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Volumn 7, Issue 1, 2017, Pages

Metabolic reconstruction and modeling microbial electrosynthesis

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; CARBON DIOXIDE;

EID: 85027846533     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-08877-z     Document Type: Article
Times cited : (94)

References (73)
  • 1
    • 77957147094 scopus 로고    scopus 로고
    • Microbial electrosynthesis - Revisiting the electrical route for microbial production
    • Rabaey, K., & Rozendal, R. A. Microbial electrosynthesis - revisiting the electrical route for microbial production. Nat. Rev. Microbiol. 8, 706-716 (2010
    • (2010) Nat. Rev. Microbiol , vol.8 , pp. 706-716
    • Rabaey, K.1    Rozendal, R.A.2
  • 3
    • 66249100237 scopus 로고    scopus 로고
    • Direct biological conversion of electrical current into methane by electromethanogenesis
    • Cheng, S., Xing, D., Call, D. F., & Logan, B. E. Direct Biological Conversion of Electrical Current into Methane by Electromethanogenesis. Environ. Sci. Technol. 43, 3953-3958 (2009
    • (2009) Environ. Sci. Technol , vol.43 , pp. 3953-3958
    • Cheng, S.1    Xing, D.2    Call, D.F.3    Logan, B.E.4
  • 4
    • 78650173757 scopus 로고    scopus 로고
    • Microbial electrosyn thesis feeding microbes electricity to convert carbon dioxide and water to multicarbon extracellular organic compounds
    • Nevin, K. P., Woodard, T. L., Franks, A. E., Summers, Z. M., & Lovley, D. R. Microbial Electrosynthesis: Feeding Microbes Electricity To Convert Carbon Dioxide and Water to Multicarbon Extracellular Organic Compounds. mBio 1, e00103-10 (2010
    • (2010) MBio , vol.1 , pp. e00103-e00110
    • Nevin, K.P.1    Woodard, T.L.2    Franks, A.E.3    Summers, Z.M.4    Lovley, D.R.5
  • 6
    • 84875903957 scopus 로고    scopus 로고
    • A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer
    • Ishii, S., et al. A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nat. Commun. 4, 1601 (2013
    • (2013) Nat. Commun , vol.4 , pp. 1601
    • Ishii, S.1
  • 7
    • 84943338696 scopus 로고    scopus 로고
    • Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach
    • Ishii, S., et al. Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach. Sci. Rep. 5 (2015
    • (2015) Sci. Rep , vol.5
    • Ishii, S.1
  • 8
    • 79957982959 scopus 로고    scopus 로고
    • The electric picnic: Synergistic requirements for exoelectrogenic microbial communities
    • Kiely, P. D., Regan, J. M., & Logan, B. E. The electric picnic: synergistic requirements for exoelectrogenic microbial communities. Curr. Opin. Biotechnol. 22, 378-385 (2011
    • (2011) Curr. Opin. Biotechnol , vol.22 , pp. 378-385
    • Kiely, P.D.1    Regan, J.M.2    Logan, B.E.3
  • 9
    • 85027867449 scopus 로고    scopus 로고
    • Electrifying microbes for the production of chemicals
    • Tremblay, P.-L., & Zhang, T. Electrifying microbes for the production of chemicals. Microb. Physiol. Metab. 201, doi: 10.3389/fmicb.2015.00201 (2015
    • (2015) Microb. Physiol. Metab , vol.201
    • Tremblay, P.-L.1    Zhang, T.2
  • 10
    • 84920720510 scopus 로고    scopus 로고
    • A previously uncharacterized nonphotosynthetic member of the chromatiaceae is the primary co2-fixing constituent in a self-regenerating biocathode
    • Wang, Z., et al. A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO2-Fixing Constituent in a Self-Regenerating Biocathode. Appl. Environ. Microbiol. 81, 699-712 (2015
    • (2015) Appl. Environ. Microbiol , vol.81 , pp. 699-712
    • Wang, Z.1
  • 11
  • 12
    • 84878648156 scopus 로고    scopus 로고
    • Long-term operation of microbial electrosynthesis systems improves acetate production by autotrophic microbiomes
    • Marshall, C. W., Ross, D. E., Fichot, E. B., Norman, R. S., & May, H. D. Long-term Operation of Microbial Electrosynthesis Systems Improves Acetate Production by Autotrophic Microbiomes. Environ. Sci. Technol. 47, 6023-6029 (2013
    • (2013) Environ. Sci. Technol , vol.47 , pp. 6023-6029
    • Marshall, C.W.1    Ross, D.E.2    Fichot, E.B.3    Norman, R.S.4    May, H.D.5
  • 13
    • 84908021230 scopus 로고    scopus 로고
    • Influence of acidic ph on hydrogen and acetate production by an electrosynthetic microbiome
    • LaBelle, E. V., Marshall, C. W., Gilbert, J. A., & May, H. D. Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome. PLoS ONE 9, e109935 (2014
    • (2014) Plos One , vol.9 , pp. e109935
    • LaBelle, E.V.1    Marshall, C.W.2    Gilbert, J.A.3    May, H.D.4
  • 14
    • 77958598358 scopus 로고    scopus 로고
    • Genomic analysis of carbon monoxide utilization and butanol production by clostridium carboxidivorans strain p7t
    • Bruant, G., Lévesque, M.-J., Peter, C., Guiot, S. R., & Masson, L. Genomic Analysis of Carbon Monoxide Utilization and Butanol Production by Clostridium carboxidivorans Strain P7T. PLoS ONE 5, e13033 (2010
    • (2010) Plos One , vol.5 , pp. e13033
    • Bruant, G.1    Lévesque, M.-J.2    Peter, C.3    Guiot, S.R.4    Masson, L.5
  • 15
    • 84911440829 scopus 로고    scopus 로고
    • Autotrophy at the thermodynamic limit of life: A model for energy conservation in acetogenic bacteria
    • Schuchmann, K., & Müller, V. Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat. Rev. Microbiol. 12, 809-821 (2014
    • (2014) Nat. Rev. Microbiol , vol.12 , pp. 809-821
    • Schuchmann, K.1    Müller, V.2
  • 16
    • 84936993627 scopus 로고    scopus 로고
    • Microbial electron transport and energy conservation -the foundation for optimizing bioelectrochemical systems
    • Kracke, F., Vassilev, I., & Krömer, J. O. Microbial electron transport and energy conservation -the foundation for optimizing bioelectrochemical systems. Front. Microbiol. 6 (2015
    • (2015) Front. Microbiol , vol.6
    • Kracke, F.1    Vassilev, I.2    Krömer, J.O.3
  • 17
    • 18144416241 scopus 로고    scopus 로고
    • Genes required for rapid expression of nitrogenase activity in azotobacter vinelandii
    • Curatti, L., Brown, C. S., Ludden, P. W., & Rubio, L. M. Genes required for rapid expression of nitrogenase activity in Azotobacter vinelandii. Proc. Natl. Acad. Sci. USA 102, 6291-6296 (2005
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6291-6296
    • Curatti, L.1    Brown, C.S.2    Ludden, P.W.3    Rubio, L.M.4
  • 18
    • 0033962472 scopus 로고    scopus 로고
    • Enhanced nitrogenase activity in strains of rhodobacter capsulatus that overexpress the rnf genes
    • Jeong, H.-S., & Jouanneau, Y. Enhanced Nitrogenase Activity in Strains of Rhodobacter capsulatus That Overexpress the rnf Genes. J. Bacteriol. 182, 1208-1214 (2000
    • (2000) J. Bacteriol , vol.182 , pp. 1208-1214
    • Jeong, H.-S.1    Jouanneau, Y.2
  • 19
    • 84897422714 scopus 로고    scopus 로고
    • Metabolic engineering of rhodobacter sphaeroides for improved hydrogen production
    • Ryu, M.-H., Hull, N. C., & Gomelsky, M. Metabolic engineering of Rhodobacter sphaeroides for improved hydrogen production. Int. J. Hydrog. Energy 39, 6384-6390 (2014
    • (2014) Int. J. Hydrog. Energy , vol.39 , pp. 6384-6390
    • Ryu, M.-H.1    Hull, N.C.2    Gomelsky, M.3
  • 20
    • 84911930262 scopus 로고    scopus 로고
    • Insights into organohalide respiration and the versatile catabolism of sulfurospirillum multivorans gained from comparative genomics and physiological studies
    • Goris, T., et al. Insights into organohalide respiration and the versatile catabolism of Sulfurospirillum multivorans gained from comparative genomics and physiological studies. Environ. Microbiol. 16, 3562-3580 (2014
    • (2014) Environ. Microbiol , vol.16 , pp. 3562-3580
    • Goris, T.1
  • 21
    • 17644414104 scopus 로고    scopus 로고
    • Evidence for autotrophic co2 fixation via the reductive tricarboxylic acid cycle by members of the e subdivision of proteobacteria
    • Hügler, M., Wirsen, C. O., Fuchs, G., Taylor, C. D., & Sievert, S. M. Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the e Subdivision of Proteobacteria. J. Bacteriol. 187, 3020-3027 (2005
    • (2005) J. Bacteriol , vol.187 , pp. 3020-3027
    • Hügler, M.1    Wirsen, C.O.2    Fuchs, G.3    Taylor, C.D.4    Sievert, S.M.5
  • 22
    • 84977579142 scopus 로고    scopus 로고
    • Comparative genomic analysis of sulfurospirillum cavolei mes reconstructed from the metagenome of an electrosynthetic microbiome
    • Ross, D. E., Marshall, C. W., May, H. D., & Norman, R. S. Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome. PLOS ONE 11, e0151214 (2016
    • (2016) Plos One , vol.11 , pp. e0151214
    • Ross, D.E.1    Marshall, C.W.2    May, H.D.3    Norman, R.S.4
  • 23
    • 80055090767 scopus 로고    scopus 로고
    • Entrance of the proton pathway in cbb3-type heme-copper oxidases
    • Lee, H. J., Gennis, R. B., & Ädelroth, P. Entrance of the proton pathway in cbb3-type heme-copper oxidases. Proc. Natl. Acad. Sci. 108, 17661-17666 (2011
    • (2011) Proc. Natl. Acad. Sci , vol.108 , pp. 17661-17666
    • Lee, H.J.1    Gennis, R.B.2    Ädelroth, P.3
  • 24
    • 0036982577 scopus 로고    scopus 로고
    • Hydrogen metabolism in desulfovibrio desulfuricans strain New Jersey (NCIMB 8313)-comparative study with D. Vulgaris and D gigas species
    • Carepo, M., et al. Hydrogen metabolism in Desulfovibrio desulfuricans strain New Jersey (NCIMB 8313)-comparative study with D. vulgaris and D. gigas species. Anaerobe 8, 325-332 (2002
    • (2002) Anaerobe , vol.8 , pp. 325-332
    • Carepo, M.1
  • 25
    • 0021220555 scopus 로고
    • Co metabolism of desulfovibrio vulgaris strain madison: Physiological function in the absence or presence of exogeneous substrates
    • Lupton, F. S., Conrad, R., & Zeikus, J. G. CO metabolism of Desulfovibrio vulgaris strain Madison: physiological function in the absence or presence of exogeneous substrates. FEMS Microbiol. Lett. 23, 263-268 (1984
    • (1984) FEMS Microbiol. Lett , vol.23 , pp. 263-268
    • Lupton, F.S.1    Conrad, R.2    Zeikus, J.G.3
  • 26
    • 84861865532 scopus 로고    scopus 로고
    • Linking bacterial metabolism to graphite cathodes: Electrochemical insights into the h2-producing capability of desulfovibrio sp
    • Aulenta, F., Catapano, L., Snip, L., Villano, M., & Majone, M. Linking Bacterial Metabolism to Graphite Cathodes: Electrochemical Insights into the H2-Producing Capability of Desulfovibrio sp. Chem. Sus. Chem 5, 1080-1085 (2012
    • (2012) Chem Sus Chem , vol.5 , pp. 1080-1085
    • Aulenta, F.1    Catapano, L.2    Snip, L.3    Villano, M.4    Majone, M.5
  • 27
    • 82355191731 scopus 로고    scopus 로고
    • Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell
    • Croese, E., Pereira, M. A., Euverink, G.-J. W., Stams, A. J. M., & Geelhoed, J. S. Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell. Appl. Microbiol. Biotechnol. 92, 1083-1093 (2011
    • (2011) Appl. Microbiol. Biotechnol , vol.92 , pp. 1083-1093
    • Croese, E.1    Pereira, M.A.2    Euverink, G.-J.W.3    Stams, A.J.M.4    Geelhoed, J.S.5
  • 28
    • 80053264714 scopus 로고    scopus 로고
    • Characteristics of hydrogen evolution and oxidation catalyzed by desulfovibrio caledoniensis biofilm on pyrolytic graphite electrode
    • Yu, L., Duan, J., Zhao, W., Huang, Y., & Hou, B. Characteristics of hydrogen evolution and oxidation catalyzed by Desulfovibrio caledoniensis biofilm on pyrolytic graphite electrode. Electrochimica Acta 56, 9041-9047 (2011
    • (2011) Electrochimica Acta , vol.56 , pp. 9041-9047
    • Yu, L.1    Duan, J.2    Zhao, W.3    Huang, Y.4    Hou, B.5
  • 29
    • 0017819828 scopus 로고
    • Growth yields and growth rates of desulfovibrio vulgaris (marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources
    • Badziong, W., & Thauer, R. K. Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources. Arch. Microbiol. 117, 209-214 (1978
    • (1978) Arch. Microbiol , vol.117 , pp. 209-214
    • Badziong, W.1    Thauer, R.K.2
  • 30
    • 0029813694 scopus 로고    scopus 로고
    • Sulfonates: Novel electron acceptors in anaerobic respiration
    • Wg Iii
    • Lie, T. J., Pitta, T., Leadbetter, E. R., Iii, W. G., & Leadbetter, J. R. Sulfonates: novel electron acceptors in anaerobic respiration. Arch. Microbiol. 166, 204-210 (1996
    • (1996) Arch. Microbiol , vol.166 , pp. 204-210
    • Lie, T.J.1    Pitta, T.2    Leadbetter, E.R.3    Leadbetter, J.R.4
  • 31
    • 14644411072 scopus 로고    scopus 로고
    • Interacting regulatory networks in the facultative photosynthetic bacterium rhodobacter sphaeroides 2.4.1
    • Kaplan, S., Eraso, J., & Roh, J. H. Interacting regulatory networks in the facultative photosynthetic bacterium, Rhodobacter sphaeroides 2.4.1. Biochem. Soc. Trans. 33, 51-55 (2005
    • (2005) Biochem. Soc. Trans , vol.33 , pp. 51-55
    • Kaplan, S.1    Eraso, J.2    Roh, J.H.3
  • 32
    • 84856429862 scopus 로고    scopus 로고
    • Transcriptional analysis of shewanella oneidensis mr-1 with an electrode compared to fe(III)citrate or oxygen as terminal electron acceptor
    • Rosenbaum, M. A., et al. Transcriptional Analysis of Shewanella oneidensis MR-1 with an Electrode Compared to Fe(III)Citrate or Oxygen as Terminal Electron Acceptor. PLoS ONE 7, e30827 (2012
    • (2012) Plos One , vol.7 , pp. e30827
    • Rosenbaum, M.A.1
  • 33
    • 27844561449 scopus 로고    scopus 로고
    • Proteiniphilum acetatigenes gen nov, sp nov, from a UASB reactor treating brewery wastewater
    • Chen, S. Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. Int. J. Syst. Evol. Microbiol. 55, 2257-2261 (2005
    • (2005) Int. J. Syst. Evol. Microbiol , vol.55 , pp. 2257-2261
    • Chen, S.1
  • 34
    • 84881663154 scopus 로고    scopus 로고
    • Relating MEC population dynamics to anode performance from DGGE and electrical data
    • Croese, E., et al. Relating MEC population dynamics to anode performance from DGGE and electrical data. Syst. Appl. Microbiol. 36, 408-416 (2013
    • (2013) Syst. Appl. Microbiol , vol.36 , pp. 408-416
    • Croese, E.1
  • 35
    • 33745202132 scopus 로고    scopus 로고
    • Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens
    • Holmes, D. E., et al. Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ. Microbiol. 8, 1805-1815 (2006
    • (2006) Environ. Microbiol , vol.8 , pp. 1805-1815
    • Holmes, D.E.1
  • 36
    • 77953645311 scopus 로고    scopus 로고
    • Alignment of the c-type cytochrome omcs along pili of geobacter sulfurreducens
    • Leang, C., Qian, X., Mester, T., & Lovley, D. R. Alignment of the c-Type Cytochrome OmcS along Pili of Geobacter sulfurreducens. Appl. Environ. Microbiol. 76, 4080-4084 (2010
    • (2010) Appl. Environ. Microbiol , vol.76 , pp. 4080-4084
    • Leang, C.1    Qian, X.2    Mester, T.3    Lovley, D.R.4
  • 37
    • 79551652545 scopus 로고    scopus 로고
    • Towards electrosynthesis in shewanella: Energetics of reversing the mtr pathway for reductive metabolism
    • Ross, D. E., Flynn, J. M., Baron, D. B., Gralnick, J. A., & Bond, D. R. Towards Electrosynthesis in Shewanella: Energetics of Reversing the Mtr Pathway for Reductive Metabolism. PLoS ONE 6, e16649 (2011
    • (2011) Plos One , vol.6 , pp. e16649
    • Ross, D.E.1    Flynn, J.M.2    Baron, D.B.3    Gralnick, J.A.4    Bond, D.R.5
  • 38
    • 79951630868 scopus 로고    scopus 로고
    • Specific localization of the c-type cytochrome omcz at the anode surface in current-producing biofilms of geobacter sulfurreducens
    • Inoue, K., et al. Specific localization of the c-type cytochrome OmcZ at the anode surface in current-producing biofilms of Geobacter sulfurreducens. Environ. Microbiol. Rep. 3, 211-217 (2011
    • (2011) Environ. Microbiol. Rep , vol.3 , pp. 211-217
    • Inoue, K.1
  • 39
    • 84857127335 scopus 로고    scopus 로고
    • Surface multiheme c-type cytochromes from thermincola potens and implications for respiratory metal reduction by gram-positive bacteria
    • Carlson, H. K., et al. Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc. Natl. Acad. Sci. 109, 1702-1707 (2012
    • (2012) Proc. Natl. Acad. Sci , vol.109 , pp. 1702-1707
    • Carlson, H.K.1
  • 40
    • 78650170320 scopus 로고    scopus 로고
    • Gene expression and deletion analysis of mechanisms for electron transfer from electrodes to geobacter sulfurreducens
    • Strycharz, S. M., et al. Gene expression and deletion analysis of mechanisms for electron transfer from electrodes to Geobacter sulfurreducens. Bioelectrochemistry 80, 142-150 (2011
    • (2011) Bioelectrochemistry , vol.80 , pp. 142-150
    • Strycharz, S.M.1
  • 41
    • 84881225162 scopus 로고    scopus 로고
    • Function of formate dehydrogenases in desulfovibrio vulgaris hildenborough energy metabolism
    • da Silva, S. M., et al. Function of formate dehydrogenases in Desulfovibrio vulgaris Hildenborough energy metabolism. Microbiology 159, 1760-1769 (2013
    • (2013) Microbiology , vol.159 , pp. 1760-1769
    • Da Silva, S.M.1
  • 42
    • 0031756314 scopus 로고    scopus 로고
    • Electron transfer between hydrogenases and mono-and multiheme cytochromes in desulfovibrio ssp
    • Pereira, I. A. C., Romão, C. V., Xavier, A. V., LeGall, J., & Teixeira, M. Electron transfer between hydrogenases and mono-and multiheme cytochromes in Desulfovibrio ssp. JBIC J. Biol. Inorg. Chem. 3, 494-498 (1998
    • (1998) JBIC J. Biol. Inorg. Chem , vol.3 , pp. 494-498
    • Pereira, I.A.C.1    Romão, C.V.2    Xavier, A.V.3    LeGall, J.4    Teixeira, M.5
  • 43
    • 32344431599 scopus 로고    scopus 로고
    • Redox interaction of cytochrome c3 with [nife] hydrogenase from desulfovibrio vulgaris miyazaki f
    • Yahata, N., et al. Redox Interaction of Cytochrome c3 with [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F. Biochemistry (Mosc) 45, 1653-1662 (2006
    • (2006) Biochemistry (Mosc , vol.45 , pp. 1653-1662
    • Yahata, N.1
  • 45
    • 84907227973 scopus 로고    scopus 로고
    • Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components
    • Pirbadian, S., et al. Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components. Proc. Natl. Acad. Sci. 111, 12883-12888 (2014
    • (2014) Proc. Natl. Acad. Sci , vol.111 , pp. 12883-12888
    • Pirbadian, S.1
  • 46
    • 84928776576 scopus 로고    scopus 로고
    • Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis
    • E00496-15
    • Deutzmann, J. S., Sahin, M., & Spormann, A. M. Extracellular Enzymes Facilitate Electron Uptake in Biocorrosion and Bioelectrosynthesis. mBio 6, e00496-15 (2015
    • (2015) MBio , vol.6
    • Deutzmann, J.S.1    Sahin, M.2    Spormann, A.M.3
  • 47
    • 84954305774 scopus 로고    scopus 로고
    • Biologically induced hydrogen production drives high rate/high efficiency microbial electrosynthesis of acetate from carbon dioxide
    • n/a-n/a
    • Jourdin, L., Lu, Y., Flexer, V., Keller, J., & Freguia, S. Biologically Induced Hydrogen Production Drives High Rate/High Efficiency Microbial Electrosynthesis of Acetate from Carbon Dioxide. ChemElectroChem n/a-n/a, doi: 10.1002/celc.201500530 (2016
    • (2016) Chem Electro Chem
    • Jourdin, L.1    Lu, Y.2    Flexer, V.3    Keller, J.4    Freguia, S.5
  • 49
    • 79956041561 scopus 로고    scopus 로고
    • Emirge: Reconstruction of full-length ribosomal genes from microbial community short read sequencing data
    • Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 12, R44 (2011
    • (2011) Genome Biol , vol.12 , pp. R44
    • Miller, C.S.1    Baker, B.J.2    Thomas, B.C.3    Singer, S.W.4    Banfield, J.F.5
  • 50
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast, C., et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013
    • (2013) Nucleic Acids Res , vol.41 , pp. D590-D596
    • Quast, C.1
  • 51
    • 84860771820 scopus 로고    scopus 로고
    • Spades: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A., et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 19, 455-477 (2012
    • (2012) J. Comput. Biol , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 52
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de bruijn graphs
    • Zerbino, D. R., & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 53
    • 84867397631 scopus 로고    scopus 로고
    • Meta velvet: An extension of velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki, T., Hachiya, T., Tanaka, H., & Sakakibara, Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40, e155-e155 (2012
    • (2012) Nucleic Acids Res , vol.40 , pp. e155-e155
    • Namiki, T.1    Hachiya, T.2    Tanaka, H.3    Sakakibara, Y.4
  • 55
    • 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
  • 56
    • 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
  • 57
    • 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
  • 58
    • 84925267288 scopus 로고    scopus 로고
    • Uniref clusters: A comprehensive and scalable alternative for improving sequence similarity searches
    • Suzek, B. E., et al. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926-932 (2015
    • (2015) Bioinformatics , vol.31 , pp. 926-932
    • Suzek, B.E.1
  • 59
    • 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
  • 60
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • Albertsen, M., et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533-538 (2013
    • (2013) Nat. Biotechnol , vol.31 , pp. 533-538
    • Albertsen, M.1
  • 61
    • 40549120596 scopus 로고    scopus 로고
    • The rast server: Rapid annotations using subsystems technology
    • Aziz, R. K., et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9, 75 (2008
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1
  • 62
    • 84938841197 scopus 로고    scopus 로고
    • Rasttk: A modular and extensible implementation of the rast algorithm for building custom annotation pipelines and annotating batches of genomes
    • Brettin, T., et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 5 (2015
    • (2015) Sci. Rep , vol.5
    • Brettin, T.1
  • 63
    • 84937040910 scopus 로고    scopus 로고
    • CheckM: Assessing the quality of microbial genomes recovered from isolates single cells and metagenomes
    • 186072.114
    • 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. gr.186072.114, doi: 10.1101/gr.186072.114 (2015
    • (2015) Genome Res. Gr
    • Parks, D.H.1    Imelfort, M.2    Skennerton, C.T.3    Hugenholtz, P.4    Tyson, G.W.5
  • 64
    • 80052606131 scopus 로고    scopus 로고
    • WebMGA a customizable web server for fast metagenomic sequence analysis
    • Wu, S., Zhu, Z., Fu, L., Niu, B., & Li, W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12, 444 (2011
    • (2011) BMC Genomics , vol.12 , pp. 444
    • Wu, S.1    Zhu, Z.2    Fu, L.3    Niu, B.4    Li, W.5
  • 65
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C., et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 66
    • 84941349095 scopus 로고    scopus 로고
    • HMMER web server: 2015 update
    • Finn, R. D., et al. HMMER web server: 2015 update. Nucleic Acids Res. 43, W30-W38 (2015
    • (2015) Nucleic Acids Res , vol.43 , pp. W30-W38
    • Finn, R.D.1
  • 67
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using targetp signalp and related tools
    • Emanuelsson, O., Brunak, S., Heijne, Gvon, & Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2, 953-971 (2007
    • (2007) Nat. Protoc , vol.2 , pp. 953-971
    • Emanuelsson, O.1    Brunak, S.2    Heijne, G.3    Nielsen, H.4
  • 68
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li, H., & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 69
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq 2
    • Love, M. I., Huber, W., & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2. Genome Biol. 15, 550 (2014
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 70
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Henry, C. S., et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 28, 977-982 (2010
    • (2010) Nat. Biotechnol , vol.28 , pp. 977-982
    • Henry, C.S.1
  • 71
    • 0033982936 scopus 로고    scopus 로고
    • Kegg kyoto encyclopedia of genes and genomes
    • Kanehisa, M., & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 73
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server -A public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer, F., et al. The metagenomics RAST server -a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1


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