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Volumn 38, Issue 4, 2015, Pages 231-236

The changing landscape of microbial biodiversity exploration and its implications for systematics

Author keywords

"Microbial dark matter" metagenomics; Candidate phyla; Candidatus taxonomy; Single cell genomics

Indexed keywords

ARCHAEON; AXENIC CULTURE; BACTERIUM; BIOSYNTHESIS; DNA DNA HYBRIDIZATION; DNA SEQUENCE; GENE AMPLIFICATION; LANDSCAPE; METAGENOMICS; MICROBIAL DIVERSITY; MOLECULAR ECOLOGY; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; TAXONOMIC RANK; TAXONOMY; TREE OF LIFE; CLASSIFICATION; GENETICS; SINGLE CELL ANALYSIS;

EID: 84999488403     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2015.03.003     Document Type: Review
Times cited : (27)

References (74)
  • 3
    • 84883870098 scopus 로고    scopus 로고
    • Omic approaches in microbial ecology: charting the unknown
    • Baker B.J., Dick G.J. Omic approaches in microbial ecology: charting the unknown. Microbe 2013, 8:353-360.
    • (2013) Microbe , vol.8 , pp. 353-360
    • Baker, B.J.1    Dick, G.J.2
  • 5
    • 84894624480 scopus 로고    scopus 로고
    • Dissecting genomic diversity, one cell at a time
    • Blainey P.C., Quake S.R. Dissecting genomic diversity, one cell at a time. Nat. Methods 2014, 11:19-21.
    • (2014) Nat. Methods , vol.11 , pp. 19-21
    • Blainey, P.C.1    Quake, S.R.2
  • 12
    • 84870035320 scopus 로고    scopus 로고
    • Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
    • Dröge J., McHardy A.C. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinform. 2012, 13:646-655.
    • (2012) Brief Bioinform. , vol.13 , pp. 646-655
    • Dröge, J.1    McHardy, A.C.2
  • 15
    • 84864324335 scopus 로고    scopus 로고
    • Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics
    • Garrity G.M., Oren A. Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics. Trends Microbiol. 2012, 20:353-354.
    • (2012) Trends Microbiol. , vol.20 , pp. 353-354
    • Garrity, G.M.1    Oren, A.2
  • 16
    • 84873146358 scopus 로고    scopus 로고
    • Response to Sutcliffe et al.: regarding the international committee on systematics of prokaryotes
    • Garrity G.M., Oren A. Response to Sutcliffe et al.: regarding the international committee on systematics of prokaryotes. Trends Microbiol. 2013, 21:53-55.
    • (2013) Trends Microbiol. , vol.21 , pp. 53-55
    • Garrity, G.M.1    Oren, A.2
  • 21
    • 82355180998 scopus 로고    scopus 로고
    • The archaeal 'TACK' superphylum and the origin of eukaryotes
    • Guy L., Ettema T.J. The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol. 2011, 19:580-587.
    • (2011) Trends Microbiol. , vol.19 , pp. 580-587
    • Guy, L.1    Ettema, T.J.2
  • 23
    • 0037007636 scopus 로고    scopus 로고
    • A new phylum of archaea represented by a nanosized hyperthermophilic symbiont
    • Huber H., Hohn M., Rachel R., Fuchs T., Wimmer V., Stetter K. A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 2002, 417:63.
    • (2002) Nature , vol.417 , pp. 63
    • Huber, H.1    Hohn, M.2    Rachel, R.3    Fuchs, T.4    Wimmer, V.5    Stetter, K.6
  • 24
    • 84907682734 scopus 로고    scopus 로고
    • GroopM: an automated tool for the recovery of population genomes from related metagenomes
    • Imelfort M., Parks D., Woodcroft B.J., Dennis P., Hugenholtz P., Tyson G.W. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2014, 2:e603.
    • (2014) PeerJ , vol.2 , pp. e603
    • Imelfort, M.1    Parks, D.2    Woodcroft, B.J.3    Dennis, P.4    Hugenholtz, P.5    Tyson, G.W.6
  • 27
    • 77952889628 scopus 로고    scopus 로고
    • En route to a genome-based classification of Archaea and Bacteria?
    • June
    • Klenk H.P., Göker M. En route to a genome-based classification of Archaea and Bacteria?. Syst. Appl. Microbiol. 2010, 33(June (4)):175-182.
    • (2010) Syst. Appl. Microbiol. , vol.33 , Issue.4 , pp. 175-182
    • Klenk, H.P.1    Göker, M.2
  • 28
    • 84884572248 scopus 로고    scopus 로고
    • Optofluidic cell selection from complex microbial communities for single-genome analysis
    • Landry Z.C., Giovanonni S.J., Quake S.R., Blainey P.C. Optofluidic cell selection from complex microbial communities for single-genome analysis. Methods Enzymol. 2013, 531:61-90.
    • (2013) Methods Enzymol. , vol.531 , pp. 61-90
    • Landry, Z.C.1    Giovanonni, S.J.2    Quake, S.R.3    Blainey, P.C.4
  • 30
    • 84864394611 scopus 로고    scopus 로고
    • Genomic sequencing of uncultured microorganisms from single cells
    • Lasken R.S. Genomic sequencing of uncultured microorganisms from single cells. Nat. Rev. Microbiol. 2012, 10:631-640.
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 631-640
    • Lasken, R.S.1
  • 32
    • 84870020971 scopus 로고    scopus 로고
    • Classification of metagenomic sequences: methods and challenges
    • Mande S.S., Mohammed M.H., Ghosh T.S. Classification of metagenomic sequences: methods and challenges. Brief Bioinform. 2012, 13:669-681.
    • (2012) Brief Bioinform. , vol.13 , pp. 669-681
    • Mande, S.S.1    Mohammed, M.H.2    Ghosh, T.S.3
  • 35
    • 84861349503 scopus 로고    scopus 로고
    • High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use
    • Mayali X., Weber P.K., Brodie E.L., Mabery S., Hoeprich P.D., Pett-Ridge J. High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. ISME J. 2012, 6:1210-1221.
    • (2012) ISME J. , vol.6 , pp. 1210-1221
    • Mayali, X.1    Weber, P.K.2    Brodie, E.L.3    Mabery, S.4    Hoeprich, P.D.5    Pett-Ridge, J.6
  • 37
    • 0028082002 scopus 로고
    • Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes
    • Murray R.G.E., Scheifer K.H. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol. 1994, 44:174-176.
    • (1994) Int. J. Syst. Bacteriol. , vol.44 , pp. 174-176
    • Murray, R.G.E.1    Scheifer, K.H.2
  • 38
    • 0028887837 scopus 로고
    • Taxonomic note: implementation of the provisional status candidatus for incompletely described procaryotes
    • Murray R.G.E., Stackebrandt E. Taxonomic note: implementation of the provisional status candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 1995, 45:186-187.
    • (1995) Int. J. Syst. Bacteriol. , vol.45 , pp. 186-187
    • Murray, R.G.E.1    Stackebrandt, E.2
  • 40
    • 34547762133 scopus 로고    scopus 로고
    • Witnessing the last supper of uncultivated microbial cells with Raman-FISH
    • Neufeld J.D., Murrell J.C. Witnessing the last supper of uncultivated microbial cells with Raman-FISH. ISME J. 2007, 1:269-270.
    • (2007) ISME J. , vol.1 , pp. 269-270
    • Neufeld, J.D.1    Murrell, J.C.2
  • 42
    • 84903985430 scopus 로고    scopus 로고
    • Then and now: a systematic review of the systematics of prokaryotes in the last 80years
    • Oren A., Garrity G.M. Then and now: a systematic review of the systematics of prokaryotes in the last 80years. Antonie Van Leeuwenhoek 2014, 106:43-56.
    • (2014) Antonie Van Leeuwenhoek , vol.106 , pp. 43-56
    • Oren, A.1    Garrity, G.M.2
  • 44
    • 84891817929 scopus 로고    scopus 로고
    • LPSN-list of prokaryotic names with standing in nomenclature
    • Parte A.C. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 2014, 42:D613-D616.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D613-D616
    • Parte, A.C.1
  • 48
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19126-191231.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 19126-191231
    • Richter, M.1    Rosselló-Móra, R.2
  • 51
    • 84856571925 scopus 로고    scopus 로고
    • Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories
    • Rosselló-Móra R. Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ. Microbiol. 2012, 14:318-334.
    • (2012) Environ. Microbiol. , vol.14 , pp. 318-334
    • Rosselló-Móra, R.1
  • 52
    • 84856496549 scopus 로고    scopus 로고
    • Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
    • Scholz M.B., Lo C.C., Chain P.S. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 2012, 23:9-15.
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 9-15
    • Scholz, M.B.1    Lo, C.C.2    Chain, P.S.3
  • 53
    • 78650591665 scopus 로고    scopus 로고
    • Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges
    • Siegl A., Kamke J., Hochmuth T., Piel J., Richter M., Liang C.G., Dandekar T., Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2011, 5:61-70.
    • (2011) ISME J. , vol.5 , pp. 61-70
    • Siegl, A.1    Kamke, J.2    Hochmuth, T.3    Piel, J.4    Richter, M.5    Liang, C.G.6    Dandekar, T.7    Hentschel, U.8
  • 54
    • 84890062467 scopus 로고    scopus 로고
    • Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution
    • Spang A., Martijn J., Saw J.H., Lind A.E., Guy L., Ettema T.J. Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. Archaea 2013, 2013:202358.
    • (2013) Archaea , vol.2013
    • Spang, A.1    Martijn, J.2    Saw, J.H.3    Lind, A.E.4    Guy, L.5    Ettema, T.J.6
  • 55
    • 84868098266 scopus 로고    scopus 로고
    • Single cell genomics: an individual look at microbes
    • Stepanauskas R. Single cell genomics: an individual look at microbes. Curr. Opin. Microbiol. 2012, 15:613-620.
    • (2012) Curr. Opin. Microbiol. , vol.15 , pp. 613-620
    • Stepanauskas, R.1
  • 56
    • 84875832926 scopus 로고    scopus 로고
    • The binning of metagenomic contigs for microbial physiology of mixed cultures
    • Strous M., Kraft B., Bisdorf R., Tegetmeyer H.E. The binning of metagenomic contigs for microbial physiology of mixed cultures. Front. Microbiol. 2012, 3:410.
    • (2012) Front. Microbiol. , vol.3 , pp. 410
    • Strous, M.1    Kraft, B.2    Bisdorf, R.3    Tegetmeyer, H.E.4
  • 57
    • 84856214874 scopus 로고    scopus 로고
    • A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa
    • Sutcliffe I.C., Trujillo M.E., Goodfellow M. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 2012, 101:13-20.
    • (2012) Antonie Van Leeuwenhoek , vol.101 , pp. 13-20
    • Sutcliffe, I.C.1    Trujillo, M.E.2    Goodfellow, M.3
  • 58
    • 79551473440 scopus 로고    scopus 로고
    • Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war
    • Sutcliffe I.C. Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war. Environ. Microbiol. 2011, 13:279-282.
    • (2011) Environ. Microbiol. , vol.13 , pp. 279-282
    • Sutcliffe, I.C.1
  • 59
    • 84873208165 scopus 로고    scopus 로고
    • A call to action for the international committee on systematics of prokaryotes
    • Sutcliffe I.C., Trujillo M.E., Whitman W.B., Goodfellow M. A call to action for the international committee on systematics of prokaryotes. Trends Microbiol. 2013, 21:51-52.
    • (2013) Trends Microbiol. , vol.21 , pp. 51-52
    • Sutcliffe, I.C.1    Trujillo, M.E.2    Whitman, W.B.3    Goodfellow, M.4
  • 65
    • 31944434615 scopus 로고    scopus 로고
    • Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays
    • Wagner M., Nielsen P.H., Loy A., Nielsen J.L., Daims H. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr. Opin. Biotechnol. 2006, 17:1-9.
    • (2006) Curr. Opin. Biotechnol. , vol.17 , pp. 1-9
    • Wagner, M.1    Nielsen, P.H.2    Loy, A.3    Nielsen, J.L.4    Daims, H.5
  • 66
    • 84907943465 scopus 로고    scopus 로고
    • Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis
    • Wang Z., Guo F., Liu L., Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis. PLOS ONE 2014, 9:1-9.
    • (2014) PLOS ONE , vol.9 , pp. 1-9
    • Wang, Z.1    Guo, F.2    Liu, L.3    Zhang, T.4
  • 74
    • 83155178364 scopus 로고    scopus 로고
    • Partial genome assembly for candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma)
    • Youssef N.H., Blainey P.C., Quake S.R., Elshahed M.S. Partial genome assembly for candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl. Environ. Microbiol. 2011, 77:7804-7814.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 7804-7814
    • Youssef, N.H.1    Blainey, P.C.2    Quake, S.R.3    Elshahed, M.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.