메뉴 건너뛰기




Volumn 2, Issue , 2016, Pages

Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC METABOLISM; BACTERIAL GENOME; CLASSIFICATION; GENETIC SELECTION; GENETICS; HETEROTROPHY; ISOLATION AND PURIFICATION; METABOLISM; METAGENOMICS; MICROBIOLOGY; MOLECULAR EVOLUTION; VERRUCOMICROBIA;

EID: 84993965453     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2016.198     Document Type: Article
Times cited : (159)

References (66)
  • 1
    • 84908132133 scopus 로고    scopus 로고
    • Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally
    • Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. Proc. R. Soc. B. 281, 20141988 (2014).
    • (2014) Proc. R. Soc. B. , vol.281 , pp. 20141988
    • Ramirez, K.S.1
  • 2
    • 33644952722 scopus 로고    scopus 로고
    • Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
    • Janssen, P. H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72, 1719-1728 (2006).
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 1719-1728
    • Janssen, P.H.1
  • 3
    • 79955980612 scopus 로고    scopus 로고
    • The under-recognized dominance of Verrucomicrobia in soil bacterial communities
    • Bergmann, G. T. et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol. Biochem. 43, 1450-1455 (2011).
    • (2011) Soil Biol. Biochem. , vol.43 , pp. 1450-1455
    • Bergmann, G.T.1
  • 4
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007).
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 5
    • 84891820094 scopus 로고    scopus 로고
    • IMG 4 version of the integrated microbial genomes comparative analysis system
    • Markowitz, V. M. et al. IMG 4 version of the Integrated Microbial Genomes comparative analysis system. Nucleic Acids Res. 42, D560-D567 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D560-D567
    • Markowitz, V.M.1
  • 6
    • 84945477915 scopus 로고    scopus 로고
    • Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils
    • Van Insberghe, D. et al. Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils. ISME J. 9, 2435-2441 (2015).
    • (2015) ISME J. , vol.9 , pp. 2435-2441
    • Van Insberghe, D.1
  • 8
    • 36849030274 scopus 로고    scopus 로고
    • Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia
    • Dunfield, P. F. et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, 879-882 (2007).
    • (2007) Nature , vol.450 , pp. 879-882
    • Dunfield, P.F.1
  • 9
    • 84878465280 scopus 로고    scopus 로고
    • Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
    • Everard, A. et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc. Natl Acad. Sci. USA 110, 9066-9071 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 9066-9071
    • Everard, A.1
  • 10
    • 84887301559 scopus 로고    scopus 로고
    • Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States
    • Fierer, N. et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621-624 (2013).
    • (2013) Science , vol.342 , pp. 621-624
    • Fierer, N.1
  • 11
    • 8144230745 scopus 로고    scopus 로고
    • Chthoniobacter flavus gen. Nov., sp. Nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia
    • Sangwan, P., Chen, X., Hugenholtz, P. & Janssen, P. H. Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl. Environ. Microbiol. 70, 5875-5881 (2004).
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 5875-5881
    • Sangwan, P.1    Chen, X.2    Hugenholtz, P.3    Janssen, P.H.4
  • 12
    • 79958161622 scopus 로고    scopus 로고
    • Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium
    • Kant, R. et al. Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium. J. Bacteriol. 193, 2902-2903 (2011).
    • (2011) J. Bacteriol. , vol.193 , pp. 2902-2903
    • Kant, R.1
  • 13
    • 84879566132 scopus 로고    scopus 로고
    • Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class spartobacteria
    • Herlemann, D. P. R. et al. Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class spartobacteria. mBio 4, e00569-12 (2013).
    • (2013) MBio , vol.4 , pp. e00569-e00612
    • Herlemann, D.P.R.1
  • 14
    • 0034521952 scopus 로고    scopus 로고
    • Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, longidoridae)
    • Vandekerckhove, T. T., Willems, A., Gillis, M. & Coomans, A. Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, longidoridae). Int. J. Syst. Evol. Microbiol. 50, 2197-2205 (2000).
    • (2000) Int. J. Syst. Evol. Microbiol. , vol.50 , pp. 2197-2205
    • Vandekerckhove, T.T.1    Willems, A.2    Gillis, M.3    Coomans, A.4
  • 15
    • 0031921271 scopus 로고    scopus 로고
    • Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils
    • Felske, A. & Akkermans, A. D. L. Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils. Lett. Appl. Microbiol. 26, 219-223 (1998).
    • (1998) Lett. Appl. Microbiol. , vol.26 , pp. 219-223
    • Felske, A.1    Akkermans, A.D.L.2
  • 16
    • 84953911745 scopus 로고    scopus 로고
    • Microbial community analysis with ribosomal gene fragments from shotgun metagenomes
    • Guo, J., Cole, J. R., Zhang, Q., Brown, C. T. & Tiedje, J. M. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl. Environ. Microbiol. 82, 157-166 (2016).
    • (2016) Appl. Environ. Microbiol. , vol.82 , pp. 157-166
    • Guo, J.1    Cole, J.R.2    Zhang, Q.3    Brown, C.T.4    Tiedje, J.M.5
  • 17
    • 84941008535 scopus 로고    scopus 로고
    • Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
    • Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl Acad. Sci. USA 112, 10967-10972 (2015).
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. 10967-10972
    • Leff, J.W.1
  • 18
    • 84871826193 scopus 로고    scopus 로고
    • Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
    • Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390-21395 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 21390-21395
    • Fierer, N.1
  • 19
    • 84897492912 scopus 로고    scopus 로고
    • Tackling soil diversity with the assembly of large, complex metagenomes
    • Howe, A. C. et al. Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl Acad. Sci. USA 111, 4904-4909 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 4904-4909
    • Howe, A.C.1
  • 20
    • 84976865403 scopus 로고    scopus 로고
    • The Pfam protein families database: Towards a more sustainable future
    • Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44, D279-D285 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. D279-D285
    • Finn, R.D.1
  • 21
    • 84946034354 scopus 로고    scopus 로고
    • Microbial species delineation using whole genome sequences
    • Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761-6771 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. 6761-6771
    • Varghese, N.J.1
  • 22
    • 84943580979 scopus 로고    scopus 로고
    • METAXA2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
    • Bengtsson-Palme, J. et al. METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol. Ecol. Resour. 15, 1403-1414 (2015).
    • (2015) Mol. Ecol. Resour. , vol.15 , pp. 1403-1414
    • Bengtsson-Palme, J.1
  • 23
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • Ciccarelli, F. D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006).
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, F.D.1
  • 24
    • 48249105854 scopus 로고    scopus 로고
    • Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
    • Hou, S. et al. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol. Direct 3, 26 (2008).
    • (2008) Biol. Direct , vol.3 , pp. 26
    • Hou, S.1
  • 25
    • 84889591423 scopus 로고    scopus 로고
    • Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation
    • Sabath, N., Ferrada, E., Barve, A. & Wagner, A. Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biol. Evol. 5, 966-977 (2013).
    • (2013) Genome Biol. Evol. , vol.5 , pp. 966-977
    • Sabath, N.1    Ferrada, E.2    Barve, A.3    Wagner, A.4
  • 27
    • 84904997234 scopus 로고    scopus 로고
    • Implications of streamlining theory for microbial ecology
    • Giovannoni, S. J., Thrash, J. C. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553-1565 (2014).
    • (2014) ISME J. , vol.8 , pp. 1553-1565
    • Giovannoni, S.J.1    Thrash, J.C.2    Temperton, B.3
  • 28
    • 84939141968 scopus 로고    scopus 로고
    • Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
    • Nayfach, S. & Pollard, K. S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 16, 51 (2015).
    • (2015) Genome Biol. , vol.16 , pp. 51
    • Nayfach, S.1    Pollard, K.S.2
  • 29
    • 1542327668 scopus 로고    scopus 로고
    • Trends between gene content and genome size in prokaryotic species with larger genomes
    • Konstantinidis, K. T. & Tiedje, J. M. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl Acad. Sci. USA 101, 3160-3165 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 3160-3165
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 30
    • 84901692094 scopus 로고    scopus 로고
    • Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
    • Barberán, A. et al. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol. Lett. 17, 794-802 (2014).
    • (2014) Ecol. Lett. , vol.17 , pp. 794-802
    • Barberán, A.1
  • 31
    • 0035317027 scopus 로고    scopus 로고
    • Determination of DNA content of aquatic bacteria by flow cytometry
    • Button, D. K. & Robertson, B. R. Determination of DNA content of aquatic bacteria by flow cytometry. Appl. Environ. Microbiol. 67, 1636-1645 (2001).
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 1636-1645
    • Button, D.K.1    Robertson, B.R.2
  • 32
    • 84875864745 scopus 로고    scopus 로고
    • Genomic and physiological analysis of carbon storage in the verrucomicrobial methanotroph 'Ca. Methylacidiphilum fumariolicum' solV
    • Khadem, A. F. et al. Genomic and physiological analysis of carbon storage in the verrucomicrobial methanotroph 'Ca. methylacidiphilum fumariolicum' solV. Front. Microbiol. 3, 345 (2012).
    • (2012) Front. Microbiol. , vol.3 , pp. 345
    • Khadem, A.F.1
  • 34
    • 85007440061 scopus 로고    scopus 로고
    • Complete genome sequence of the Opitutaceae bacterium strain TAV5, a potential facultative methylotroph of the wood-feeding termite Reticulitermes flavipes
    • Kotak, M. et al. Complete genome sequence of the Opitutaceae bacterium strain TAV5, a potential facultative methylotroph of the wood-feeding termite Reticulitermes flavipes. Genome Announc. 3, e00060-15 (2015).
    • (2015) Genome Announc. , vol.3 , pp. e00015-e00060
    • Kotak, M.1
  • 35
    • 84907962466 scopus 로고    scopus 로고
    • Less is more: Selective advantages can explain the prevalent loss of biosynthetic genes in bacteria
    • D'Souza, G. et al. Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria. Evolution 68, 2559-2570 (2014).
    • (2014) Evolution , vol.68 , pp. 2559-2570
    • D'Souza, G.1
  • 36
    • 45749083062 scopus 로고    scopus 로고
    • Increased fitness of Pseudomonas fluorescens Pf0-1 leucine auxotrophs in soil
    • Wook, K. & Levy, S. B. Increased fitness of Pseudomonas fluorescens Pf0-1 leucine auxotrophs in soil. Appl. Environ. Microbiol. 74, 3644-3651 (2008).
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 3644-3651
    • Wook, K.1    Levy, S.B.2
  • 37
    • 70449227735 scopus 로고
    • Soil bacteria and growth promoting substances
    • Lochhead, A. G. Soil bacteria and growth promoting substances. Bacteriol. Rev. 22, 145-153 (1958).
    • (1958) Bacteriol. Rev. , vol.22 , pp. 145-153
    • Lochhead, A.G.1
  • 38
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi, H. & Gojobori, T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl Acad. Sci. USA 99, 3695-3700 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 39
    • 84905719886 scopus 로고    scopus 로고
    • Survival of mycobacteria depends on proteasome-mediated amino acid recycling under nutrient limitation
    • Elharar, Y. et al. Survival of mycobacteria depends on proteasome-mediated amino acid recycling under nutrient limitation. EMBO J. 33, 1802-1814 (2014).
    • (2014) EMBO J. , vol.33 , pp. 1802-1814
    • Elharar, Y.1
  • 40
    • 84911807786 scopus 로고    scopus 로고
    • Reductive genome evolution at both ends of the bacterial population size spectrum
    • Batut, B., Knibbe, C., Marais, G. & Daubin, V. Reductive genome evolution at both ends of the bacterial population size spectrum. Nat. Rev. Microbiol. 12, 841-850 (2014).
    • (2014) Nat. Rev. Microbiol. , vol.12 , pp. 841-850
    • Batut, B.1    Knibbe, C.2    Marais, G.3    Daubin, V.4
  • 41
    • 84887151854 scopus 로고    scopus 로고
    • Small genomes and sparse metabolisms of sedimentassociated bacteria from four candidate phyla
    • Kantor, R. S. et al. Small genomes and sparse metabolisms of sedimentassociated bacteria from four candidate phyla. mBio 4, e00708-13 (2013).
    • (2013) MBio , vol.4 , pp. e00708-e00713
    • Kantor, R.S.1
  • 43
    • 79952751932 scopus 로고    scopus 로고
    • The generation and maintenance of diversity in microbial communities
    • Fierer, N. & Lennon, J. T. The generation and maintenance of diversity in microbial communities. Am. J. Bot. 98, 439-448 (2011).
    • (2011) Am. J. Bot. , vol.98 , pp. 439-448
    • Fierer, N.1    Lennon, J.T.2
  • 44
    • 84857029292 scopus 로고    scopus 로고
    • Seasonality in ocean microbial communities
    • Giovannoni, S. J. & Vergin, K. L. Seasonality in ocean microbial communities. Science 335, 671-676 (2012).
    • (2012) Science , vol.335 , pp. 671-676
    • Giovannoni, S.J.1    Vergin, K.L.2
  • 45
    • 0036177929 scopus 로고    scopus 로고
    • Composition of hydrolysable amino acids in soil organic matter and soil microbial biomass
    • Friedel, J. K. & Scheller, E. Composition of hydrolysable amino acids in soil organic matter and soil microbial biomass. Soil Biol. Biochem. 34, 315-325 (2002).
    • (2002) Soil Biol. Biochem. , vol.34 , pp. 315-325
    • Friedel, J.K.1    Scheller, E.2
  • 46
    • 84872842601 scopus 로고    scopus 로고
    • Oligopeptides represent a preferred source of organic N uptake: A global phenomenon?
    • Farrell, M. et al. Oligopeptides represent a preferred source of organic N uptake: a global phenomenon? Ecosystems 16, 133-145 (2013).
    • (2013) Ecosystems , vol.16 , pp. 133-145
    • Farrell, M.1
  • 48
    • 84860511582 scopus 로고    scopus 로고
    • The black queen hypothesis: Evolution of dependencies through adaptive gene loss
    • Morris, J. J., Lenski, R. E. & Zinser, E. R. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012).
    • (2012) MBio , vol.3 , pp. e00012-e00036
    • Morris, J.J.1    Lenski, R.E.2    Zinser, E.R.3
  • 50
    • 84876460076 scopus 로고    scopus 로고
    • Nutrient requirments for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium
    • Carini, P., Steindler, L., Beszteri, S. & Giovannoni S. J. Nutrient requirments for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium. ISME J. 7, 592-602 (2013).
    • (2013) ISME J. , vol.7 , pp. 592-602
    • Carini, P.1    Steindler, L.2    Beszteri, S.3    Giovannoni, S.J.4
  • 51
    • 84905119356 scopus 로고    scopus 로고
    • Predicting the responsiveness of soil biodiversity to deforestation: A cross-biome study
    • Crowther, T. W. et al. Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study. Glob. Change Biol. 20, 2983-2994 (2014).
    • (2014) Glob. Change Biol. , vol.20 , pp. 2983-2994
    • Crowther, T.W.1
  • 52
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1
  • 53
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate phylotype sequences from microbial amplicon reads
    • Edgar, R. C. UPARSE: highly accurate phylotype sequences from microbial amplicon reads. Nat. Methods 10, 996-998 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 54
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 55
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • De Santis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072 (2006).
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 5069-5072
    • De Santis, T.Z.1
  • 56
    • 84873564282 scopus 로고    scopus 로고
    • Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments
    • Miller, C. S. et al. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS ONE 8, e56018 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e56018
    • Miller, C.S.1
  • 57
    • 75249107844 scopus 로고    scopus 로고
    • PyNAST: A flexible tool for aligning sequences to a template alignment
    • Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 266-267
    • Caporaso, J.G.1
  • 58
    • 84937442075 scopus 로고    scopus 로고
    • Compact graphical representation of phylogenetic data and metadata with GraPhlAn
    • Asnicar, F., Weingart, G., Tickle, C. H., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Peer J 3, e1029 (2015).
    • (2015) Peer J , vol.3 , pp. e1029
    • Asnicar, F.1    Weingart, G.2    Tickle, C.H.3    Huttenhower, C.4    Segata, N.5
  • 59
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.M.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 60
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1
  • 61
    • 34347388470 scopus 로고    scopus 로고
    • Uniref: Comprehensive and non-redundant uniProt reference clusters
    • Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. Uniref: comprehensive and non-redundant uniProt reference clusters. Bioinformatics 23, 1282-1288 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 62
    • 70350015324 scopus 로고    scopus 로고
    • Community-wide analysis of microbial genome sequence signatures
    • Dick, G. J. et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10, R85 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R85
    • Dick, G.J.1
  • 63
    • 84930531751 scopus 로고    scopus 로고
    • Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center
    • Anantharaman, K., Breier, J. A. & Dick, G. J. Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME J. 10, 225-239 (2016).
    • (2016) ISME J. , vol.10 , pp. 225-239
    • Anantharaman, K.1    Breier, J.A.2    Dick, G.J.3
  • 64
    • 84937040910 scopus 로고    scopus 로고
    • CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    • Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043-1055 (2015).
    • (2015) Genome Res. , vol.25 , pp. 1043-1055
    • Parks, D.H.1    Imelfort, M.2    Skennerton, C.T.3    Hugenholtz, P.4    Tyson, G.W.5
  • 65
    • 84967271535 scopus 로고    scopus 로고
    • Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
    • Baker, B. J. et al. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat. Microbiol. 1, 16002 (2016).
    • (2016) Nat. Microbiol. , vol.1 , pp. 16002
    • Baker, B.J.1
  • 66
    • 84940446833 scopus 로고    scopus 로고
    • Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community
    • Garcia, S. L. et al. Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community. Mol. Ecol. 24, 4449-4459 (2015).
    • (2015) Mol. Ecol. , vol.24 , pp. 4449-4459
    • Garcia, S.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.