메뉴 건너뛰기




Volumn 5, Issue AUG, 2014, Pages

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

Author keywords

Gene content; Genus boundaries; Marine microbiology; Phylogenomics; Roseobacter group; Supermatrix

Indexed keywords

CLADISTICS; COMB; GENOME; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROBIOLOGY; NEW GENUS; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; ROSEOBACTER; SPECIES;

EID: 84987811377     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00416     Document Type: Article
Times cited : (43)

References (75)
  • 1
    • 84878413043 scopus 로고    scopus 로고
    • Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema
    • Abt, B., Göker, M., Scheuner, C., Han, C., Lu, M., Misra, M., et al. (2013). Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Stand. Genomic Sci. 8, 88-105. doi: 10.4056/sigs.3096473
    • (2013) Stand. Genomic Sci. , vol.8 , pp. 88-105
    • Abt, B.1    Göker, M.2    Scheuner, C.3    Han, C.4    Lu, M.5    Misra, M.6
  • 2
    • 84863601275 scopus 로고    scopus 로고
    • Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta
    • Abt, B., Han, C., Scheuner, C., Lu, M., Lapidus, A., Nolan, M., et al. (2012). Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand. Genomic Sci. 6, 194-209. doi: 10.4056/sigs.2796069
    • (2012) Stand. Genomic Sci. , vol.6 , pp. 194-209
    • Abt, B.1    Han, C.2    Scheuner, C.3    Lu, M.4    Lapidus, A.5    Nolan, M.6
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6
  • 4
    • 79957438170 scopus 로고    scopus 로고
    • Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
    • Anderson, I. J., Scheuner, C., Göker, M., Mavromatis, K., Hooper, S. D., Porat, I., et al. (2011). Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS ONE 6:e20237. doi: 10.1371/journal.pone.0020237
    • (2011) PLoS ONE , vol.6
    • Anderson, I.J.1    Scheuner, C.2    Göker, M.3    Mavromatis, K.4    Hooper, S.D.5    Porat, I.6
  • 5
    • 27844580665 scopus 로고    scopus 로고
    • Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov
    • Arahal, D. R., Macian, M. C., Garay, E., and Pujalte, M. J. (2005). Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int. J. Syst. Evol. Microbiol. 55, 2371-2376. doi: 10.1099/ijs.0.63842-0
    • (2005) Int. J. Syst. Evol. Microbiol. , vol.55 , pp. 2371-2376
    • Arahal, D.R.1    Macian, M.C.2    Garay, E.3    Pujalte, M.J.4
  • 6
    • 77952891045 scopus 로고    scopus 로고
    • Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
    • Auch, A. F., Klenk, H.-P., and Göker, M. (2010a). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand. Genomic Sci. 2, 142-148. doi: 10.4056/sigs.541628
    • (2010) Stand. Genomic Sci. , vol.2 , pp. 142-148
    • Auch, A.F.1    Klenk, H.-P.2    Göker, M.3
  • 7
    • 77952891913 scopus 로고    scopus 로고
    • Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
    • Auch, A. F., Von Jan, M., Klenk, H.-P., and Göker, M. (2010b). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2, 117-134. doi: 10.4056/sigs.531120
    • (2010) Stand. Genomic Sci. , vol.2 , pp. 117-134
    • Auch, A.F.1    Von Jan, M.2    Klenk, H.-P.3    Göker, M.4
  • 8
    • 84855367993 scopus 로고    scopus 로고
    • Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing
    • Berger, M., Neumann, A., Schulz, S., Simon, M., and Brinkhoff, T. (2011). Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J. Bacteriol. 193, 6576-6585. doi: 10.1128/JB.05818-11
    • (2011) J. Bacteriol. , vol.193 , pp. 6576-6585
    • Berger, M.1    Neumann, A.2    Schulz, S.3    Simon, M.4    Brinkhoff, T.5
  • 9
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten, J. (2006). A review of long-branch attraction. Cladistics 21, 163-193. doi: 10.1111/j.1096-0031.2005.00059.x
    • (2006) Cladistics , vol.21 , pp. 163-193
    • Bergsten, J.1
  • 10
    • 84881043340 scopus 로고    scopus 로고
    • Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade
    • Beyersmann, P. G., Chertkov, O., Petersen, J., Fiebig, A., Chen, A., Pati, A., et al. (2013). Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand. Genomic Sci. 8, 403-419. doi: 10.4056/sigs.3927626
    • (2013) Stand. Genomic Sci. , vol.8 , pp. 403-419
    • Beyersmann, P.G.1    Chertkov, O.2    Petersen, J.3    Fiebig, A.4    Chen, A.5    Pati, A.6
  • 11
    • 84893377192 scopus 로고    scopus 로고
    • Genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment
    • Breider, S., Teshima, H., Petersen, J., Chertkov, O., Dalingault, H., Chen, A., et al. (2014). Genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment. Stand. Genomic Sci. 9, 687-703. doi: 10.4056/sigs.3828824
    • (2014) Stand. Genomic Sci. , vol.9 , pp. 687-703
    • Breider, S.1    Teshima, H.2    Petersen, J.3    Chertkov, O.4    Dalingault, H.5    Chen, A.6
  • 12
    • 43949120140 scopus 로고    scopus 로고
    • Diversity, ecology, and genomics of the Roseobacter clade: a short overview
    • Brinkhoff, T., Giebel, H. A., and Simon, M. (2008). Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch. Microbiol. 189, 531-539. doi: 10.1007/s00203-008-0353-y
    • (2008) Arch. Microbiol. , vol.189 , pp. 531-539
    • Brinkhoff, T.1    Giebel, H.A.2    Simon, M.3
  • 13
    • 26844510681 scopus 로고    scopus 로고
    • Overview of the marine Roseobacter lineage
    • Buchan, A., Gonzalez, J. M., and Moran, M. A. (2005). Overview of the marine Roseobacter lineage. Appl. Environ. Microb. 71, 5665-5677. doi: 10.1128/AEM.71.10.5665-5677.2005
    • (2005) Appl. Environ. Microb. , vol.71 , pp. 5665-5677
    • Buchan, A.1    Gonzalez, J.M.2    Moran, M.A.3
  • 14
    • 84887093261 scopus 로고    scopus 로고
    • Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a member of the Roseobacter clade
    • Buddruhs, N., Chertkov, O., Petersen, J., Fiebig, A., Chen, A., Pati, A., et al. (2013a). Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a member of the Roseobacter clade. Stand. Genomic Sci. 9, 128-141. doi: 10.4056/sigs.4297965
    • (2013) Stand. Genomic Sci. , vol.9 , pp. 128-141
    • Buddruhs, N.1    Chertkov, O.2    Petersen, J.3    Fiebig, A.4    Chen, A.5    Pati, A.6
  • 15
    • 84887071726 scopus 로고    scopus 로고
    • Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395
    • Buddruhs, N., Pradella, S., Göker, M., Päuker, O., Michael, V., Pukall, R., et al. (2013b). Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395. Int. J. Syst. Evol. Microbiol. 63, 4340-4349. doi: 10.1099/ijs.0.053900-0
    • (2013) Int. J. Syst. Evol. Microbiol. , vol.63 , pp. 4340-4349
    • Buddruhs, N.1    Pradella, S.2    Göker, M.3    Päuker, O.4    Michael, V.5    Pukall, R.6
  • 16
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552. doi: 10.1093/oxfordjournals.molbev.a026334
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 17
    • 84865717815 scopus 로고    scopus 로고
    • Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS)
    • Chen, Y. (2012). Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environ. Microbiol. 14, 2308-2322. doi: 10.1111/j.1462-2920.2012.02765.x
    • (2012) Environ. Microbiol. , vol.14 , pp. 2308-2322
    • Chen, Y.1
  • 18
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., and Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287. doi: 10.1126/science.1123061
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    von Mering, C.3    Creevey, C.J.4    Snel, B.5    Bork, P.6
  • 19
    • 84887052328 scopus 로고    scopus 로고
    • Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis
    • Dogs, M., Teshima, H., Petersen, J., Chertkov, O., Dalingault, H., Chen, A., et al. (2013a). Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand. Genomic Sci. 9, 142-159. doi: 10.4056/sigs.4287962
    • (2013) Stand. Genomic Sci. , vol.9 , pp. 142-159
    • Dogs, M.1    Teshima, H.2    Petersen, J.3    Chertkov, O.4    Dalingault, H.5    Chen, A.6
  • 20
    • 84890658016 scopus 로고    scopus 로고
    • Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary-metabolite producing member of the marine Roseobacter clade, and emendation of the species Phaeobacter inhibens
    • Dogs, M., Voget, S., Teshima, H., Petersen, J., Fiebig, A., Davenport, K., et al. (2013b). Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary-metabolite producing member of the marine Roseobacter clade, and emendation of the species Phaeobacter inhibens. Stand. Genomic Sci. 9, 334-350. doi: 10.4056/sigs.4448212
    • (2013) Stand. Genomic Sci. , vol.9 , pp. 334-350
    • Dogs, M.1    Voget, S.2    Teshima, H.3    Petersen, J.4    Fiebig, A.5    Davenport, K.6
  • 21
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 22
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A. J., Van Dongen, S. M., and Ouzounis, C. A. (2002). An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584. doi: 10.1093/nar/30.7.1575
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.M.2    Ouzounis, C.A.3
  • 23
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376. doi: 10.1007/BF01734359
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 25
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: minimum change on a specified tree topology
    • Fitch, W. M. (1977). Toward defining the course of evolution: minimum change on a specified tree topology. Syst. Zool. 20, 406-416. doi: 10.2307/2412116
    • (1977) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 26
    • 84954121175 scopus 로고    scopus 로고
    • Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T)
    • Frank, O., Pradella, S., Rohde, M., Scheuner, C., Klenk, H.-P., Göker, M., et al. (2014). Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T). Stand. Genomic Sci. 9. doi: 10.4056/sigs.5179110
    • (2014) Stand. Genomic Sci , pp. 9
    • Frank, O.1    Pradella, S.2    Rohde, M.3    Scheuner, C.4    Klenk, H.-P.5    Göker, M.6
  • 27
    • 84881042980 scopus 로고    scopus 로고
    • Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T
    • Freese, H., Dalingault, H., Petersen, J., Pradella, S., Davenport, K., Teshima, H., et al. (2013). Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T. Stand. Genomic Sci. 8, 450-464. doi: 10.4056/sigs.383362
    • (2013) Stand. Genomic Sci. , vol.8 , pp. 450-464
    • Freese, H.1    Dalingault, H.2    Petersen, J.3    Pradella, S.4    Davenport, K.5    Teshima, H.6
  • 29
    • 40549094625 scopus 로고    scopus 로고
    • Genetic dissection of tropodithietic acid biosynthesis in marine roseobacters
    • Geng, H., Bruhn, J. B., Nielsen, K. F., Gram, L., and Belas, R. (2008). Genetic dissection of tropodithietic acid biosynthesis in marine roseobacters. Appl. Environ. Microb. 74, 1535-1545. doi: 10.1128/AEM.02339-07
    • (2008) Appl. Environ. Microb. , vol.74 , pp. 1535-1545
    • Geng, H.1    Bruhn, J.B.2    Nielsen, K.F.3    Gram, L.4    Belas, R.5
  • 30
    • 84879351437 scopus 로고    scopus 로고
    • Phylogeny-driven target selection for genome-sequencing (and other) projects
    • Göker, M., and Klenk, H.-P. (2013). Phylogeny-driven target selection for genome-sequencing (and other) projects. Stand. Genomic Sci. 8, 360-374. doi: 10.4056/sigs.3446951
    • (2013) Stand. Genomic Sci. , vol.8 , pp. 360-374
    • Göker, M.1    Klenk, H.-P.2
  • 32
    • 0038048942 scopus 로고    scopus 로고
    • Parsimony, likelihood, and simplicity
    • Goloboff, P. A. (2003). Parsimony, likelihood, and simplicity. Cladistics 19, 91-103. doi: 10.1111/j.1096-0031.2003.tb00297.x
    • (2003) Cladistics , vol.19 , pp. 91-103
    • Goloboff, P.A.1
  • 33
    • 79958232736 scopus 로고    scopus 로고
    • Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach
    • Jin, H.-M., Lee, H.-J., Kim, J.-M., Park, M.-S., Lee, K., and Jeon, C. E. (2011). Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int. J. Syst. Evol. Microbiol. 61, 1392-1396. doi: 10.1099/ijs.0.025007-0
    • (2011) Int. J. Syst. Evol. Microbiol. , vol.61 , pp. 1392-1396
    • Jin, H.-M.1    Lee, H.-J.2    Kim, J.-M.3    Park, M.-S.4    Lee, K.5    Jeon, C.E.6
  • 34
    • 53749103374 scopus 로고    scopus 로고
    • Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea
    • Kim, Y.-G., Hwang, C. Y., and Cho, B. C. (2008). Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea. Int. J. Syst. Evol. Microbiol. 58, 2102-2106. doi: 10.1099/ijs.0.65820-0
    • (2008) Int. J. Syst. Evol. Microbiol. , vol.58 , pp. 2102-2106
    • Kim, Y.-G.1    Hwang, C.Y.2    Cho, B.C.3
  • 35
    • 77952889628 scopus 로고    scopus 로고
    • En route to a genome-based taxonomy of Archaea and Bacteria?
    • Klenk, H.-P., and Göker, M. (2010). En route to a genome-based taxonomy of Archaea and Bacteria? Syst. Appl. Microbiol. 33, 175-182. doi: 10.1016/j.syapm.2010.03.003
    • (2010) Syst. Appl. Microbiol. , vol.33 , pp. 175-182
    • Klenk, H.-P.1    Göker, M.2
  • 36
    • 84959806898 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)
    • Kluge, A. G. (1989). A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7-25. doi: 10.2307/2992432
    • (1989) Syst. Zool. , vol.38 , pp. 7-25
    • Kluge, A.G.1
  • 37
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le, S. Q., and Gascuel, O. (2008). An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307-1320. doi: 10.1093/molbev/msn067
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 38
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee, C., Grasso, C., and Sharlow, M. F. (2002). Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452-464. doi: 10.1093/bioinformatics/18.3.452
    • (2002) Bioinformatics , vol.18 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 39
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. Jr., and Roos, D. S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189. doi: 10.1101/gr.1224503
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 40
    • 67651146722 scopus 로고    scopus 로고
    • Evidence, content and corroboration and the tree of life
    • Lienau, E. K., and DeSalle, R. (2009). Evidence, content and corroboration and the tree of life. Acta Biotheor. 57, 187-199. doi: 10.1007/s10441-008-9066-5
    • (2009) Acta Biotheor. , vol.57 , pp. 187-199
    • Lienau, E.K.1    DeSalle, R.2
  • 41
    • 84900009480 scopus 로고    scopus 로고
    • Puniceibacterium antarcticum gen. nov., sp. nov., isolated from Antarctic seawater
    • Liu, C., Zhang, X.-Y., Su, H.-N., Zhou, M.-Y., Chen, B., Li, H., et al. (2014). Puniceibacterium antarcticum gen. nov., sp. nov., isolated from Antarctic seawater. Int. J. Syst. Evol. Microbiol. 64, 1566-1572. doi: 10.1099/ijs.0.057695-0
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 1566-1572
    • Liu, C.1    Zhang, X.-Y.2    Su, H.-N.3    Zhou, M.-Y.4    Chen, B.5    Li, H.6
  • 42
    • 84859713729 scopus 로고    scopus 로고
    • Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater
    • Lucena, T., Pujalte, M. J., Ruvira, M. A., Garay, E., Macián, M. C., and Arahal, D. R. (2012). Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater. Int. J. Syst. Evol. Microbiol. 62, 844-848. doi: 10.1099/ijs.0.030973-0
    • (2012) Int. J. Syst. Evol. Microbiol. , vol.62 , pp. 844-848
    • Lucena, T.1    Pujalte, M.J.2    Ruvira, M.A.3    Garay, E.4    Macián, M.C.5    Arahal, D.R.6
  • 43
    • 34249935530 scopus 로고    scopus 로고
    • Fast and reliable MALDI-TOF MS-based microorganism identification
    • Maier, T., and Kostrzewa, M. (2007). Fast and reliable MALDI-TOF MS-based microorganism identification. Chem. Today 25, 68-71. doi: 10.1038/nmeth870
    • (2007) Chem. Today , vol.25 , pp. 68-71
    • Maier, T.1    Kostrzewa, M.2
  • 44
    • 33745300025 scopus 로고    scopus 로고
    • Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al., 1998 as Phaeobacter gallaeciensis ge. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al., 1995) Uchino et al., 1999 as Marinovum algicola gen. nov., comb. nov., and emended description of the genera Roseobacter, Ruegeria and Leisingera
    • Martens, T., Heidorn, T., Pukall, R., Simon, M., Tindall, B. J., and Brinkhoff, T. (2006). Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al., 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al., 1995) Uchino et al., 1999 as Marinovum algicola gen. nov., comb. nov., and emended description of the genera Roseobacter, Ruegeria and Leisingera. Int. J. Syst. Evol. Microbiol. 56, 1293-1304. doi: 10.1099/ijs.0.63724-0
    • (2006) Int. J. Syst. Evol. Microbiol. , vol.56 , pp. 1293-1304
    • Martens, T.1    Heidorn, T.2    Pukall, R.3    Simon, M.4    Tindall, B.J.5    Brinkhoff, T.6
  • 45
    • 84874011652 scopus 로고    scopus 로고
    • Genome sequence-based species delimitation with confidence intervals and improved distance functions
    • Meier-Kolthoff, J. P., Auch, A. F., Klenk, H.-P., and Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14:60. doi: 10.1186/1471-2105-14-60
    • (2013) BMC Bioinform. , vol.14 , pp. 60
    • Meier-Kolthoff, J.P.1    Auch, A.F.2    Klenk, H.-P.3    Göker, M.4
  • 46
    • 84890634795 scopus 로고    scopus 로고
    • Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age
    • Meier-Kolthoff, J. P., Klenk, H.-P., and Göker, M. (2014). Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age. Int. J. Syst. Evol. Microbiol. 64, 352-356. doi: 10.1099/ijs.0.056994-0
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 352-356
    • Meier-Kolthoff, J.P.1    Klenk, H.-P.2    Göker, M.3
  • 50
    • 77952674525 scopus 로고    scopus 로고
    • Genome characteristics of a generalist marine bacterial lineage
    • Newton, R. J., Griffin, L. E., Bowles, M. M., Meile, C., Gifford, S., Givens, C. E., et al. (2010). Genome characteristics of a generalist marine bacterial lineage. ISME J. 4, 784-798. doi: 10.1038/ismej.2009.150
    • (2010) ISME J. , vol.4 , pp. 784-798
    • Newton, R.J.1    Griffin, L.E.2    Bowles, M.M.3    Meile, C.4    Gifford, S.5    Givens, C.E.6
  • 51
    • 84897941816 scopus 로고    scopus 로고
    • Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring
    • Park, S., Park, D.-S., Bae, K. S., and Yoon, J.-H. (2014). Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int. J. Syst. Evol. Microbiol. 64, 1378-1383. doi: 10.1099/ijs.0.057646-0
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 1378-1383
    • Park, S.1    Park, D.-S.2    Bae, K.S.3    Yoon, J.-H.4
  • 53
    • 84881031716 scopus 로고    scopus 로고
    • Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements
    • Riedel, T., Teshima, H., Petersen, J., Fiebig, A., Davenport, K., Daligault, H., et al. (2013). Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand. Genomic Sci. 8, 389-402. doi: 10.4056/sigs.3858183
    • (2013) Stand. Genomic Sci. , vol.8 , pp. 389-402
    • Riedel, T.1    Teshima, H.2    Petersen, J.3    Fiebig, A.4    Davenport, K.5    Daligault, H.6
  • 54
    • 0031798779 scopus 로고    scopus 로고
    • Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus
    • Ruiz-Ponte, C., Cilia, V., Lambert, C., and Nicolas, J. L. (1998). Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. Int. J. Syst. Bacteriol. 48, 537-542. doi: 10.1099/00207713-48-2-537
    • (1998) Int. J. Syst. Bacteriol. , vol.48 , pp. 537-542
    • Ruiz-Ponte, C.1    Cilia, V.2    Lambert, C.3    Nicolas, J.L.4
  • 55
    • 0035989518 scopus 로고    scopus 로고
    • Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide
    • Schaefer, J. K., Goodwin, K. D., McDonald, I. R., Murrell, J. C., and Oremland, R. S. (2002). Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int. J. Syst. Evol. Microbiol. 52, 851-859. doi: 10.1099/ijs.0.01960-0
    • (2002) Int. J. Syst. Evol. Microbiol. , vol.52 , pp. 851-859
    • Schaefer, J.K.1    Goodwin, K.D.2    McDonald, I.R.3    Murrell, J.C.4    Oremland, R.S.5
  • 56
    • 0033102131 scopus 로고    scopus 로고
    • Long-branch abstractions
    • Siddall, M. E., and Whiting, M. F. (1999). Long-branch abstractions. Cladistics 15, 9-24. doi: 10.1111/j.1096-0031.1999.tb00391.x
    • (1999) Cladistics , vol.15 , pp. 9-24
    • Siddall, M.E.1    Whiting, M.F.2
  • 57
    • 79952176138 scopus 로고    scopus 로고
    • The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments
    • Spring, S., Scheuner, C., Lapidus, A., Lucas, S., Glavina Del Rio, T., Tice, H., et al. (2010). The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010:690737. doi: 10.1155/2010/690737
    • (2010) Archaea , vol.2010 , pp. 690737
    • Spring, S.1    Scheuner, C.2    Lapidus, A.3    Lucas, S.4    Glavina Del Rio, T.5    Tice, H.6
  • 58
    • 84929880666 scopus 로고    scopus 로고
    • 'Family Intrasporangiaceae, '
    • eds E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson (Berlin: Springer), in press
    • Stackebrandt, E., Scheuner, C., Göker, M., and Schumann, P. (2014). "Family Intrasporangiaceae". in The Prokaryotes-Actinobacteria, 4th Edn., eds E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson (Berlin: Springer), in press.
    • (2014) The Prokaryotes-Actinobacteria, 4th Edn.
    • Stackebrandt, E.1    Scheuner, C.2    Göker, M.3    Schumann, P.4
  • 59
    • 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. doi: 10.1093/bioinformatics/btl446
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 60
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • Stamatakis, A., Hoover, P., and Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 57, 758-771. doi: 10.1080/10635150802429642
    • (2008) Syst. Biol. , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 61
    • 76549121926 scopus 로고    scopus 로고
    • Leisingera nanhaiensis sp. nov., isolated from marine sediment
    • Sun, F., Wang, B., Liu, X., Lai, Q., Du, Y., Li, G., et al. (2010). Leisingera nanhaiensis sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 60, 275-280. doi: 10.1099/ijs.0.010439-0
    • (2010) Int. J. Syst. Evol. Microbiol. , vol.60 , pp. 275-280
    • Sun, F.1    Wang, B.2    Liu, X.3    Lai, Q.4    Du, Y.5    Li, G.6
  • 63
    • 0038391401 scopus 로고    scopus 로고
    • RASCAL: rapid scanning and correction of multiple sequence alignments
    • Thompson, J. D., Thierry, J.-C. C., and Poch, O. (2003). RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 19, 1155-1161. doi: 10.1093/bioinformatics/btg133
    • (2003) Bioinformatics , vol.19 , pp. 1155-1161
    • Thompson, J.D.1    Thierry, J.-C.C.2    Poch, O.3
  • 64
    • 47249128107 scopus 로고    scopus 로고
    • Wohlfahrtiimonas chitiniclastica gen. nov., sp. nov., a new gammaproteobacterium isolated from Wohlfahrtia magnifica (Diptera: Sarcophagidae)
    • Tóth, E. M., Schumann, P., Borsodi, A. K., Kéki, Z., Kovács, A. L., and Márialigeti, K. (2008). Wohlfahrtiimonas chitiniclastica gen. nov., sp. nov., a new gammaproteobacterium isolated from Wohlfahrtia magnifica (Diptera: Sarcophagidae). Int. J. Syst. Evol. Microbiol. 58, 976-981. doi: 10.1099/ijs.0.65324-0
    • (2008) Int. J. Syst. Evol. Microbiol. , vol.58 , pp. 976-981
    • Tóth, E.M.1    Schumann, P.2    Borsodi, A.K.3    Kéki, Z.4    Kovács, A.L.5    Márialigeti, K.6
  • 65
    • 0031729883 scopus 로고    scopus 로고
    • Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev
    • Uchino, Y., Hirata, A., Yokota, A., and Sugiyama, J. (1998). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J. Gen. Appl. Microbiol. 44, 201-210. doi: 10.2323/jgam.44.201
    • (1998) J. Gen. Appl. Microbiol. , vol.44 , pp. 201-210
    • Uchino, Y.1    Hirata, A.2    Yokota, A.3    Sugiyama, J.4
  • 66
    • 58949090084 scopus 로고    scopus 로고
    • Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al., 2002, Phaeobacter daeponensis Yoon et al., 2007 and Phaeobacter inhibens Martens et al., 2006
    • Vandecandelaere, I., Segaert, E., Mollica, A., Faimali, M., and Vandamme, P. (2008). Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al., 2002, Phaeobacter daeponensis Yoon et al., 2007 and Phaeobacter inhibens Martens et al., 2006. Int. J. Syst. Evol. Microbiol. 58, 2788-2793. doi: 10.1099/ijs.0.65844-0
    • (2008) Int. J. Syst. Evol. Microbiol , vol.58 , pp. 2788-2793
    • Vandecandelaere, I.1    Segaert, E.2    Mollica, A.3    Faimali, M.4    Vandamme, P.5
  • 67
    • 67649785258 scopus 로고    scopus 로고
    • Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm
    • Vandecandelaere, I., Segaert, E., Mollica, A., Faimali, M., and Vandamme, P. (2009). Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm. Int. J. Syst. Evol. Microbiol. 59, 1209-1214. doi: 10.1099/ijs.0.002642-0
    • (2009) Int. J. Syst. Evol. Microbiol. , vol.59 , pp. 1209-1214
    • Vandecandelaere, I.1    Segaert, E.2    Mollica, A.3    Faimali, M.4    Vandamme, P.5
  • 68
    • 84929677280 scopus 로고    scopus 로고
    • 'The families Erysipelotrichaceae emend., Coprobacillaceae fam nov., and Turicibacteraceae fam. nov., '
    • eds E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson (Berlin: Springer), in press
    • Verbarg, S., Göker, M., Scheuner, S., Schumann, P., and Stackebrandt, E. (2014). "The families Erysipelotrichaceae emend., Coprobacillaceae fam nov., and Turicibacteraceae fam. nov.". in The Prokaryotes, 4th Edn., eds E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson (Berlin: Springer), in press.
    • (2014) The Prokaryotes, 4th Edn.
    • Verbarg, S.1    Göker, M.2    Scheuner, S.3    Schumann, P.4    Stackebrandt, E.5
  • 70
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M., and Eisen, J. A. (2008). A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:R151. doi: 10.1186/gb-2008-9-10-r151
    • (2008) Genome Biol. , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 71
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang, Z. (1993). Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10, 1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 72
    • 34248198910 scopus 로고    scopus 로고
    • Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
    • Yoon, J.-H., Kang, S.-J., Lee, S.-Y., and Oh, T.-K. (2007). Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 57, 856-861. doi: 10.1099/ijs.0.64779-0
    • (2007) Int. J. Syst. Evol. Microbiol. , vol.57 , pp. 856-861
    • Yoon, J.-H.1    Kang, S.-J.2    Lee, S.-Y.3    Oh, T.-K.4
  • 73
    • 70450263295 scopus 로고    scopus 로고
    • Seohaeicola saemankumensis gen. nov., sp. nov., isolated from a tidal flat
    • Yoon, J.-H., Kang, S.-J., Lee, S.-Y., Oh, K.-H., and Oh, T.-K. (2009). Seohaeicola saemankumensis gen. nov., sp. nov., isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 59, 2675-2679. doi: 10.1099/ijs.0.011312-0
    • (2009) Int. J. Syst. Evol. Microbiol. , vol.59 , pp. 2675-2679
    • Yoon, J.-H.1    Kang, S.-J.2    Lee, S.-Y.3    Oh, K.-H.4    Oh, T.-K.5
  • 74
    • 0031665356 scopus 로고    scopus 로고
    • Aerobic anoxygenic phototrophic bacteria
    • Yurkov, V. V., and Beatty, J. T. (1998). Aerobic anoxygenic phototrophic bacteria. Microbiol. Mol. Biol. Rev. 62, 695-724.
    • (1998) Microbiol. Mol. Biol. Rev. , vol.62 , pp. 695-724
    • Yurkov, V.V.1    Beatty, J.T.2
  • 75
    • 48549101142 scopus 로고    scopus 로고
    • Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic
    • Zhang, D. C., Li, H. R., Xin, Y. H., Liu, H. C., Chi, Z. M., Zhou, P. J., et al. (2008). Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic. Int. J. Syst. Evol. Microbiol. 58, 1384-1387. doi: 10.1099/ijs.0.65708-0
    • (2008) Int. J. Syst. Evol. Microbiol. , vol.58 , pp. 1384-1387
    • Zhang, D.C.1    Li, H.R.2    Xin, Y.H.3    Liu, H.C.4    Chi, Z.M.5    Zhou, P.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.