메뉴 건너뛰기




Volumn 551, Issue 7681, 2017, Pages 457-463

A communal catalogue reveals Earth's multiscale microbial diversity

(303)  Thompson, Luke R a,b,c   Sanders, Jon G a   McDonald, Daniel a   Amir, Amnon a   Ladau, Joshua d   Locey, Kenneth J e   Prill, Robert J f   Tripathi, Anupriya a,g,h   Gibbons, Sean M i,j   Ackermann, Gail a   Navas Molina, Jose A a,k   Janssen, Stefan a   Kopylova, Evguenia a   Vázquez Baeza, Yoshiki a,k   González, Antonio a   Morton, James T a,k   Mirarab, Siavash l   Xu, Zhenjiang Zech a   Jiang, Lingjing a,m   Haroon, Mohamed F n   more..


Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; DATABASE; META-ANALYSIS; MICROBIAL COMMUNITY; RNA; SPECIES DIVERSITY;

EID: 85034804875     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature24621     Document Type: Article
Times cited : (1729)

References (84)
  • 1
    • 34547433545 scopus 로고    scopus 로고
    • Global patterns in bacterial diversity
    • Lozupone, C. A., Knight, R. Global patterns in bacterial diversity. Proc. Natl Acad. Sci. USA 104, 11436-11440 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 11436-11440
    • Lozupone, C.A.1    Knight, R.2
  • 3
    • 31444447130 scopus 로고    scopus 로고
    • The diversity and biogeography of soil bacterial communities
    • Fierer, N., Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626-631 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 626-631
    • Fierer, N.1    Jackson, R.B.2
  • 4
    • 80052061077 scopus 로고    scopus 로고
    • Marine bacterial, archaeal and protistan association networks reveal ecological linkages
    • Steele, J. A. et al. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. 5, 1414-1425 (2011).
    • (2011) ISME J , vol.5 , pp. 1414-1425
    • Steele, J.A.1
  • 6
    • 84929997716 scopus 로고    scopus 로고
    • Ocean plankton Determinants of community structure in the global plankton interactome
    • Lima-Mendez, G. et al. Ocean plankton. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).
    • (2015) Science , vol.348 , pp. 1262073
    • Lima-Mendez, G.1
  • 7
    • 80052722544 scopus 로고    scopus 로고
    • Meeting report: The terabase metagenomics workshop and the vision of an Earth microbiome project
    • Gilbert, J. A. et al. Meeting report: The terabase metagenomics workshop and the vision of an Earth microbiome project. Stand. Genomic Sci. 3, 243-248 (2010).
    • (2010) Stand. Genomic Sci. , vol.3 , pp. 243-248
    • Gilbert, J.A.1
  • 8
    • 84906829581 scopus 로고    scopus 로고
    • The Earth Microbiome project: Successes and aspirations
    • Gilbert, J. A., Jansson, J. K., Knight, R. The Earth Microbiome project: Successes and aspirations. BMC Biol. 12, 69 (2014).
    • (2014) BMC Biol , vol.12 , pp. 69
    • Gilbert, J.A.1    Jansson, J.K.2    Knight, R.3
  • 9
    • 84880917983 scopus 로고    scopus 로고
    • A metaanalysis of changes in bacterial and archaeal communities with time
    • Shade, A., Caporaso, J. G., Handelsman, J., Knight, R., Fierer, N. A metaanalysis of changes in bacterial and archaeal communities with time. ISME J. 7, 1493-1506 (2013).
    • (2013) ISME J. , vol.7 , pp. 1493-1506
    • Shade, A.1    Caporaso, J.G.2    Handelsman, J.3    Knight, R.4    Fierer, N.5
  • 10
    • 79955749319 scopus 로고    scopus 로고
    • Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
    • Yilmaz, P. et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29, 415-420 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 415-420
    • Yilmaz, P.1
  • 13
    • 85020132416 scopus 로고    scopus 로고
    • DNA sequencing as a tool to monitor marine ecological status
    • Goodwin, K. D. et al. DNA sequencing as a tool to monitor marine ecological status. Front. Mar. Sci. https://doi.org/10.3389/fmars.2017.00107 (2017).
    • (2017) Front. Mar. Sci.
    • Goodwin, K.D.1
  • 14
    • 79952005915 scopus 로고    scopus 로고
    • Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    • Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4516-4522 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 4516-4522
    • Caporaso, J.G.1
  • 15
    • 84978941037 scopus 로고    scopus 로고
    • Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
    • Eloe-Fadrosh, E. A., Ivanova, N. N., Woyke, T., Kyrpides, N. C. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat. Microbiol. 1, 15032 (2016).
    • (2016) Nat. Microbiol. , vol.1 , pp. 15032
    • Eloe-Fadrosh, E.A.1    Ivanova, N.N.2    Woyke, T.3    Kyrpides, N.C.4
  • 16
    • 84966929319 scopus 로고    scopus 로고
    • A new view of the tree of life
    • Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).
    • (2016) Nat. Microbiol. , vol.1 , pp. 16048
    • Hug, L.A.1
  • 17
    • 84969814805 scopus 로고    scopus 로고
    • Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
    • Apprill, A., McNally, S., Parsons, R., Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129-137 (2015).
    • (2015) Aquat. Microb. Ecol. , vol.75 , pp. 129-137
    • Apprill, A.1    McNally, S.2    Parsons, R.3    Weber, L.4
  • 18
    • 84952035459 scopus 로고    scopus 로고
    • Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
    • Parada, A. E., Needham, D. M., Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403-1414 (2016).
    • (2016) Environ. Microbiol. , vol.18 , pp. 1403-1414
    • Parada, A.E.1    Needham, D.M.2    Fuhrman, J.A.3
  • 19
    • 85041902876 scopus 로고    scopus 로고
    • Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys
    • Walters, W. et al. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1, e00009-15 (2016).
    • (2016) MSystems , vol.1 , pp. e00009-15
    • Walters, W.1
  • 20
    • 33747073504 scopus 로고    scopus 로고
    • Microbial diversity in the deep sea and the underexplored rare biosphere
    • Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl Acad. Sci. USA 103, 12115-12120 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 12115-12120
    • Sogin, M.L.1
  • 21
    • 85020080492 scopus 로고    scopus 로고
    • Deblur rapidly resolves single-nucleotide community sequence patterns
    • Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2, e00191-16 (2017).
    • (2017) MSystems , vol.2 , pp. e00191-e00216
    • Amir, A.1
  • 22
    • 85029421971 scopus 로고    scopus 로고
    • Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
    • Callahan, B. J., McMurdie, P. J., Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. http://dx.doi.org/10.1038/ismej.2017.119 (2017).
    • (2017) ISME J
    • Callahan, B.J.1    McMurdie, P.J.2    Holmes, S.P.3
  • 23
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse, S. M., Welch, D. M., Morrison, H. G., Sogin, M. L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889-1898 (2010).
    • (2010) Environ. Microbiol. , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 24
    • 84920644670 scopus 로고    scopus 로고
    • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
    • Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
    • (2014) BMC Biol , vol.12 , pp. 87
    • Salter, S.J.1
  • 25
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618 (2012).
    • (2012) ISME J. , vol.6 , pp. 610-618
    • McDonald, D.1
  • 26
    • 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
  • 27
    • 84946811744 scopus 로고    scopus 로고
    • Decreases in average bacterial community rRNA operon copy number during succession
    • Nemergut, D. R. et al. Decreases in average bacterial community rRNA operon copy number during succession. ISME J. 10, 1147-1156 (2016).
    • (2016) ISME J , vol.10 , pp. 1147-1156
    • Nemergut, D.R.1
  • 28
    • 85034833781 scopus 로고    scopus 로고
    • Invasive plants rapidly reshape soil properties in a grassland ecosystem
    • Gibbons, S. M. et al. Invasive plants rapidly reshape soil properties in a grassland ecosystem. mSystems 2, e00178-16 (2017).
    • (2017) MSystems , vol.2 , pp. e00178-e00216
    • Gibbons, S.M.1
  • 29
    • 0034074410 scopus 로고    scopus 로고
    • RRNA operon copy number reflects ecological strategies of bacteria
    • Klappenbach, J. A., Dunbar, J. M., Schmidt, T. M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 1328-1333 (2000).
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 1328-1333
    • Klappenbach, J.A.1    Dunbar, J.M.2    Schmidt, T.M.3
  • 30
    • 1542438057 scopus 로고    scopus 로고
    • On the generality of the latitudinal diversity gradient
    • Hillebrand, H. On the generality of the latitudinal diversity gradient. Am. Nat. 163, 192-211 (2004).
    • (2004) Am. Nat. , vol.163 , pp. 192-211
    • Hillebrand, H.1
  • 31
    • 45549109457 scopus 로고    scopus 로고
    • A latitudinal diversity gradient in planktonic marine bacteria
    • Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl Acad. Sci. USA 105, 7774-7778 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7774-7778
    • Fuhrman, J.A.1
  • 32
    • 84883172257 scopus 로고    scopus 로고
    • Global marine bacterial diversity peaks at high latitudes in winter
    • Ladau, J. et al. Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 7, 1669-1677 (2013).
    • (2013) ISME J , vol.7 , pp. 1669-1677
    • Ladau, J.1
  • 33
    • 84954102971 scopus 로고    scopus 로고
    • Low diversity of planktonic bacteria in the tropical ocean
    • Milici, M. et al. Low diversity of planktonic bacteria in the tropical ocean. Sci. Rep. 6, 19054 (2016).
    • (2016) Sci. Rep. , vol.6 , pp. 19054
    • Milici, M.1
  • 34
    • 78349260124 scopus 로고    scopus 로고
    • Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes
    • Chu, H. et al. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 12, 2998-3006 (2010).
    • (2010) Environ. Microbiol. , vol.12 , pp. 2998-3006
    • Chu, H.1
  • 35
    • 85008414669 scopus 로고    scopus 로고
    • PH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution
    • Wu, Y., Zeng, J., Zhu, Q., Zhang, Z., Lin, X. pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution. Sci. Rep. 7, srep40093 (2017).
    • (2017) Sci. Rep. , vol.7 , pp. 40093
    • Wu, Y.1    Zeng, J.2    Zhu, Q.3    Zhang, Z.4    Lin, X.5
  • 36
    • 84977270544 scopus 로고    scopus 로고
    • Temperature mediates continental-scale diversity of microbes in forest soils
    • Zhou, J. et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat. Commun. 7, 12083 (2016).
    • (2016) Nat. Commun. , vol.7 , pp. 12083
    • Zhou, J.1
  • 37
    • 85021432139 scopus 로고    scopus 로고
    • Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales
    • Hendershot, J. N., Read, Q. D., Henning, J. A., Sanders, N. J., Classen, A. T. Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales. Ecology 98, 1757-1763 (2017).
    • (2017) Ecology , vol.98 , pp. 1757-1763
    • Hendershot, J.N.1    Read, Q.D.2    Henning, J.A.3    Sanders, N.J.4    Classen, A.T.5
  • 38
    • 84877046025 scopus 로고    scopus 로고
    • Measuring fractions of beta diversity and their relationships to nestedness: A theoretical and empirical comparison of novel approaches
    • Carvalho, J. C., Cardoso, P., Borges, P., Schmera, D. Measuring fractions of beta diversity and their relationships to nestedness: A theoretical and empirical comparison of novel approaches. Oikos 122, 825-834 (2013).
    • (2013) Oikos , vol.122 , pp. 825-834
    • Carvalho, J.C.1    Cardoso, P.2    Borges, P.3    Schmera, D.4
  • 39
    • 84954099831 scopus 로고    scopus 로고
    • Diet-induced extinctions in the gut microbiota compound over generations
    • Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212-215 (2016).
    • (2016) Nature , vol.529 , pp. 212-215
    • Sonnenburg, E.D.1
  • 40
    • 0027331799 scopus 로고
    • The measure of order and disorder in the distribution of species in fragmented habitat
    • Atmar, W., Patterson, B. D. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia 96, 373-382 (1993).
    • (1993) Oecologia , vol.96 , pp. 373-382
    • Atmar, W.1    Patterson, B.D.2
  • 41
    • 0030303315 scopus 로고    scopus 로고
    • Investigating causality of nestedness of insular communities: Selective immigrations or extinctions
    • Lomolino, M. V. Investigating causality of nestedness of insular communities: Selective immigrations or extinctions? J. Biogeogr. 23, 699-703 (1996).
    • (1996) J Biogeogr , vol.23 , pp. 699-703
    • Lomolino, M.V.1
  • 44
    • 84899491894 scopus 로고    scopus 로고
    • Assemblage time series reveal biodiversity change but not systematic loss
    • Dornelas, M. et al. Assemblage time series reveal biodiversity change but not systematic loss. Science 344, 296-299 (2014).
    • (2014) Science , vol.344 , pp. 296-299
    • Dornelas, M.1
  • 45
    • 84973441865 scopus 로고    scopus 로고
    • Spatial gaps in global biodiversity information and the role of citizen science
    • Amano, T., Lamming, J. D. L., Sutherland, W. J. Spatial gaps in global biodiversity information and the role of citizen science. Bioscience 66, 393-400 (2016).
    • (2016) Bioscience , vol.66 , pp. 393-400
    • Amano, T.1    Lamming, J.D.L.2    Sutherland, W.J.3
  • 46
    • 84987732826 scopus 로고    scopus 로고
    • The mass production of redundant, misleading, and conflicted systematic reviews and meta-analyses
    • Ioannidis, J. P. A. The mass production of redundant, misleading, and conflicted systematic reviews and meta-analyses. Milbank Q. 94, 485-514 (2016).
    • (2016) Milbank Q. , vol.94 , pp. 485-514
    • Ioannidis, J.P.A.1
  • 47
    • 84920397295 scopus 로고    scopus 로고
    • The founding charter of the Genomic Observatories Network
    • Davies, N. et al. The founding charter of the Genomic Observatories Network. Gigascience 3, 2 (2014).
    • (2014) Gigascience , vol.3 , pp. 2
    • Davies, N.1
  • 48
    • 84945537929 scopus 로고    scopus 로고
    • MICROBIOME A unified initiative to harness Earth's microbiomes
    • Alivisatos, A. P. et al. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 350, 507-508 (2015).
    • (2015) Science , vol.350 , pp. 507-508
    • Alivisatos, A.P.1
  • 49
    • 84986538850 scopus 로고    scopus 로고
    • Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
    • Gohl, D. M. et al. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat. Biotechnol. 34, 942-949 (2016).
    • (2016) Nat. Biotechnol. , vol.34 , pp. 942-949
    • Gohl, D.M.1
  • 50
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    • Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624 (2012).
    • (2012) ISME J , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1
  • 51
    • 84988625177 scopus 로고    scopus 로고
    • The Environment Ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation
    • Buttigieg, P. L., Pafilis, E., Lewis, S. E. The Environment Ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation. J. Biomed. Semant. 7, 57 (2016).
    • (2016) J. Biomed. Semant. , vol.7 , pp. 57
    • Buttigieg, P.L.1    Pafilis, E.2    Lewis, S.E.3
  • 52
    • 84868270724 scopus 로고    scopus 로고
    • The biological observation matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome
    • McDonald, D. et al. The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. Gigascience 1, 7 (2012).
    • (2012) Gigascience , vol.1 , pp. 7
    • McDonald, D.1
  • 53
    • 84920714710 scopus 로고    scopus 로고
    • Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
    • Rideout, J. R. et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2, e545 (2014).
    • (2014) PeerJ , vol.2 , pp. e545
    • Rideout, J.R.1
  • 54
    • 73449128271 scopus 로고    scopus 로고
    • Fast Uni Frac: Facilitating highthroughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    • Hamady, M., Lozupone, C., Knight, R. Fast UniFrac: Facilitating highthroughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 4, 17-27 (2010).
    • (2010) ISME J , vol.4 , pp. 17-27
    • Hamady, M.1    Lozupone, C.2    Knight, R.3
  • 55
    • 84864010118 scopus 로고    scopus 로고
    • SEPP: SATé-enabled phylogenetic placement
    • Mirarab, S., Nguyen, N., Warnow, T. SEPP: SATé-enabled phylogenetic placement. Pac. Symp. Biocomput. 2012, 247-258 (2012).
    • (2012) Pac. Symp. Biocomput. , vol.2012 , pp. 247-258
    • Mirarab, S.1    Nguyen, N.2    Warnow, T.3
  • 56
    • 84991526597 scopus 로고    scopus 로고
    • EMPeror: A tool for visualizing high-throughput microbial community data
    • Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A., Knight, R. EMPeror: A tool for visualizing high-throughput microbial community data. Gigascience 2, 16 (2013).
    • (2013) Gigascience , vol.2 , pp. 16
    • Vázquez-Baeza, Y.1    Pirrung, M.2    Gonzalez, A.3    Knight, R.4
  • 58
    • 84874265271 scopus 로고    scopus 로고
    • The plant ontology as a tool for comparative plant anatomy and genomic analyses
    • Cooper, L. et al. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 54, e1 (2013).
    • (2013) Plant Cell Physiol , vol.54 , pp. e1
    • Cooper, L.1
  • 59
    • 84964314624 scopus 로고    scopus 로고
    • An ontology for microbial phenotypes
    • Chibucos, M. C. et al. An ontology for microbial phenotypes. BMC Microbiol. 14, 294 (2014).
    • (2014) BMC Microbiol , vol.14 , pp. 294
    • Chibucos, M.C.1
  • 60
    • 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
  • 61
    • 84870814915 scopus 로고    scopus 로고
    • Sort Me RNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
    • Kopylova, E., Noé, L., Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211-3217 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 3211-3217
    • Kopylova, E.1    Noé, L.2    Touzet, H.3
  • 62
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss, P. D., Gevers, D., Westcott, S. L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6, e27310 (2011).
    • (2011) PLoS One , vol.6 , pp. e27310
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 63
    • 84994444665 scopus 로고    scopus 로고
    • VSEARCH: A versatile open source tool for metagenomics
    • Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
    • (2016) PeerJ , vol.4 , pp. e2584
    • Rognes, T.1    Flouri, T.2    Nichols, B.3    Quince, C.4    Mahé, F.5
  • 64
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23, 205-211 (2009).
    • (2009) Genome Inform , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 65
    • 77958610660 scopus 로고    scopus 로고
    • Pplacer: Linear time maximumlikelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen, F. A., Kodner, R. B., Armbrust, E. V. pplacer: Linear time maximumlikelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 66
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 67
    • 79952600759 scopus 로고    scopus 로고
    • Cython: The best of both worlds
    • Behnel, S. et al. Cython: The best of both worlds. Comput. Sci. Eng. 13, 31-39 (2011).
    • (2011) Comput. Sci. Eng. , vol.13 , pp. 31-39
    • Behnel, S.1
  • 69
    • 84964850604 scopus 로고    scopus 로고
    • Simple and efficient fully-functional succinct trees
    • Cordova, J., Navarro, G. Simple and efficient fully-functional succinct trees. Theor. Comput. Sci. 656, 135-145 (2016).
    • (2016) Theor. Comput. Sci. , vol.656 , pp. 135-145
    • Cordova, J.1    Navarro, G.2
  • 70
    • 84940644968 scopus 로고
    • A mathematical theory of communication
    • Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423 (1948).
    • (1948) Bell Syst. Tech. J. , vol.27 , pp. 379-423
    • Shannon, C.E.1
  • 71
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao, A. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11, 265-270 (1984).
    • (1984) Scand. J. Stat. , vol.11 , pp. 265-270
    • Chao, A.1
  • 72
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • Faith, D. P. Conservation evaluation and phylogenetic diversity. Bio. Conserv. 61, 1-10 (1992).
    • (1992) Bio. Conserv. , vol.61 , pp. 1-10
    • Faith, D.P.1
  • 73
    • 77953019375 scopus 로고    scopus 로고
    • Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories
    • Guo, W., Sarkar, S. K., Peddada, S. D. Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories. Biometrics 66, 485-492 (2010).
    • (2010) Biometrics , vol.66 , pp. 485-492
    • Guo, W.1    Sarkar, S.K.2    Peddada, S.D.3
  • 74
    • 84959177668 scopus 로고    scopus 로고
    • A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies
    • Grandhi, A., Guo, W., Peddada, S. D. A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies. BMC Bioinformatics 17, 104 (2016).
    • (2016) BMC Bioinformatics , vol.17 , pp. 104
    • Grandhi, A.1    Guo, W.2    Peddada, S.D.3
  • 76
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 814-821
    • Langille, M.G.1
  • 77
    • 56249113343 scopus 로고    scopus 로고
    • Building predictive models in R using the caret package
    • Kuhn, M. Building predictive models in R using the caret package. J. Stat. Soft. 28, 1-26 (2008).
    • (2008) J. Stat. Soft. , vol.28 , pp. 1-26
    • Kuhn, M.1
  • 78
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw, A., Wiener, M. Classification and regression by randomForest. R News 2-3, 18-22 (2002).
    • (2002) R News , vol.2-3 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 79
    • 80052301430 scopus 로고    scopus 로고
    • Bayesian community-wide culture-independent microbial source tracking
    • Knights, D. et al. Bayesian community-wide culture-independent microbial source tracking. Nat. Methods 8, 761-763 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 761-763
    • Knights, D.1
  • 80
    • 49249087447 scopus 로고    scopus 로고
    • A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement
    • Almeida-Neto, M., Guimaraes, P., Guimaraes, P. R. J., Loyola, R. D., Ulrich, W. A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement. Oikos 117, 1227-1239 (2008).
    • (2008) Oikos , vol.117 , pp. 1227-1239
    • Almeida-Neto, M.1    Guimaraes, P.2    Guimaraes, P.R.J.3    Loyola, R.D.4    Ulrich, W.5
  • 81
    • 58149122738 scopus 로고    scopus 로고
    • A consumer's guide to nestedness analysis
    • Ulrich, W., Almeida-Neto, M., Gotelli, N. J. A consumer's guide to nestedness analysis. Oikos 118, 3-17 (2009).
    • (2009) Oikos , vol.118 , pp. 3-17
    • Ulrich, W.1    Almeida-Neto, M.2    Gotelli, N.J.3
  • 82
    • 84891787231 scopus 로고    scopus 로고
    • Ribosomal Database Project: Data and tools for high throughput rRNA analysis
    • Cole, J. R. et al. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633-D642 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D633-D642
    • Cole, J.R.1
  • 83
    • 0020043415 scopus 로고
    • Pasteurella multocida- The major cause of hand infections following domestic animal bites
    • Arons, M. S., Fernando, L., Polayes, I. M. Pasteurella multocida-the major cause of hand infections following domestic animal bites. J. Hand Surg. Am. 7, 47-52 (1982).
    • (1982) J. Hand Surg. Am. , vol.7 , pp. 47-52
    • Arons, M.S.1    Fernando, L.2    Polayes, I.M.3
  • 84
    • 84997541867 scopus 로고    scopus 로고
    • Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
    • Ormerod, K. L. et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome 4, 36 (2016).
    • (2016) Microbiome , vol.4 , pp. 36
    • Ormerod, K.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.