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Volumn 8, Issue 5, 2005, Pages 564-571

How genomics has affected the concept of microbiology

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIOPHAGE; DNA SEQUENCE; DNA VIRUS; EUKARYOTE; GENOME; GENOME ANALYSIS; GENOME SIZE; GENOMICS; GRAM NEGATIVE BACTERIUM; MICROBIAL DIVERSITY; MICROBIOLOGY; NONHUMAN; PHYLOGENETIC TREE; PROKARYOTE; PUBLICATION; REVIEW; TAXONOMY;

EID: 25144491745     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2005.08.011     Document Type: Review
Times cited : (36)

References (48)
  • 2
    • 8844266097 scopus 로고    scopus 로고
    • The 1.2-Mb genome sequence of mimivirus
    • D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto, H. Ogata, B. La Scola, M. Susan, and J.M. Claverie The 1.2-Mb genome sequence of mimivirus Science 306 2004 1344 1350 This article reports the genome sequencing of a giant virus found in amoebae; both the particle size and genome size of this virus distinguish it from other viruses, together with the unusual presence of genes that encode components of the protein translation apparatus and DNA repair functions. The size and composition of the mimivirus genome raise interesting questions about how we distinguish viruses from cellular parasites.
    • (2004) Science , vol.306 , pp. 1344-1350
    • Raoult, D.1    Audic, S.2    Robert, C.3    Abergel, C.4    Renesto, P.5    Ogata, H.6    La Scola, B.7    Susan, M.8    Claverie, J.M.9
  • 3
    • 16844363764 scopus 로고    scopus 로고
    • New evolutionary frontiers from unusual virus genomes
    • C. Desjardins, J.A. Eisen, and V. Nene New evolutionary frontiers from unusual virus genomes Genome Biol 6 2005 212
    • (2005) Genome Biol , vol.6 , pp. 212
    • Desjardins, C.1    Eisen, J.A.2    Nene, V.3
  • 4
    • 0023025688 scopus 로고
    • Studies on polydnavirus transmission
    • D.B. Stoltz, D. Guzo, and D. Cook Studies on polydnavirus transmission Virology 155 1986 120 131
    • (1986) Virology , vol.155 , pp. 120-131
    • Stoltz, D.B.1    Guzo, D.2    Cook, D.3
  • 5
    • 0029860741 scopus 로고    scopus 로고
    • Host haemocyte inactivation by an insect parasitoid: Transient expression of a polydnavirus gene
    • S. Asgari, M. Hellers, and O. Schmidt Host haemocyte inactivation by an insect parasitoid: transient expression of a polydnavirus gene J Gen Virol 77 1996 2653 2662
    • (1996) J Gen Virol , vol.77 , pp. 2653-2662
    • Asgari, S.1    Hellers, M.2    Schmidt, O.3
  • 6
    • 5044234323 scopus 로고    scopus 로고
    • Genome sequence of a polydnavirus: Insights into symbiotic virus evolution
    • E. Espagne, C. Dupuy, E. Huguet, L. Cattolico, B. Provost, N. Martins, M. Poirie, G. Periquet, and J.M. Drezen Genome sequence of a polydnavirus: insights into symbiotic virus evolution Science 306 2004 286 289 Analysis of this 0.6 Mb genome, which originated from a virus transferred by a parasitoid wasp to its leptidopteran prey, revealed a segmented structural organization and features unusual in viral genomes, such as a wide range of coding density and the presence of introns. As in the case of the mimivirus genome, the polydnavirus genome challenges our assumptions of what constitutes a virus and a viral genome.
    • (2004) Science , vol.306 , pp. 286-289
    • Espagne, E.1    Dupuy, C.2    Huguet, E.3    Cattolico, L.4    Provost, B.5    Martins, N.6    Poirie, M.7    Periquet, G.8    Drezen, J.M.9
  • 8
    • 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
    • P.H. Janssen, A. Schuhmann, E. Morschel, and F.A. Rainey Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil Appl Environ Microbiol 63 1997 1382 1388
    • (1997) Appl Environ Microbiol , vol.63 , pp. 1382-1388
    • Janssen, P.H.1    Schuhmann, A.2    Morschel, E.3    Rainey, F.A.4
  • 9
    • 0037007636 scopus 로고    scopus 로고
    • A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
    • H. Huber, M.J. Hohn, R. Rachel, T. Fuchs, V.C. Wimmer, and K.O. Stetter A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont Nature 417 2002 63 67
    • (2002) Nature , vol.417 , pp. 63-67
    • Huber, H.1    Hohn, M.J.2    Rachel, R.3    Fuchs, T.4    Wimmer, V.C.5    Stetter, K.O.6
  • 10
    • 1542327668 scopus 로고    scopus 로고
    • Trends between gene content and genome size in prokaryotic species with larger genomes
    • K.T. Konstantinidis, and J.M. Tiedje Trends between gene content and genome size in prokaryotic species with larger genomes Proc Natl Acad Sci USA 101 2004 3160 3165
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3160-3165
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 21
    • 18544368222 scopus 로고    scopus 로고
    • In vitro assembly and GTP hydrolysis by bacterial tubulins BtubA and BtubB
    • C.A. Sontag, J.T. Staley, and H.P. Erickson In vitro assembly and GTP hydrolysis by bacterial tubulins BtubA and BtubB J Cell Biol 169 2005 233 238
    • (2005) J Cell Biol , vol.169 , pp. 233-238
    • Sontag, C.A.1    Staley, J.T.2    Erickson, H.P.3
  • 22
    • 0037022287 scopus 로고    scopus 로고
    • The origin of the eukaryotic cell: A genomic investigation
    • H. Hartman, and A. Fedorov The origin of the eukaryotic cell: a genomic investigation Proc Natl Acad Sci USA 99 2002 1420 1425
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 1420-1425
    • Hartman, H.1    Fedorov, A.2
  • 23
    • 12844268310 scopus 로고    scopus 로고
    • Eukaryotic signature proteins of Prosthecobacter dejongeii and Gemmata sp. Wa-1 as revealed by in silico analysis
    • J.T. Staley, H. Bouzek, and C. Jenkins Eukaryotic signature proteins of Prosthecobacter dejongeii and Gemmata sp. Wa-1 as revealed by in silico analysis FEMS Microbiol Lett 243 2005 9 14
    • (2005) FEMS Microbiol Lett , vol.243 , pp. 9-14
    • Staley, J.T.1    Bouzek, H.2    Jenkins, C.3
  • 24
    • 0345701347 scopus 로고    scopus 로고
    • Genes required for mycobacterial growth defined by high density mutagenesis
    • C.M. Sassetti, D.H. Boyd, and E.J. Rubin Genes required for mycobacterial growth defined by high density mutagenesis Mol Microbiol 48 2003 77 84
    • (2003) Mol Microbiol , vol.48 , pp. 77-84
    • Sassetti, C.M.1    Boyd, D.H.2    Rubin, E.J.3
  • 25
    • 0347990454 scopus 로고    scopus 로고
    • Evolution of minimal-gene-sets in host-dependent bacteria
    • L. Klasson, and S.G. Andersson Evolution of minimal-gene-sets in host-dependent bacteria Trends Microbiol 12 2004 37 43
    • (2004) Trends Microbiol , vol.12 , pp. 37-43
    • Klasson, L.1    Andersson, S.G.2
  • 26
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics, minimal gene-sets and the last universal common ancestor
    • E.V. Koonin Comparative genomics, minimal gene-sets and the last universal common ancestor Nat Rev Microbiol 1 2003 127 136
    • (2003) Nat Rev Microbiol , vol.1 , pp. 127-136
    • Koonin, E.V.1
  • 27
    • 0035917471 scopus 로고    scopus 로고
    • Structure, function, and assembly of the terminal organelle of Mycoplasma pneumoniae
    • D.C. Krause, and M.F. Balish Structure, function, and assembly of the terminal organelle of Mycoplasma pneumoniae FEMS Microbiol Lett 198 2001 1 7
    • (2001) FEMS Microbiol Lett , vol.198 , pp. 1-7
    • Krause, D.C.1    Balish, M.F.2
  • 28
    • 1442300837 scopus 로고    scopus 로고
    • Cellular engineering in a minimal microbe: Structure and assembly of the terminal organelle of Mycoplasma pneumoniae
    • D.C. Krause, and M.F. Balish Cellular engineering in a minimal microbe: structure and assembly of the terminal organelle of Mycoplasma pneumoniae Mol Microbiol 51 2004 917 924
    • (2004) Mol Microbiol , vol.51 , pp. 917-924
    • Krause, D.C.1    Balish, M.F.2
  • 31
    • 12244258510 scopus 로고    scopus 로고
    • Experimental evolution of conflict mediation between genomes
    • J.L. Sachs, and J.J. Bull Experimental evolution of conflict mediation between genomes Proc Natl Acad Sci USA 102 2005 390 395 A fascinating study of competition and cooperation in bacteriophages, in which the authors engineered phage to contain antibiotic resistance markers and then selected for the presence of both markers, resulting in drastic reduction of one genome and co-packaging of both phage genomes in a single particle.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 390-395
    • Sachs, J.L.1    Bull, J.J.2
  • 32
    • 0031912606 scopus 로고    scopus 로고
    • Novel division level bacterial diversity in a Yellowstone hot spring
    • P. Hugenholtz, C. Pitulle, K.L. Hershberger, and N.R. Pace Novel division level bacterial diversity in a Yellowstone hot spring J Bacteriol 180 1998 366 376
    • (1998) J Bacteriol , vol.180 , pp. 366-376
    • Hugenholtz, P.1    Pitulle, C.2    Hershberger, K.L.3    Pace, N.R.4
  • 33
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: Application of genomics to uncultured microorganisms
    • J. Handelsman Metagenomics: application of genomics to uncultured microorganisms Microbiol Mol Biol Rev 68 2004 669 685
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 669-685
    • Handelsman, J.1
  • 34
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: Genomic analysis of microbial communities
    • C.S. Riesenfeld, P.D. Schloss, and J. Handelsman Metagenomics: genomic analysis of microbial communities Annu Rev Genet 38 2004 525 552
    • (2004) Annu Rev Genet , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1    Schloss, P.D.2    Handelsman, J.3
  • 35
    • 4644354371 scopus 로고    scopus 로고
    • Metagenomics - The key to the uncultured microbes
    • W.R. Streit, and R.A. Schmitz Metagenomics - the key to the uncultured microbes Curr Opin Microbiol 7 2004 492 498
    • (2004) Curr Opin Microbiol , vol.7 , pp. 492-498
    • Streit, W.R.1    Schmitz, R.A.2
  • 36
    • 1342300599 scopus 로고    scopus 로고
    • Environmental genomics, the big picture?
    • F. Rodriguez-Valera Environmental genomics, the big picture? FEMS Microbiol Lett 231 2004 153 158
    • (2004) FEMS Microbiol Lett , vol.231 , pp. 153-158
    • Rodriguez-Valera, F.1
  • 37
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • G.W. Tyson, J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar, and J.F. Banfield Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 428 2004 37 43 First report of the use of shotgun sequencing to reconstruct the genomes of uncultivated microbes. Two almost-complete genomes and three partial genomes were assembled from an acidic biofilm that harbors a relatively low-diversity microbial community.
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5    Richardson, P.M.6    Solovyev, V.V.7    Rubin, E.M.8    Rokhsar, D.S.9    Banfield, J.F.10
  • 38
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • J.C. Venter, K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu, I. Paulsen, K.E. Nelson, and W. Nelson Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74 First attempt at extremely high-volume sequencing (of more than one billion base pairs) from an environmental sample. More than 1.2 million genes were predicted from the sequence data, estimated to originate from at least 1800 genomic species. This study provided a large and important dataset that continues to be mined for new findings.
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1    Remington, K.2    Heidelberg, J.F.3    Halpern, A.L.4    Rusch, D.5    Eisen, J.A.6    Wu, D.7    Paulsen, I.8    Nelson, K.E.9    Nelson, W.10
  • 39
    • 0037043731 scopus 로고    scopus 로고
    • Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
    • M.S. Rappé, S.A. Connon, K.L. Vergin, and S.J. Giovannoni Cultivation of the ubiquitous SAR11 marine bacterioplankton clade Nature 418 2002 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
  • 40
    • 18744382447 scopus 로고    scopus 로고
    • Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys
    • M. Sait, P. Hugenholtz, and P.H. Janssen Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys Environ Microbiol 4 2002 654 666
    • (2002) Environ Microbiol , vol.4 , pp. 654-666
    • Sait, M.1    Hugenholtz, P.2    Janssen, P.H.3
  • 43
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • K.T. Konstantinidis, and J.M. Tiedje Genomic insights that advance the species definition for prokaryotes Proc Natl Acad Sci USA 102 2005 2567 2572 First attempt at using quantitative genome data to establish a genome-based species definition for prokaryotes.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2567-2572
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 44
    • 0037407566 scopus 로고    scopus 로고
    • Genome diversification in Staphylococcus aureus: Molecular evolution of a highly variable chromosomal region encoding the Staphylococcal exotoxin-like family of proteins
    • J.R. Fitzgerald, S.D. Reid, E. Ruotsalainen, T.J. Tripp, M. Liu, R. Cole, P. Kuusela, P.M. Schlievert, A. Jarvinen, and J.M. Musser Genome diversification in Staphylococcus aureus: molecular evolution of a highly variable chromosomal region encoding the Staphylococcal exotoxin-like family of proteins Infect Immun 71 2003 2827 2838
    • (2003) Infect Immun , vol.71 , pp. 2827-2838
    • Fitzgerald, J.R.1    Reid, S.D.2    Ruotsalainen, E.3    Tripp, T.J.4    Liu, M.5    Cole, R.6    Kuusela, P.7    Schlievert, P.M.8    Jarvinen, A.9    Musser, J.M.10
  • 45
    • 0036335361 scopus 로고    scopus 로고
    • Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima
    • C.L. Nesbo, K.E. Nelson, and W.F. Doolittle Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima J Bacteriol 184 2002 4475 4488
    • (2002) J Bacteriol , vol.184 , pp. 4475-4488
    • Nesbo, C.L.1    Nelson, K.E.2    Doolittle, W.F.3
  • 46
    • 0038613121 scopus 로고    scopus 로고
    • The molecular evolution of catalatic hydroperoxidases: Evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota
    • M.G. Klotz, and P.C. Loewen The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota Mol Biol Evol 20 2003 1098 1112
    • (2003) Mol Biol Evol , vol.20 , pp. 1098-1112
    • Klotz, M.G.1    Loewen, P.C.2
  • 47
    • 0642312312 scopus 로고    scopus 로고
    • The source of laterally transferred genes in bacterial genomes
    • V. Daubin, E. Lerat, and G. Perriere The source of laterally transferred genes in bacterial genomes Genome Biol 4 2003 R57
    • (2003) Genome Biol , vol.4 , pp. 57
    • Daubin, V.1    Lerat, E.2    Perriere, G.3
  • 48
    • 0242490943 scopus 로고    scopus 로고
    • Lateral gene transfer: When will adolescence end?
    • J.G. Lawrence, and H. Hendrickson Lateral gene transfer: when will adolescence end? Mol Microbiol 50 2003 739 749
    • (2003) Mol Microbiol , vol.50 , pp. 739-749
    • Lawrence, J.G.1    Hendrickson, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.