메뉴 건너뛰기




Volumn 9, Issue 8, 2014, Pages

MediaDB: A database of microbial growth conditions in defined media

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM CULTURE; BIOMASS; CLINICAL DATA REPOSITORY; CULTURE MEDIUM; DATA BASE; GENE SEQUENCE; HAEMOPHILUS INFLUENZAE; HIGH THROUGHPUT SEQUENCING; MEDIADB DATABASE; METHANOCOCCUS MARIPALUDIS; MICROBIAL GROWTH; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; SHEWANELLA ONEIDENSIS; STREPTOMYCES COELICOLOR; SYNECHOCYSTIS; UNINDEXED SEQUENCE; ARCHAEON; BACTERIA; CHEMISTRY; EUKARYOTIC CELL; FACTUAL DATABASE; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; PHYSIOLOGY; PROCEDURES;

EID: 84905455190     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103548     Document Type: Article
Times cited : (21)

References (49)
  • 1
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, et al. (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature Biotechnology 28: 977-982.
    • (2010) Nature Biotechnology , vol.28 , pp. 977-982
    • Henry, C.S.1    DeJongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5
  • 2
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BØ (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols 5: 93-121.
    • (2010) Nature Protocols , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.Ø.2
  • 3
    • 0034018128 scopus 로고    scopus 로고
    • Who is out there? Microbial aspects of biodiversity
    • Amann R (2000) Who is out there? Microbial aspects of biodiversity. Systematic and Applied Microbiology 23: 1-8.
    • (2000) Systematic and Applied Microbiology , vol.23 , pp. 1-8
    • Amann, R.1
  • 4
    • 1842560595 scopus 로고    scopus 로고
    • Tapping into microbial diversity
    • DOI 10.1038/nrmicro819
    • Keller M, Zengler K (2004) Tapping into microbial diversity. Nature Reviews Microbiology 2: 141-150. (Pubitemid 39490067)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.2 , pp. 141-150
    • Keller, M.1    Zengler, K.2
  • 5
    • 70349448695 scopus 로고    scopus 로고
    • Cultivating the uncultured: Limits, advances and future challenges
    • Alain K, Querellou J (2009) Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13: 583-594.
    • (2009) Extremophiles , vol.13 , pp. 583-594
    • Alain, K.1    Querellou, J.2
  • 7
    • 77955911147 scopus 로고    scopus 로고
    • Culturing marine bacteria-an essential prerequisite for biodiscovery
    • Joint I, Mühling M, Querellou J (2010) Culturing marine bacteria-an essential prerequisite for biodiscovery. Microbial Biotechnology 3: 564-575.
    • (2010) Microbial Biotechnology , vol.3 , pp. 564-575
    • Joint, I.1    Mühling, M.2    Querellou, J.3
  • 10
    • 0037052320 scopus 로고    scopus 로고
    • Isolating "uncultivabte" microorganisms in pure culture in a simulated natural environment
    • DOI 10.1126/science.1070633
    • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating " uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129. (Pubitemid 34517131)
    • (2002) Science , vol.296 , Issue.5570 , pp. 1127-1129
    • Kaeberlein, T.1    Lewis, K.2    Epstein, S.S.3
  • 11
    • 29144482711 scopus 로고    scopus 로고
    • Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria
    • DOI 10.1128/AEM.71.12.8714-8720.2005
    • Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Applied and Environmental Microbiology 71: 8714-8720. (Pubitemid 41804007)
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.12 , pp. 8714-8720
    • Ferrari, B.C.1    Binnerup, S.J.2    Gillings, M.3
  • 12
    • 33745080668 scopus 로고    scopus 로고
    • Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam
    • DOI 10.1007/s10126-005-5015-3
    • Yasumoto-Hirose M, Nishijima M, Ngirchechol MK, Kanoh K, Shizuri Y, et al. (2006) Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Marine Biotechnology 8: 227-237. (Pubitemid 43881827)
    • (2006) Marine Biotechnology , vol.8 , Issue.3 , pp. 227-237
    • Yasumoto-Hirose, M.1    Nishijima, M.2    Ngirchechol, M.K.3    Kanoh, K.4    Shizuri, Y.5    Miki, W.6
  • 13
    • 35448948699 scopus 로고    scopus 로고
    • Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates
    • DOI 10.1128/AEM.01309-07
    • Bollmann A, Lewis K, Epstein SS (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Applied and Environmental Microbiology 73: 6386-6390. (Pubitemid 47623695)
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.20 , pp. 6386-6390
    • Bollmann, A.1    Lewis, K.2    Epstein, S.S.3
  • 14
    • 0036323967 scopus 로고    scopus 로고
    • Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea
    • DOI 10.1128/AEM.68.8.3978-3987.2002
    • Bruns A, Cypionka H, Overmann J (2002) Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Applied and Environmental Microbiology 68: 3978-3987. (Pubitemid 34836711)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.8 , pp. 3978-3987
    • Bruns, A.1    Cypionka, H.2    Overmann, J.3
  • 15
    • 0242684409 scopus 로고    scopus 로고
    • Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton
    • DOI 10.1128/AEM.69.4.1980-1989.2003
    • Bruns A, Nübel U, Cypionka H, Overmann J (2003) Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Applied and Environmental Microbiology 69: 1980-1989. (Pubitemid 36443610)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.4 , pp. 1980-1989
    • Bruns, A.1    Nubel, U.2    Cypionka, H.3    Overmann, J.4
  • 17
    • 77949545789 scopus 로고    scopus 로고
    • Siderophores from neighboring organisms promote the growth of uncultured bacteria
    • D'Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, et al. (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry & Biology 17: 254-264.
    • (2010) Chemistry & Biology , vol.17 , pp. 254-264
    • D'Onofrio, A.1    Crawford, J.M.2    Stewart, E.J.3    Witt, K.4    Gavrish, E.5
  • 18
    • 0030613344 scopus 로고    scopus 로고
    • Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil
    • Janssen PH, Schuhmann A, Mörschel E, Rainey FA (1997) Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Applied and Environmental Microbiology 63: 1382-1388.
    • (1997) Applied and Environmental Microbiology , vol.63 , pp. 1382-1388
    • Janssen, P.H.1    Schuhmann, A.2    Mörschel, E.3    Rainey, F.A.4
  • 19
  • 20
    • 0036250036 scopus 로고    scopus 로고
    • Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia
    • DOI 10.1128/AEM.68.5.2391-2396.2002
    • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Applied and Environmental Microbiology 68: 2391-2396. (Pubitemid 34477836)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.5 , pp. 2391-2396
    • Janssen, P.H.1    Yates, P.S.2    Grinton, B.E.3    Taylor, P.M.4    Sait, M.5
  • 21
    • 0036324056 scopus 로고    scopus 로고
    • High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates
    • DOI 10.1128/AEM.68.8.3878-3885.2002
    • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Applied and Environmental Microbiology 68: 3878-3885. (Pubitemid 34836698)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.8 , pp. 3878-3885
    • Connon, S.A.1    Giovannoni, S.J.2
  • 22
    • 0037043731 scopus 로고    scopus 로고
    • Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
    • Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
    • (2002) Nature , vol.418 , pp. 630-633
    • Rappé, M.S.1    Connon, S.A.2    Vergin, K.L.3    Giovannoni, S.J.4
  • 24
  • 25
    • 18744382447 scopus 로고    scopus 로고
    • Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys
    • DOI 10.1046/j.1462-2920.2002.00352.x
    • Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivationin-dependent surveys. Environmental Microbiology 4: 654-666. (Pubitemid 35442253)
    • (2002) Environmental Microbiology , vol.4 , Issue.11 , pp. 654-666
    • Sait, M.1    Hugenholtz, P.2    Janssen, P.H.3
  • 27
    • 13544277388 scopus 로고    scopus 로고
    • Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria
    • DOI 10.1128/AEM.71.2.826-834.2005
    • Davis KE, Joseph SJ, Janssen PH (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Applied and Environmental Microbiology 71: 826-834. (Pubitemid 40223569)
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.2 , pp. 826-834
    • Davis, K.E.R.1    Joseph, S.J.2    Janssen, P.H.3
  • 28
    • 55949124350 scopus 로고    scopus 로고
    • Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand
    • Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S, et al. (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environmental Microbiology 10: 2030-2041.
    • (2008) Environmental Microbiology , vol.10 , pp. 2030-2041
    • Stott, M.B.1    Crowe, M.A.2    Mountain, B.W.3    Smirnova, A.V.4    Hou, S.5
  • 32
    • 84876460076 scopus 로고    scopus 로고
    • Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium
    • Carini P, Steindler L, Beszteri S, Giovannoni SJ (2012) Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium. The ISME Journal 7: 592-602.
    • (2012) The ISME Journal , vol.7 , pp. 592-602
    • Carini, P.1    Steindler, L.2    Beszteri, S.3    Giovannoni, S.J.4
  • 33
  • 34
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • DOI 10.1038/nrmicro1023
    • Price ND, Reed JL, Palsson BØ (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews Microbiology 2: 886-897. (Pubitemid 39567269)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 35
    • 0347762745 scopus 로고    scopus 로고
    • Identifying Constraints that Govern Cell Behavior: A Key to Converting Conceptual to Computational Models in Biology?
    • DOI 10.1002/bit.10849
    • Covert MW, Famili I, Palsson BO (2003) Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and Bioengineering 84: 763-772. (Pubitemid 38089692)
    • (2003) Biotechnology and Bioengineering , vol.84 , Issue.7 , pp. 763-772
    • Covert, M.W.1    Famili, I.2    Palsson, B.O.3
  • 40
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger J, Park JO, Conrad TM, Palsson BØ (2010) BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.Ø.4
  • 41
    • 84876560358 scopus 로고    scopus 로고
    • The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013
    • Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Research 41: D456-D463.
    • (2013) Nucleic Acids Research , vol.41
    • Hastings, J.1    De Matos, P.2    Dekker, A.3    Ennis, M.4    Harsha, B.5
  • 43
    • 67849110019 scopus 로고    scopus 로고
    • Hyperlink management system and ID converter system: Enabling maintenance-free hyperlinks among major biological databases
    • Imanishi T, Nakaoka H (2009) Hyperlink management system and ID converter system: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Research 37: W17-W22.
    • (2009) Nucleic Acids Research , vol.37
    • Imanishi, T.1    Nakaoka, H.2
  • 44
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4: R54.
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 45
    • 84857080094 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A
    • Benedict MN, Gonnerman MC, Metcalf WW, Price ND (2012) Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. Journal of Bacteriology 194: 855-865.
    • (2012) Journal of Bacteriology , vol.194 , pp. 855-865
    • Benedict, M.N.1    Gonnerman, M.C.2    Metcalf, W.W.3    Price, N.D.4
  • 46
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596.
    • (2013) Nucleic Acids Research , vol.41
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3    Gerken, J.4    Schweer, T.5
  • 47
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 49
    • 0032127358 scopus 로고    scopus 로고
    • The Biology Workbench - A seamless database and analysis environment for the biologist
    • Subramaniam S (1998) The Biology Workbench - a seamless database and analysis environment for the biologist. Proteins: Structure, Function, and Bioinformatics 32: 1-2.
    • (1998) Proteins: Structure, Function, and Bioinformatics , vol.32 , pp. 1-2
    • Subramaniam, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.