/science.276.5313.734 (Pubitemid 27199842)
19. Detection of intracellular bacterial communities in human urinary tract infection. Rosen DA, Hooton TM, Stamm WE, Humphrey PA, Hultgren SJ, PLoS medicine 2007 4 12 329 10.1371/journal.pmed.0040329 18092884
20. Biofilm formation by asymptomatic and virulent urinary tract infectious Escherichia coli strains. Hancock V, Ferrieres L, Klemm P, FEMS microbiology letters 2007 267 1 30 37 10.1111/j.1574-6968.2006.00507.x 17166230 (Pubitemid 46066536)
21. Biofilm formation by Escherichia coli isolated from patients with urinary tract infections. Salo J, Sevander JJ, Tapiainen T, Ikaheimo I, Pokka T, Koskela M, Uhari M, Clinical nephrology 2009 71 5 501 507 19473609
22. Viable but nonculturable bacteria are present in mouse and human urine specimens. Anderson M, Bollinger D, Hagler A, Hartwell H, Rivers B, Ward K, Steck TR, J Clin Microbiol 2004 42 2 753 758 10.1128/JCM.42.2.753-758.2004 14766848 (Pubitemid 38222658)
23. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY, Clin Microbiol Infect 2008 14 10 908 934 10.1111/j.1469-0691.2008.02070.x 18828852
24. Detection of eubacteria in interstitial cystitis by 16S rDNA amplification. Heritz DM, Lacroix JM, Batra SD, Jarvi KA, Beheshti B, Mittelman MW, J Urol 1997 158 6 2291 2295 10.1016/S0022-5347(01)68237-5 9366378 (Pubitemid 27481392)
25. PCR-based technique for the detection of bacteria in semen and urine. Lacroix JM, Jarvic K, Batrab SD, Heritze DM, Mittelman MW, J Microbiol Methods 1996 26 1-2 61 71 10.1016/0167-7012(96)00844-5 (Pubitemid 26246341)
26. Microbial population diversity in the urethras of healthy males and males suffering from nonchlamydial, nongonococcal urethritis. Riemersma WA, van der Schee CJ, van der Meijden WI, Verbrugh HA, van Belkum A, J Clin Microbiol 2003 41 5 1977 1986 10.1128/JCM.41.5.1977-1986.2003 12734237 (Pubitemid 36576523)
27. Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD, PLoS ONE 2010 5 11 14116 10.1371/journal.pone.0014116 21124791
28. The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van Der Pol B, PLoS ONE 2011 6 5 19709 10.1371/journal.pone. 0019709 21603636
29. Genome sequencing in microfabricated high-density picolitre reactors. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Nature 2005 437 7057 376 380 16056220 (Pubitemid 41613494)
30. Microbial diversity in the deep sea and the underexplored "rare biosphere". Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ, Proc Natl Acad Sci USA 2006 103 32 12115 12120 10.1073/pnas.0605127103 16880384 (Pubitemid 44215820)
31. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD, PLoS Pathog 2008 4 2 20 10.1371/journal.ppat.0040020 18248093 (Pubitemid 351340722)
32. Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, Ronaghi M, BMC Microbiol 2007 7 1 108 10.1186/1471-2180-7-108 18047683 (Pubitemid 351253128)
33. Comparative analysis of human gut microbiota by barcoded pyrosequencing. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L, PLoS ONE 2008 3 7 2836 10.1371/journal.pone.0002836 18665274
34. Accurate determination of microbial diversity from 454 pyrosequencing data. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT, Nature methods 2009 6 9 639 641 10.1038/nmeth.1361 19668203
35. ESPRIT. http://www.biotech.ufl.edu/people/sun/esprit.html
36. MEtaGenome ANalyzer. http://www-ab.informatik.uni-tuebingen.de/software/ megan/welcome.html
37. MEGAN analysis of metagenomic data. Huson DH, Auch AF, Qi J, Schuster SC, Genome Res 2007 17 3 377 386 http://www-ab.informatik.uni-tuebingen.de/ software/megan software freely available for academic purposes from 10.1101/gr.5969107 17255551 (Pubitemid 46376747)
38. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC, PLoS ONE 2008 3 6 2527 10.1371/journal.pone. 0002527 18575584
39. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Appl Environ Microbiol 2009 75 23 7537 7541 10.1128/AEM.01541-09 19801464
40. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Huse SM, Welch DM, Morrison HG, Sogin ML, Environmental microbiology 2010 12 7 1889 1898 10.1111/j.1462-2920.2010.02193.x 20236171
41. Rethinking microbial diversity analysis in the high throughput sequencing era. Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF, J Microbiol Methods 2011 86 1 42 51 10.1016/j.mimet.2011.03.014 21457733
42. Aerococcus christensenii sp. nov., from the human vagina. Collins MD, Jovita MR, Hutson RA, Ohlen M, Falsen E, Int J Syst Bacteriol 1999 49 Pt 3 1125 1128 10425770 (Pubitemid 29320763)
43. Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus. Ezaki T, Kawamura Y, Li N, Li ZY, Zhao L, Shu S, Int J Syst Evol Microbiol 2001 51 Pt 4 1521 1528 11491354 (Pubitemid 32700650)
44. "Actinobaculum massiliae," a new species causing chronic urinary tract infection. Greub G, Raoult D, J Clin Microbiol 2002 40 11 3938 3941 10.1128/JCM.40.11.3938-3941.2002 12409355 (Pubitemid 35291122)
45. Vaginal indicators of amniotic fluid infection in preterm labor. Hitti J, Hillier SL, Agnew KJ, Krohn MA, Reisner DP, Eschenbach DA, Obstet Gynecol 2001 97 2 211 219 10.1016/S0029-7844(00)01146-7 11165584 (Pubitemid 32126335)
46. Six cases of Aerococcus sanguinicola infection: clinical relevance and bacterial identification. Ibler K, Truberg Jensen K, Ostergaard C, Sonksen UW, Bruun B, Schonheyder HC, Kemp M, Dargis R, Andresen K, Christensen JJ, Scand J Infect Dis 2008 40 9 761 765 10.1080/00365540802078059 19086249
47. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. Malinen E, Krogius-Kurikka L, Lyra A, Nikkila J, Jaaskelainen A, Rinttila T, Vilpponen-Salmela T, von Wright AJ, Palva A, World J Gastroenterol 2010 16 36 4532 4540 10.3748/wjg.v16.i36.4532 20857523
48. Actinobaculum schaalii: a common cause of urinary tract infection in the elderly population. Bacteriological and clinical characteristics. Nielsen HL, Soby KM, Christensen JJ, Prag J, Scand J Infect Dis 2010 42 1 43 47 10.3109/00365540903289662 19883165
49. Enteropathogens in adult patients with diarrhea and healthy control subjects: a 1-year prospective study in a Swedish clinic for infectious diseases. Svenungsson B, Lagergren A, Ekwall E, Evengard B, Hedlund KO, Karnell A, Lofdahl S, Svensson L, Weintraub A, Clin Infect Dis 2000 30 5 770 778 10.1086/313770 10816147
50. Corynebacterium pseudogenitalium urinary tract infection. Vedel G, Toussaint G, Riegel P, Fouilladieu JL, Billoet A, Poyart C, Emerg Infect Dis 2006 12 2 355 356 17080582
51. Development of 16S rRNA-based probes for the identification of Gram-positive anaerobic cocci isolated from human clinical specimens. Wildeboer-Veloo AC, Harmsen HJ, Welling GW, Degener JE, Clin Microbiol Infect 2007 13 10 985 992 10.1111/j.1469-0691.2007.01803.x 17714522 (Pubitemid 47382254)
52. Aerococcus urinae in urinary tract infections. Zhang Q, Kwoh C, Attorri S, Clarridge JE, J Clin Microbiol 2000 38 4 1703 1705 10747177 (Pubitemid 30216723)
53. Eubacterium sp. oral clone BU061. http://www.ncbi.nlm.nih.gov/nuccore/ AF385567
54. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Bjornsson L, Hugenholtz P, Tyson GW, Blackall LL, Microbiology 2002 148 Pt 8 2309 2318 12177325
55. Phenotypic and phylogenetic characterization of some Globicatella-like organisms from human sources: description of Facklamia hominis gen. nov., sp. nov. Collins MD, Falsen E, Lemozy J, Akervall E, Sjoden B, Lawson PA, Int J Syst Bacteriol 1997 47 3 880 882 10.1099/00207713-47-3-880 9226922 (Pubitemid 27327788)
56. Molecular analysis of human forearm superficial skin bacterial biota. Gao Z, Tseng CH, Pei Z, Blaser MJ, Proc Natl Acad Sci USA 2007 104 8 2927 2932 10.1073/pnas.0607077104 17293459 (Pubitemid 46327980)
57. The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Hansen J, Gulati A, Sartor RB, Curr Opin Gastroenterol 2010 26 6 564 571 10.1097/MOG.0b013e32833f1195 20871399
58. Facklamia hominis causing chorioamnionitis and puerperal bacteraemia. Healy B, Beukenholt RW, Tuthill D, Ribeiro CD, The Journal of infection 2005 50 4 353 355 10.1016/j.jinf.2004.05.013 15845436 (Pubitemid 40533375)
59. Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae. Kalyuzhnaya MG, Bowerman S, Lara JC, Lidstrom ME, Chistoserdova L, Int J Syst Evol Microbiol 2006 56 Pt 12 2819 2823 17158982 (Pubitemid 44970992)
60. SufA-a bacterial enzyme that cleaves fibrinogen and blocks fibrin network formation. Karlsson C, Morgelin M, Collin M, Lood R, Andersson ML, Schmidtchen A, Bjorck L, Frick IM, Microbiology 2009 155 Pt 1 238 248 19118364
61. Molecular and cultural analysis of the microflora associated with endodontic infections. Munson MA, Pitt-Ford T, Chong B, Weightman A, Wade WG, Journal of dental research 2002 81 11 761 766 10.1177/154405910208101108 12407091
62. The lower genital tract microbiota in relation to cytokine-, SLPI- and endotoxin levels: application of checkerboard DNA-DNA hybridization (CDH). Nikolaitchouk N, Andersch B, Falsen E, Strombeck L, Mattsby-Baltzer I, APMIS 2008 116 4 263 277 10.1111/j.1600-0463.2008.00808.x 18397461 (Pubitemid 351499157)
63. Lactobacillus coleohominis sp. nov., isolated from human sources. Nikolaitchouk N, Wacher C, Falsen E, Andersch B, Collins MD, Lawson PA, Int J Syst Evol Microbiol 2001 51 Pt 6 2081 2085 11760950 (Pubitemid 33107429)
64. Vaginal microbiome of reproductive-age women. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, et al. Proc Natl Acad Sci USA 2011 108 Suppl 1 4680 4687 20534435
65. Identification of bacteria associated with spreading odontogenic infections by 16S rRNA gene sequencing. Riggio MP, Aga H, Murray CA, Jackson MS, Lennon A, Hammersley N, Bagg J, Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2007 103 5 610 617 10.1016/j.tripleo.2006.08.009 17141534
66. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Shah HN, Collins DM, Int J Syst Bacteriol 1990 40 2 205 208 10.1099/00207713-40-2-205 2223612 (Pubitemid 20143193)
67. Propionimicrobium gen. nov., a new genus to accommodate Propionibacterium lymphophilum (Torrey 1916) Johnson and Cummins 1972, 1057AL as Propionimicrobium lymphophilum comb. nov. Stackebrandt E, Schumann P, Schaal KP, Weiss N, Int J Syst Evol Microbiol 2002 52 Pt 6 1925 1927 12508849 (Pubitemid 36004169)
68. Porphyromonas somerae sp. nov., a pathogen isolated from humans and distinct from porphyromonas levii. Summanen PH, Durmaz B, Vaisanen ML, Liu C, Molitoris D, Eerola E, Helander IM, Finegold SM, J Clin Microbiol 2005 43 9 4455 4459 10.1128/JCM.43.9.4455-4459.2005 16145091 (Pubitemid 41298227)
69. Human Microbiome Project catalog. http://www.hmpdacc.org
70. Human Oral Microbiome Database. http://www.homd.org
71. European urinalysis guidelines. Scand J Clin Lab Invest Suppl 2000 231 1 86 12647764
72. Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species. Butler JE, Young ND, Lovley DR, BMC genomics 2009 10 103 10.1186/1471-2164-10-103 19284579
73. Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling. Dekio I, Hayashi H, Sakamoto M, Kitahara M, Nishikawa T, Suematsu M, Benno Y, J Med Microbiol 2005 54 Pt 12 1231 1238 16278439 (Pubitemid 41783833)
74. A metagenomic beta-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Gloux K, Berteau O, El Oumami H, Beguet F, Leclerc M, Dore J, Proc Natl Acad Sci USA 2011 108 Suppl 1 4539 4546 20615998
75. Factors affecting human supragingival biofilm composition. I. Plaque mass. Haffajee AD, Teles RP, Patel MR, Song X, Veiga N, Socransky SS, J Periodontal Res 2009 44 4 511 519 10.1111/j.1600-0765.2008.01154.x 18973540
76. Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation. Hayashi H, Sakamoto M, Benno Y, Microbiol Immunol 2002 46 12 819 831 12597356 (Pubitemid 36019156)
77. Bacterial diversity in the human saliva from different ages. Kang JG, Kim SH, Ahn TY, J Microbiol 2006 44 5 572 576 17082753
78. Neisseria and Branhamella. Knapp JS, Koumans EH, Manual of Clinical Microbiology Washington, DC, USA: ASM press, Murray PR, Baron EJ, Pfaller MAea, 7 1999 586 603
79. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. Ling Z, Kong J, Liu F, Zhu H, Chen X, Wang Y, Li L, Nelson KE, Xia Y, Xiang C, BMC genomics 2010 11 488 10.1186/1471-2164-11-488 20819230
80. Helicobacter pylori transiently in the mouth may participate in the transmission of infection. Silva DG, Tinoco EM, Rocha GA, Rocha AM, Guerra JB, Saraiva IE, Queiroz DM, Mem Inst Oswaldo Cruz 2010 105 5 657 660 10.1590/S0074-02762010000500009 20835612
81. Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Will C, Thurmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R, Appl Environ Microbiol 2010 76 20 6751 6759 10.1128/AEM.01063-10 20729324
82. A novel midstream urine-collection device reduces contamination rates in urine cultures amongst women. Jackson SR, Dryden M, Gillett P, Kearney P, Weatherall R, BJU international 2005 96 3 360 364 10.1111/j.1464-410X.2005. 05631.x 16042730 (Pubitemid 41097682)
83. Urine culture contamination: a College of American Pathologists Q-Probes study of 127 laboratories. Bekeris LG, Jones BA, Walsh MK, Wagar EA, Arch Pathol Lab Med 2008 132 6 913 917 18517272 (Pubitemid 351918695)
84. Transrenal DNA testing: progress and perspectives. Umansky SR, Tomei LD, Expert review of molecular diagnostics 2006 6 2 153 163 10.1586/14737159.6.2.153 16512776 (Pubitemid 44167145)
85. The effects of circumcision on the penis microbiome. Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ, et al. PLoS ONE 2010 5 1 8422 10.1371/journal.pone.0008422 20066050
86. A catalog of reference genomes from the human microbiome. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, et al. Science (New York, NY) 2010 328 5981 994 999
87. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE, Database (Oxford) 2010 2010 aq013
88. The gastrointestinal microbiome: a malleable, third genome of mammals. Carroll IM, Threadgill DW, Threadgill DS, Mamm Genome 2009 20 7 395 403 10.1007/s00335-009-9204-7 19629594
89. Enterotypes of the human gut microbiome. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, et al. Nature 2011
90. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW, PLoS ONE 2009 4 8 6669 10.1371/journal.pone.0006669 19693277
91. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Liu Z, DeSantis TZ, Andersen GL, Knight R, Nucleic Acids Res 2008 36 18 120 10.1093/nar/gkn491 18723574
92. Study of inter- and intra-individual variations in the salivary microbiota. Lazarevic V, Whiteson K, Hernandez D, Francois P, Schrenzel J, BMC genomics 2010 11 523 10.1186/1471-2164-11-523 20920195
93. The epidemiology of urinary tract infection. Foxman B, Nat Rev Urol 2010 7 12 653 660 10.1038/nrurol.2010.190 21139641
94. Molecular identification of bacteria associated with bacterial vaginosis. Fredricks DN, Fiedler TL, Marrazzo JM, N Engl J Med 2005 353 18 1899 1911 10.1056/NEJMoa043802 16267321 (Pubitemid 41565955)
95. High vaginal concentrations of Atopobium vaginae and Gardnerella vaginalis in women undergoing preterm labor. Menard JP, Mazouni C, Salem-Cherif I, Fenollar F, Raoult D, Boubli L, Gamerre M, Bretelle F, Obstet Gynecol 2010 115 1 134 140 10.1097/AOG.0b013e3181c391d7 20027045
96. Culture-independent identification of pathogenic bacteria and polymicrobial infections in the genitourinary tract of renal transplant recipients. Domann E, Hong G, Imirzalioglu C, Turschner S, Kuhle J, Watzel C, Hain T, Hossain H, Chakraborty T, J Clin Microbiol 2003 41 12 5500 5510 10.1128/JCM.41.12.5500-5510.2003 14662931 (Pubitemid 37543236)
97. Three cases of serious infection caused by Aerococcus urinae. Schuur PM, Sabbe L, van der Wouw AJ, Montagne GJ, Buiting AG, Eur J Clin Microbiol Infect Dis 1999 18 5 368 371 10.1007/PL00015022 10421047 (Pubitemid 29531176)
98. Culture-negative infective endocarditis caused by Aerococcus urinae. Slany M, Freiberger T, Pavlik P, Cerny J, J Heart Valve Dis 2007 16 2 203 205 17484472
99. Symptomatic bacteriuria due to Ureaplasma and Mycoplasma in adults. Pedraza Aviles AG, Ortiz Zaragoza MC, Rev Latinoam Microbiol 1998 40 1-2 9 13 10932729
100. Prevalence of Ureaplasma urealyticum and Mycoplasma hominis in women with chronic urinary symptoms. Baka S, Kouskouni E, Antonopoulou S, Sioutis D, Papakonstantinou M, Hassiakos D, Logothetis E, Liapis A, Urology 2009 74 1 62 66 10.1016/j.urology.2009.02.014 19371925
101. Guide To Amplicon Sequencing. http://www.my454.com/downloads/protocols/ Guide-To-Amplicon-Sequencing.pdf