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Volumn 4, Issue 3, 2013, Pages

Random sampling process leads to overestimation ofβ-diversity of microbial communities

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BETA DIVERSITY; CONTROLLED STUDY; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NORMAL DISTRIBUTION; OPERATIONAL TAXONOMIC UNIT; POISSON DISTRIBUTION; POPULATION ABUNDANCE; PRIORITY JOURNAL; PROCESS MODEL; RANDOM SAMPLE; REPRODUCIBILITY; RNA SEQUENCE; SPECIES COMPOSITION; SPECIES DISTRIBUTION; TAXONOMY; BIOTA; METAGENOMICS; MICROBIOLOGY; MOLECULAR BIOLOGY; PROCEDURES; SELECTION BIAS; THEORETICAL MODEL;

EID: 84879595619     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00324-13     Document Type: Article
Times cited : (76)

References (74)
  • 2
    • 79952136790 scopus 로고    scopus 로고
    • Functional molecular ecological networks
    • Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X. 2010. Functional molecular ecological networks. mBio 1(4):e00169-10. http://dx.doi.org/10.1128/mBio.00169-10/.
    • (2010) MBio , vol.1 , Issue.4
    • Zhou, J.1    Deng, Y.2    Luo, F.3    He, Z.4    Tu, Q.5    Zhi, X.6
  • 3
    • 84858748000 scopus 로고    scopus 로고
    • 2
    • Zhou J, Deng Y, Luo F, He Z, Yang Y. 2011. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio 2(4):e00122-11. http://dx.doi.org/10.1128/mBio.00122-11/.
    • (2011) MBio , vol.2 , Issue.4
    • Zhou, J.1    Deng, Y.2    Luo, F.3    He, Z.4    Yang, Y.5
  • 5
    • 0029475680 scopus 로고
    • Soil microbial diversity and the sustainability of agricultural soils
    • Kennedy AC, Smith KL. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75-86.
    • (1995) Plant Soil , vol.170 , pp. 75-86
    • Kennedy, A.C.1    Smith, K.L.2
  • 8
    • 33845901507 scopus 로고    scopus 로고
    • Microbial ecology: Human gut microbes associated with obesity
    • Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022-1023.
    • (2006) Nature , vol.444 , pp. 1022-1023
    • Ley, R.E.1    Turnbaugh, P.J.2    Klein, S.3    Gordon, J.I.4
  • 9
    • 33748605034 scopus 로고    scopus 로고
    • Fundamental questions in biology
    • Levin SA. 2006. Fundamental questions in biology. PLoS Biol. 4:e300. http://dx.doi.org/10.1371/journal.pbio.0040300/.
    • (2006) PLoS Biol , vol.4
    • Levin, S.A.1
  • 13
    • 84866040222 scopus 로고    scopus 로고
    • A direct PCR approach to accelerate analyses of human-associated microbial communities
    • Flores GE, Henley JB, Fierer N. 2012. A direct PCR approach to accelerate analyses of human-associated microbial communities. PLoS One 7:e44563. http://dx.doi.org/10.1371/journal.pone.0044563/.
    • (2012) PLoS One , vol.7
    • Flores, G.E.1    Henley, J.B.2    Fierer, N.3
  • 14
    • 52649090774 scopus 로고    scopus 로고
    • An invitation to the marriage of metagenomics and metabolomics
    • Turnbaugh PJ, Gordon JI. 2008. An invitation to the marriage of metagenomics and metabolomics. Cell 134:708-713.
    • (2008) Cell , vol.134 , pp. 708-713
    • Turnbaugh, P.J.1    Gordon, J.I.2
  • 17
    • 85027927719 scopus 로고    scopus 로고
    • Enterotypes of the human gut microbiome
    • Arumugam M, et al. 2011. Enterotypes of the human gut microbiome. Nature 473:174-180.
    • (2011) Nature , vol.473 , pp. 174-180
    • Arumugam, M.1
  • 19
    • 84856011484 scopus 로고    scopus 로고
    • Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
    • Greenblum S, Turnbaugh PJ, Borenstein E. 2012. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Natl. Acad. Sci. U. S. A. 109:594-599.
    • (2012) Proc. Natl. Acad. Sci. U. S. A , vol.109 , pp. 594-599
    • Greenblum, S.1    Turnbaugh, P.J.2    Borenstein, E.3
  • 31
    • 84863739532 scopus 로고    scopus 로고
    • Testing the limits of 454 pyrotag sequencing: Reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes
    • Pilloni G, Granitsiotis MS, Engel M, Lueders T. 2012. Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS One 7:e40467. http://dx.doi.org/10.1371/journal.pone.0040467/.
    • (2012) PLoS One , vol.7
    • Pilloni, G.1    Granitsiotis, M.S.2    Engel, M.3    Lueders, T.4
  • 34
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project Consortium
    • Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature 486:215-221.
    • (2012) Nature , vol.486 , pp. 215-221
  • 35
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium
    • Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 40
    • 66149130975 scopus 로고    scopus 로고
    • Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
    • Shi Y, Tyson GW, DeLong EF. 2009. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459:266-269.
    • (2009) Nature , vol.459 , pp. 266-269
    • Shi, Y.1    Tyson, G.W.2    Delong, E.F.3
  • 43
    • 84866174523 scopus 로고    scopus 로고
    • Genomic approaches to studying the human microbiota
    • Weinstock GM. 2012. Genomic approaches to studying the human microbiota. Nature 489:250-256.
    • (2012) Nature , vol.489 , pp. 250-256
    • Weinstock, G.M.1
  • 44
    • 79960502648 scopus 로고    scopus 로고
    • Disentangling the importance of ecological niches from stochastic processes across scales
    • Chase JM, Myers JA. 2011. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366:2351-2363.
    • (2011) Philos. Trans. R. Soc. Lond. B Biol. Sci , vol.366 , pp. 2351-2363
    • Chase, J.M.1    Myers, J.A.2
  • 45
    • 36849062509 scopus 로고    scopus 로고
    • Drought mediates the importance of stochastic community assembly
    • Chase JM. 2007. Drought mediates the importance of stochastic community assembly. Proc. Natl. Acad. Sci. U. S. A. 104:17430-17434.
    • (2007) Proc. Natl. Acad. Sci. U. S. A , vol.104 , pp. 17430-17434
    • Chase, J.M.1
  • 46
    • 77953577612 scopus 로고    scopus 로고
    • Stochastic community assembly causes higher biodiversity in more productive environments
    • Chase JM. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science 328:1388-1391.
    • (2010) Science , vol.328 , pp. 1388-1391
    • Chase, J.M.1
  • 51
    • 84865060813 scopus 로고    scopus 로고
    • PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
    • Pinto AJ, Raskin L. 2012. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE 7:e43093. http://dx.doi.org/10.1371/journal.pone.0043093/.
    • (2012) PLoS ONE , vol.7
    • Pinto, A.J.1    Raskin, L.2
  • 53
    • 34548523806 scopus 로고    scopus 로고
    • A statistical theory for sampling species abundances
    • Green JL, Plotkin JB. 2007. A statistical theory for sampling species abundances. Ecol. Lett. 10:1037-1045.
    • (2007) Ecol. Lett , vol.10 , pp. 1037-1045
    • Green, J.L.1    Plotkin, J.B.2
  • 54
    • 0013400753 scopus 로고    scopus 로고
    • Sampling the species composition of a landscape
    • Plotkin JB, Muller-Landau HC. 2002. Sampling the species composition of a landscape. Ecology 83:3344-3356.
    • (2002) Ecology , vol.83 , pp. 3344-3356
    • Plotkin, J.B.1    Muller-Landau, H.C.2
  • 55
    • 34447503403 scopus 로고    scopus 로고
    • Sampling species abundance distributions: Resolving the veil-line debate
    • Chisholm RA. 2007. Sampling species abundance distributions: resolving the veil-line debate. J. Theor. Biol. 247:600-607.
    • (2007) J. Theor. Biol , vol.247 , pp. 600-607
    • Chisholm, R.A.1
  • 56
    • 0032421795 scopus 로고    scopus 로고
    • A general theory of the sampling process with applications to the "veil line."
    • Dewdney AK. 1998. A general theory of the sampling process with applications to the "veil line." Theor. Popul. Biol. 54:294-302.
    • (1998) Theor. Popul. Biol , vol.54 , pp. 294-302
    • Dewdney, A.K.1
  • 57
    • 53849104257 scopus 로고    scopus 로고
    • The rational exploration of microbial diversity
    • Quince C, Curtis TP, Sloan WT. 2008. The rational exploration of microbial diversity. ISME J. 2:997-1006.
    • (2008) ISME J , vol.2 , pp. 997-1006
    • Quince, C.1    Curtis, T.P.2    Sloan, W.T.3
  • 58
    • 0003456793 scopus 로고    scopus 로고
    • 2nd ed. Benjamin/Cummings, Menlo Park, CA
    • Krebs CJ. 1999. Ecological methodology, 2nd ed. Benjamin/Cummings, Menlo Park, CA.
    • (1999) Ecological Methodology
    • Krebs, C.J.1
  • 59
    • 5344251750 scopus 로고    scopus 로고
    • Sampling Hubbell's neutral theory of biodiversity
    • Alonso D, McKane AJ. 2004. Sampling Hubbell's neutral theory of biodiversity. Ecol. Lett. 7:901-910.
    • (2004) Ecol. Lett , vol.7 , pp. 901-910
    • Alonso, D.1    McKane, A.J.2
  • 61
    • 80054855719 scopus 로고    scopus 로고
    • Bugs, stool, and the irritable bowel syndrome: Too much is as bad as too little?
    • Talley NJ, Fodor AA. 2011. Bugs, stool, and the irritable bowel syndrome: too much is as bad as too little? Gastroenterology 141:1555-1559.
    • (2011) Gastroenterology , vol.141 , pp. 1555-1559
    • Talley, N.J.1    Fodor, A.A.2
  • 62
    • 84865501143 scopus 로고    scopus 로고
    • Low sequencing efforts bias analyses of shared taxa in microbial communities
    • Lemos LN, Fulthorpe RR, Roesch LF. 2012. Low sequencing efforts bias analyses of shared taxa in microbial communities. Folia Microbiol. (Praha) 57:409-413.
    • (2012) Folia Microbiol. (Praha) , vol.57 , pp. 409-413
    • Lemos, L.N.1    Fulthorpe, R.R.2    Roesch, L.F.3
  • 63
    • 79961081161 scopus 로고    scopus 로고
    • Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads
    • Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. 2011. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77:3846-3852.
    • (2011) Appl. Environ. Microbiol , vol.77 , pp. 3846-3852
    • Bartram, A.K.1    Lynch, M.D.2    Stearns, J.C.3    Moreno-Hagelsieb, G.4    Neufeld, J.D.5
  • 64
    • 84859829470 scopus 로고    scopus 로고
    • High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples
    • Kauserud H, Kumar S, Brysting AK, Nordén J, Carlsen T. 2012. High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples. Mycorrhiza 22:309-315.
    • (2012) Mycorrhiza , vol.22 , pp. 309-315
    • Kauserud, H.1    Kumar, S.2    Brysting, A.K.3    Nordén, J.4    Carlsen, T.5
  • 65
    • 80052868933 scopus 로고    scopus 로고
    • Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops
    • Mao Y, Yannarell AC, Mackie RI. 2011. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 6:e24750. http://dx.doi.org/10.1371/journal.pone.0024750/.
    • (2011) PLoS One , vol.6
    • Mao, Y.1    Yannarell, A.C.2    Mackie, R.I.3
  • 66
    • 83055163369 scopus 로고    scopus 로고
    • Influence of DNA extraction and PCR amplification on studies of soil fungal communities based on amplicon sequencing
    • Xu LH, Ravnskov S, Larsen J, Nicolaisen M. 2011. Influence of DNA extraction and PCR amplification on studies of soil fungal communities based on amplicon sequencing. Can. J. Microbiol. 57:1062-1066.
    • (2011) Can. J. Microbiol , vol.57 , pp. 1062-1066
    • Xu, L.H.1    Ravnskov, S.2    Larsen, J.3    Nicolaisen, M.4
  • 67
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss PD, Gevers D, Westcott SL. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6:e27310. http://dx.doi.org/10.1371/journal.pone.0027310/.
    • (2011) PLoS One , vol.6
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 68
    • 83155178360 scopus 로고    scopus 로고
    • Barcoded primers used in multiplex amplicon pyrosequencing bias amplification
    • Berry D, Ben Mahfoudh K, Wagner M, Loy A. 2011. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 77:7846-7849.
    • (2011) Appl. Environ. Microbiol , vol.77 , pp. 7846-7849
    • Berry, D.1    Ben, M.K.2    Wagner, M.3    Loy, A.4
  • 70
    • 70350294348 scopus 로고    scopus 로고
    • Systematic artifacts in metagenomes from complex microbial communities
    • Gomez-Alvarez V, Teal TK, Schmidt TM. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3:1314-1317.
    • (2009) ISME J , vol.3 , pp. 1314-1317
    • Gomez-Alvarez, V.1    Teal, T.K.2    Schmidt, T.M.3
  • 72
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-123.
    • (2010) Environ. Microbiol , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 73
    • 0037630010 scopus 로고    scopus 로고
    • Disentangling sampling and ecological explanations underlying species area relationships
    • Cam E, Nichols JD, Hines JE, Sauer JR, Jara A, Flather CH. 2002. Disentangling sampling and ecological explanations underlying species area relationships. Ecology 83:1118-1130.
    • (2002) Ecology , vol.83 , pp. 1118-1130
    • Cam, E.1    Nichols, J.D.2    Hines, J.E.3    Sauer, J.R.4    Jara, A.5    Flather, C.H.6
  • 74
    • 0035846111 scopus 로고    scopus 로고
    • Acclimatization of soil respiration to warming in a tall grass prairie
    • Luo Y, Wan S, Hui D, Wallace LL. 2001. Acclimatization of soil respiration to warming in a tall grass prairie. Nature 413:622-625.
    • (2001) Nature , vol.413 , pp. 622-625
    • Luo, Y.1    Wan, S.2    Hui, D.3    Wallace, L.L.4


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