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Volumn 81, Issue 2, 2012, Pages 427-437

Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction

Author keywords

16S rRNA; Correlation network; Faecal bacteria; Within individual variation

Indexed keywords

BACTERIAL DNA; RNA 16S;

EID: 84863779749     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01368.x     Document Type: Article
Times cited : (21)

References (49)
  • 2
    • 85027927719 scopus 로고    scopus 로고
    • Enterotypes of the human gut microbiome
    • Arumugam M, Raes J, Pelletier E et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180.
    • (2011) Nature , vol.473 , pp. 174-180
    • Arumugam, M.1    Raes, J.2    Pelletier, E.3
  • 4
    • 78449296237 scopus 로고    scopus 로고
    • Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors
    • Benson AK, Kelly SA, Legge R et al. (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. P Natl Acad Sci USA 107: 18933-18938.
    • (2010) P Natl Acad Sci USA , vol.107 , pp. 18933-18938
    • Benson, A.K.1    Kelly, S.A.2    Legge, R.3
  • 6
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
    • (2010) Nat Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3
  • 8
    • 79952757721 scopus 로고    scopus 로고
    • Composition, variability, and temporal stability of the intestinal microbiota of the elderly
    • Claesson MJ, Cusack S, O'Sullivan O et al. (2010) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. P Natl Acad Sci USA 108: 4586-4591.
    • (2010) P Natl Acad Sci USA , vol.108 , pp. 4586-4591
    • Claesson, M.J.1    Cusack, S.2    O'Sullivan, O.3
  • 10
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    • Cole JR, Wang Q, Cardenas E et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(Database issue): D141-D145.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3
  • 13
    • 79952756960 scopus 로고    scopus 로고
    • Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
    • Dethlefsen L & Relman DA (2010) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. P Natl Acad Sci USA 108: 4554-4561.
    • (2010) P Natl Acad Sci USA , vol.108 , pp. 4554-4561
    • Dethlefsen, L.1    Relman, D.A.2
  • 15
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen L, Huse S, Sogin ML & Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280.
    • (2008) PLoS Biol , vol.6
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 16
    • 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
  • 17
    • 0036135946 scopus 로고    scopus 로고
    • Molecular Monitoring of Succession of Bacterial Communities in Human Neonates
    • Favier CF, Vaughan EE, Vos WMD & Akkermans ADL (2002) Molecular Monitoring of Succession of Bacterial Communities in Human Neonates. Society 68: 219-226.
    • (2002) Society , vol.68 , pp. 219-226
    • Favier, C.F.1    Vaughan, E.E.2    Vos, W.M.D.3    Akkermans, A.D.L.4
  • 18
    • 0031692488 scopus 로고    scopus 로고
    • Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes
    • Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F & Welling GW (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 64: 3336-3345.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3336-3345
    • Franks, A.H.1    Harmsen, H.J.2    Raangs, G.C.3    Jansen, G.J.4    Schut, F.5    Welling, G.W.6
  • 19
    • 0141767040 scopus 로고    scopus 로고
    • Proper multivariate conditional autoregressive models for spatial data analysis
    • Gelfand A & Vounatsou P (2003) Proper multivariate conditional autoregressive models for spatial data analysis. Biostatistics 4: 11-25.
    • (2003) Biostatistics , vol.4 , pp. 11-25
    • Gelfand, A.1    Vounatsou, P.2
  • 21
    • 0037425743 scopus 로고    scopus 로고
    • Gut flora in health and disease
    • Guarner F & Malagelada J-R (2003) Gut flora in health and disease. Lancet 361: 512-519.
    • (2003) Lancet , vol.361 , pp. 512-519
    • Guarner, F.1    Malagelada, J.-R.2
  • 24
    • 34547685588 scopus 로고    scopus 로고
    • Importance of microbial colonization of the gut in early life to the development of immunity
    • Kelly D, King T & Aminov R (2007) Importance of microbial colonization of the gut in early life to the development of immunity. Mutat Res 622: 58-69.
    • (2007) Mutat Res , vol.622 , pp. 58-69
    • Kelly, D.1    King, T.2    Aminov, R.3
  • 26
    • 1542469537 scopus 로고    scopus 로고
    • A bivariate Bayes method for improving the estimates of mortality rates with 2-fold CAR model
    • Kim H, Sun D & Tsutakawa RK (2001) A bivariate Bayes method for improving the estimates of mortality rates with 2-fold CAR model. J Am Stat Assoc 96: 1506-1521.
    • (2001) J Am Stat Assoc , vol.96 , pp. 1506-1521
    • Kim, H.1    Sun, D.2    Tsutakawa, R.K.3
  • 28
    • 0006407254 scopus 로고    scopus 로고
    • Winbugs - a Bayesian modelling framework: concepts, structure, and extensibility
    • Lunn DJ, Thomas A, Best N & Spiegelhalter D (2000) Winbugs - a Bayesian modelling framework: concepts, structure, and extensibility. Stat Comput 10: 325-337.
    • (2000) Stat Comput , vol.10 , pp. 325-337
    • Lunn, D.J.1    Thomas, A.2    Best, N.3    Spiegelhalter, D.4
  • 29
    • 71549146864 scopus 로고    scopus 로고
    • Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces
    • Mulder IE, Schmidt B, Stokes CR et al. (2009) Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol 7: 79.
    • (2009) BMC Biol , vol.7 , pp. 79
    • Mulder, I.E.1    Schmidt, B.2    Stokes, C.R.3
  • 30
    • 59849113547 scopus 로고    scopus 로고
    • Microbes in gastrointestinal health and disease
    • Neish AS (2009) Microbes in gastrointestinal health and disease. Gastroenterology 136: 65-80.
    • (2009) Gastroenterology , vol.136 , pp. 65-80
    • Neish, A.S.1
  • 32
    • 34848903220 scopus 로고    scopus 로고
    • From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
    • Opgen-Rhein R & Strimmer K (2007) From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol 1: 37.
    • (2007) BMC Syst Biol , vol.1 , pp. 37
    • Opgen-Rhein, R.1    Strimmer, K.2
  • 34
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3
  • 36
    • 79951480123 scopus 로고    scopus 로고
    • R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria.
    • R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2010) R: A Language and Environment for Statistical Computing
  • 38
    • 15944364151 scopus 로고    scopus 로고
    • An empirical bayes approach to inferring large-scale gene association networks
    • Schäfer J & Strimmer K (2005a) An empirical bayes approach to inferring large-scale gene association networks. Bioinformatics 21: 754-764.
    • (2005) Bioinformatics , vol.21 , pp. 754-764
    • Schäfer, J.1    Strimmer, K.2
  • 39
    • 27844521293 scopus 로고    scopus 로고
    • A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
    • Schäfer J & Strimmer K (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4:Article32.
    • (2005) Stat Appl Genet Mol Biol , vol.4
    • Schäfer, J.1    Strimmer, K.2
  • 41
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3
  • 42
    • 13444302396 scopus 로고    scopus 로고
    • R2winbugs: a package for running winbugs from r
    • Sturtz S, Ligges U & Gelman A (2005) R2winbugs: a package for running winbugs from r. J Stat Softw 12: 1-16.
    • (2005) J Stat Softw , vol.12 , pp. 1-16
    • Sturtz, S.1    Ligges, U.2    Gelman, A.3
  • 44
    • 58749112734 scopus 로고    scopus 로고
    • A core gut microbiome in obese and lean twins
    • Turnbaugh PJ, Hamady M, Yatsunenko T et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
    • (2009) Nature , vol.457 , pp. 480-484
    • Turnbaugh, P.J.1    Hamady, M.2    Yatsunenko, T.3
  • 45
    • 79958056338 scopus 로고    scopus 로고
    • The host selects mucosal and luminal associations of co-evolved gut microbes: a novel concept
    • Van den Abbeele P, Van de Wiele T, Verstraete W & Possemiers S (2011) The host selects mucosal and luminal associations of co-evolved gut microbes: a novel concept. FEMS Microbiol Rev 35: 681-704.
    • (2011) FEMS Microbiol Rev , vol.35 , pp. 681-704
    • Van den Abbeele, P.1    Van de Wiele, T.2    Verstraete, W.3    Possemiers, S.4
  • 46
    • 2442616728 scopus 로고    scopus 로고
    • Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers
    • Vanhoutte T, Huys G, Brandt E & Swings J (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48: 437-446.
    • (2004) FEMS Microbiol Ecol , vol.48 , pp. 437-446
    • Vanhoutte, T.1    Huys, G.2    Brandt, E.3    Swings, J.4
  • 47
    • 67651121491 scopus 로고    scopus 로고
    • Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut
    • van Vliet MJ, Tissing WJE, Dun CAJ, Meessen NEL, Kamps WA, de Bont ESJM & Harmsen HJM (2009) Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut. Clin Infect Dis 49: 262-270.
    • (2009) Clin Infect Dis , vol.49 , pp. 262-270
    • van Vliet, M.J.1    Tissing, W.J.E.2    Dun, C.A.J.3    Meessen, N.E.L.4    Kamps, W.A.5    de Bont, E.S.J.M.6    Harmsen, H.J.M.7
  • 48
    • 34247384151 scopus 로고    scopus 로고
    • Intestinal bacteria and ageing
    • Woodmansey EJ (2007) Intestinal bacteria and ageing. J Appl Microbiol 102: 1178-1186.
    • (2007) J Appl Microbiol , vol.102 , pp. 1178-1186
    • Woodmansey, E.J.1
  • 49
    • 0031684010 scopus 로고    scopus 로고
    • Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria
    • Zoetendal EG, Akkermans ADL & Vos WMD (1998) Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria. Appl Environ Microbiol 64: 3854-3859.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3854-3859
    • Zoetendal, E.G.1    Akkermans, A.D.L.2    Vos, W.M.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.