메뉴 건너뛰기




Volumn 7, Issue 5, 2012, Pages

Comparison of storage conditions for human vaginal microbiome studies

Author keywords

[No Author keywords available]

Indexed keywords

LACTIC ACID; RNA 16S;

EID: 84861385390     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036934     Document Type: Article
Times cited : (58)

References (50)
  • 2
    • 29144436277 scopus 로고    scopus 로고
    • Microbial community fingerprints of composts stored under different conditions
    • Klammer S, Mondini C, Insam H, (2005) Microbial community fingerprints of composts stored under different conditions. Ann Microbiol 55: 299-305.
    • (2005) Ann Microbiol , vol.55 , pp. 299-305
    • Klammer, S.1    Mondini, C.2    Insam, H.3
  • 3
    • 38049080602 scopus 로고    scopus 로고
    • Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces
    • Nechvatal JM, Ram JL, Basson MD, Namprachan P, Niec SR, et al. (2008) Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods 72: 124-132.
    • (2008) J Microbiol Methods , vol.72 , pp. 124-132
    • Nechvatal, J.M.1    Ram, J.L.2    Basson, M.D.3    Namprachan, P.4    Niec, S.R.5
  • 5
    • 77951941062 scopus 로고    scopus 로고
    • Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
    • Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N, (2010) Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 307: 80-86.
    • (2010) FEMS Microbiol Lett , vol.307 , pp. 80-86
    • Lauber, C.L.1    Zhou, N.2    Gordon, J.I.3    Knight, R.4    Fierer, N.5
  • 6
    • 61449237181 scopus 로고    scopus 로고
    • Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity
    • Tzeneva VA, Salles JF, Naumova N, de Vos WM, Kuikman PJ, et al. (2009) Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity. Res Microbiol 160: 89-98.
    • (2009) Res Microbiol , vol.160 , pp. 89-98
    • Tzeneva, V.A.1    Salles, J.F.2    Naumova, N.3    de Vos, W.M.4    Kuikman, P.J.5
  • 8
    • 84934443407 scopus 로고    scopus 로고
    • Biorepository standards and protocols for collecting, processing, and storing human tissues
    • Troyer D, (2008) Biorepository standards and protocols for collecting, processing, and storing human tissues. Methods Mol Biol 441: 193-220.
    • (2008) Methods Mol Biol , vol.441 , pp. 193-220
    • Troyer, D.1
  • 9
    • 41849083955 scopus 로고    scopus 로고
    • High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study
    • Barton RH, Nicholson JK, Elliott P, Holmes E, (2008) High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study. Int J Epidemiol 37 (Suppl 1): i31-40.
    • (2008) Int J Epidemiol , vol.37 , Issue.SUPPL. 1
    • Barton, R.H.1    Nicholson, J.K.2    Elliott, P.3    Holmes, E.4
  • 10
    • 41849087888 scopus 로고    scopus 로고
    • The UK Biobank sample handling and storage validation studies
    • Peakman TC, Elliott P, (2008) The UK Biobank sample handling and storage validation studies. Int J Epidemiol 37 (Suppl 1): i2-6.
    • (2008) Int J Epidemiol , vol.37 , Issue.SUPPL. 1
    • Peakman, T.C.1    Elliott, P.2
  • 11
    • 41849111818 scopus 로고    scopus 로고
    • A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols
    • Dunn WB, Broadhurst D, Ellis DI, Brown M, Halsall A, et al. (2008) A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols. Int J Epidemiol 37 (Suppl 1): i23-30.
    • (2008) Int J Epidemiol , vol.37 , Issue.SUPPL. 1
    • Dunn, W.B.1    Broadhurst, D.2    Ellis, D.I.3    Brown, M.4    Halsall, A.5
  • 12
    • 33947392610 scopus 로고    scopus 로고
    • Urine stability for metabolomics studies: effects of preparation and storage
    • Saude EJ, Sykes, D B, (2007) Urine stability for metabolomics studies: effects of preparation and storage. Metabolomics 3: 19-27.
    • (2007) Metabolomics , vol.3 , pp. 19-27
    • Saude, E.J.1    Sykes, D.B.2
  • 13
    • 0023217720 scopus 로고
    • Short-chain fatty acids and succinate in feces of healthy human volunteers and their correlation with anaerobe cultural counts
    • Meijer-Severs GJ, van Santen E, (1987) Short-chain fatty acids and succinate in feces of healthy human volunteers and their correlation with anaerobe cultural counts. Scand J Gastroenterol 22: 672-676.
    • (1987) Scand J Gastroenterol , vol.22 , pp. 672-676
    • Meijer-Severs, G.J.1    van Santen, E.2
  • 14
    • 38649108480 scopus 로고    scopus 로고
    • Species variation in the fecal metabolome gives insight into differential gastrointestinal function
    • Saric J, Wang Y, Li J, Coen M, Utzinger J, et al. (2008) Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res 7: 352-360.
    • (2008) J Proteome Res , vol.7 , pp. 352-360
    • Saric, J.1    Wang, Y.2    Li, J.3    Coen, M.4    Utzinger, J.5
  • 17
    • 34548768221 scopus 로고    scopus 로고
    • Effect of magnetic field strength on NMR-based metabonomic human urine data. Comparative study of 250, 400, 500, and 800 MHz
    • Bertram HC, Malmendal A, Petersen BO, Madsen JC, Pedersen H, et al. (2007) Effect of magnetic field strength on NMR-based metabonomic human urine data. Comparative study of 250, 400, 500, and 800 MHz. Anal Chem 79: 7110-7115.
    • (2007) Anal Chem , vol.79 , pp. 7110-7115
    • Bertram, H.C.1    Malmendal, A.2    Petersen, B.O.3    Madsen, J.C.4    Pedersen, H.5
  • 18
    • 0141625930 scopus 로고    scopus 로고
    • Self-collected versus provider-collected vaginal swabs for the diagnosis of bacterial vaginosis: an assessment of validity and reliability
    • Nelson DB, Bellamy S, Gray TS, Nachamkin I, (2003) Self-collected versus provider-collected vaginal swabs for the diagnosis of bacterial vaginosis: an assessment of validity and reliability. J Clin Epidemiol 56: 862-866.
    • (2003) J Clin Epidemiol , vol.56 , pp. 862-866
    • Nelson, D.B.1    Bellamy, S.2    Gray, T.S.3    Nachamkin, I.4
  • 19
    • 77951866199 scopus 로고    scopus 로고
    • Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis
    • Forney LJ, Gajer P, Williams CJ, Schneider GM, Koenig SS, et al. (2010) Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. J Clin Microbiol 48: 1741-1748.
    • (2010) J Clin Microbiol , vol.48 , pp. 1741-1748
    • Forney, L.J.1    Gajer, P.2    Williams, C.J.3    Schneider, G.M.4    Koenig, S.S.5
  • 20
    • 0026088584 scopus 로고
    • Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation
    • Nugent RP, Krohn MA, Hillier SL, (1991) Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. JClinMicrobiol 29: 297-301.
    • (1991) JClinMicrobiol , vol.29 , pp. 297-301
    • Nugent, R.P.1    Krohn, M.A.2    Hillier, S.L.3
  • 21
    • 0031596222 scopus 로고    scopus 로고
    • Inverse association of H2O2-producing lactobacilli and vaginal Escherichia coli colonization in women with recurrent urinary tract infections
    • Gupta K, Stapleton AE, Hooton TM, Roberts PL, Fennell CL, et al. (1998) Inverse association of H2O2-producing lactobacilli and vaginal Escherichia coli colonization in women with recurrent urinary tract infections. J Infect Dis 178: 446-450.
    • (1998) J Infect Dis , vol.178 , pp. 446-450
    • Gupta, K.1    Stapleton, A.E.2    Hooton, T.M.3    Roberts, P.L.4    Fennell, C.L.5
  • 24
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 26
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 27
    • 33644810067 scopus 로고    scopus 로고
    • Evaluating distance functions for clustering tandem repeats
    • Rao S, Rodriguez A, Benson G, (2005) Evaluating distance functions for clustering tandem repeats. Genome Inform 16: 3-12.
    • (2005) Genome Inform , vol.16 , pp. 3-12
    • Rao, S.1    Rodriguez, A.2    Benson, G.3
  • 28
    • 34247990255 scopus 로고
    • On the Kolmogorov-Smirnov Test for Normality with Mean and Variance Unknown
    • Lilliefors HW, (1967) On the Kolmogorov-Smirnov Test for Normality with Mean and Variance Unknown. Journal of the American Statistical Association 62: 399-402.
    • (1967) Journal of the American Statistical Association , vol.62 , pp. 399-402
    • Lilliefors, H.W.1
  • 29
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss PD, Gevers D, Westcott SL, (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS one 6: e27310.
    • (2011) PloS One , vol.6
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 30
    • 0001312511 scopus 로고
    • Algorithm AS 183: An Efficient and Portable Pseudo-Random Number Generator
    • Wichman BA, Hill ID, (1982) Algorithm AS 183: An Efficient and Portable Pseudo-Random Number Generator. Applied Statistics 31: 188-190.
    • (1982) Applied Statistics , vol.31 , pp. 188-190
    • Wichman, B.A.1    Hill, I.D.2
  • 31
    • 0023308154 scopus 로고
    • Building a Random-Number Generator
    • Wichman BA, Hill ID, (1987) Building a Random-Number Generator. BYTE pp. 127-128.
    • (1987) BYTE , pp. 127-128
    • Wichman, B.A.1    Hill, I.D.2
  • 33
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME journal 6: 610-618.
    • (2012) The ISME Journal , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    DeSantis, T.Z.5
  • 34
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 35
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: a new phylogenetic method for comparing microbial communities
    • Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 36
    • 77951056974 scopus 로고    scopus 로고
    • Approaching clinical reality: markers for monitoring systemic inflammation and sepsis
    • Claus RA, Otto GP, Deigner HP, Bauer M, (2010) Approaching clinical reality: markers for monitoring systemic inflammation and sepsis. Curr Mol Med 10: 227-235.
    • (2010) Curr Mol Med , vol.10 , pp. 227-235
    • Claus, R.A.1    Otto, G.P.2    Deigner, H.P.3    Bauer, M.4
  • 37
    • 5144233105 scopus 로고
    • MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy
    • Bax A, Davis DG, (1985) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J Magn Reson 65: 355-360.
    • (1985) J Magn Reson , vol.65 , pp. 355-360
    • Bax, A.1    Davis, D.G.2
  • 38
    • 0029400480 scopus 로고
    • NMRPipe: a multidimensional spectral processing system based on UNIX pipes
    • Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293.
    • (1995) J Biomol NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5
  • 39
    • 0346142279 scopus 로고
    • Individual comparisons of grouped data by ranking methods
    • Wilcoxon F, (1946) Individual comparisons of grouped data by ranking methods. J Econ Entomol 39: 269.
    • (1946) J Econ Entomol , vol.39 , pp. 269
    • Wilcoxon, F.1
  • 42
    • 0032879164 scopus 로고    scopus 로고
    • Acid production by vaginal flora in vitro is consistent with the rate and extent of vaginal acidification
    • Boskey ER, Telsch KM, Whaley KJ, Moench TR, Cone RA, (1999) Acid production by vaginal flora in vitro is consistent with the rate and extent of vaginal acidification. Infect Immun 67: 5170-5175.
    • (1999) Infect Immun , vol.67 , pp. 5170-5175
    • Boskey, E.R.1    Telsch, K.M.2    Whaley, K.J.3    Moench, T.R.4    Cone, R.A.5
  • 43
    • 0034817210 scopus 로고    scopus 로고
    • Origins of vaginal acidity: high D/L lactate ratio is consistent with bacteria being the primary source
    • Boskey ER, Cone RA, Whaley KJ, Moench TR, (2001) Origins of vaginal acidity: high D/L lactate ratio is consistent with bacteria being the primary source. Hum Reprod 16: 1809-1813.
    • (2001) Hum Reprod , vol.16 , pp. 1809-1813
    • Boskey, E.R.1    Cone, R.A.2    Whaley, K.J.3    Moench, T.R.4
  • 44
    • 70350306659 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 is trapped by acidic but not by neutralized human cervicovaginal mucus
    • Lai SK, Hida K, Shukair S, Wang YY, Figueiredo A, et al. (2009) Human immunodeficiency virus type 1 is trapped by acidic but not by neutralized human cervicovaginal mucus. J Virol 83: 11196-11200.
    • (2009) J Virol , vol.83 , pp. 11196-11200
    • Lai, S.K.1    Hida, K.2    Shukair, S.3    Wang, Y.Y.4    Figueiredo, A.5
  • 45
    • 79960558598 scopus 로고    scopus 로고
    • In vaginal fluid, bacteria associated with bacterial vaginosis can be suppressed with lactic acid but not hydrogen peroxide
    • O'Hanlon DE, Moench TR, Cone RA, (2011) In vaginal fluid, bacteria associated with bacterial vaginosis can be suppressed with lactic acid but not hydrogen peroxide. BMC Infect Dis 11: 200.
    • (2011) BMC Infect Dis , vol.11 , pp. 200
    • O'Hanlon, D.E.1    Moench, T.R.2    Cone, R.A.3
  • 46
    • 8644281117 scopus 로고    scopus 로고
    • Analysis of vaginal acetic acid in patients undergoing treatment for bacterial vaginosis
    • Chaudry AN, Travers PJ, Yuenger J, Colletta L, Evans P, et al. (2004) Analysis of vaginal acetic acid in patients undergoing treatment for bacterial vaginosis. J Clin Microbiol 42: 5170-5175.
    • (2004) J Clin Microbiol , vol.42 , pp. 5170-5175
    • Chaudry, A.N.1    Travers, P.J.2    Yuenger, J.3    Colletta, L.4    Evans, P.5
  • 47
    • 0033760002 scopus 로고    scopus 로고
    • Inhibition of chemotaxis by organic acids from anaerobes may prevent a purulent response in bacterial vaginosis
    • Al-Mushrif S, Eley A, Jones BM, (2000) Inhibition of chemotaxis by organic acids from anaerobes may prevent a purulent response in bacterial vaginosis. J Med Microbiol 49: 1023-1030.
    • (2000) J Med Microbiol , vol.49 , pp. 1023-1030
    • Al-Mushrif, S.1    Eley, A.2    Jones, B.M.3
  • 48
    • 84859701470 scopus 로고    scopus 로고
    • Short-Chain Fatty Acids Induce Pro-Inflammatory Cytokine Production Alone and in Combination with Toll-Like Receptor Ligands
    • Mirmonsef P, Zariffard MR, Gilbert D, Makinde H, Landay AL, et al. (2011) Short-Chain Fatty Acids Induce Pro-Inflammatory Cytokine Production Alone and in Combination with Toll-Like Receptor Ligands. Am J Reprod Immunol.
    • (2011) Am J Reprod Immunol
    • Mirmonsef, P.1    Zariffard, M.R.2    Gilbert, D.3    Makinde, H.4    Landay, A.L.5
  • 49
    • 79551641738 scopus 로고    scopus 로고
    • The effects of commensal bacteria on innate immune responses in the female genital tract
    • Mirmonsef P, Gilbert D, Zariffard MR, Hamaker BR, Kaur A, et al. (2011) The effects of commensal bacteria on innate immune responses in the female genital tract. Am J Reprod Immunol 65: 190-195.
    • (2011) Am J Reprod Immunol , vol.65 , pp. 190-195
    • Mirmonsef, P.1    Gilbert, D.2    Zariffard, M.R.3    Hamaker, B.R.4    Kaur, A.5
  • 50
    • 78650404794 scopus 로고    scopus 로고
    • Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection
    • Brotman RM, Klebanoff MA, Nansel TR, Yu KF, Andrews WW, et al. (2010) Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection. J Infect Dis 202: 1907-1915.
    • (2010) J Infect Dis , vol.202 , pp. 1907-1915
    • Brotman, R.M.1    Klebanoff, M.A.2    Nansel, T.R.3    Yu, K.F.4    Andrews, W.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.