메뉴 건너뛰기




Volumn 2, Issue 7, 2008, Pages 689-695

The tragedy of the uncommon: Understanding limitations in the analysis of microbial diversity

Author keywords

Communities; Diversity; Diversity indices

Indexed keywords

BACTERIUM; BACTERIUM IDENTIFICATION; BIODIVERSITY; CLASSIFICATION; COMPARATIVE STUDY; DNA FINGERPRINTING; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PHYLOGENY; SHORT SURVEY;

EID: 46749150088     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2008.44     Document Type: Short Survey
Times cited : (232)

References (56)
  • 1
    • 33645450631 scopus 로고    scopus 로고
    • Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes
    • Abdo Z, Schütte UME, Bent SJ, Williams CJ, Forney LJ, Joyce P. (2006). Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8: 929-938.
    • (2006) Environ Microbiol , vol.8 , pp. 929-938
    • Abdo, Z.1    Schütte, U.M.E.2    Bent, S.J.3    Williams, C.J.4    Forney, L.J.5    Joyce, P.6
  • 2
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain-specific 16S primers
    • Baker GC, Smith JJ, Cowan DA. (2003). Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
    • (2003) J Microbiol Methods , vol.55 , pp. 541-555
    • Baker, G.C.1    Smith, J.J.2    Cowan, D.A.3
  • 3
    • 0005687347 scopus 로고
    • Diversity of planktonic Foraminifera in deep sea sediments
    • Berger W, Parker FL. (1970). Diversity of planktonic Foraminifera in deep sea sediments. Science 168: 1345-1347.
    • (1970) Science , vol.168 , pp. 1345-1347
    • Berger, W.1    Parker, F.L.2
  • 4
    • 0037388225 scopus 로고    scopus 로고
    • Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity
    • passim
    • Crosby LD, Criddle CS. (2003). Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-794, 796, 798 passim.
    • (2003) Biotechniques , vol.34
    • Crosby, L.D.1    Criddle, C.S.2
  • 7
    • 2942566096 scopus 로고    scopus 로고
    • Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology
    • Curtis TP, Sloan WT. (2004). Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7: 221-226.
    • (2004) Curr Opin Microbiol , vol.7 , pp. 221-226
    • Curtis, T.P.1    Sloan, W.T.2
  • 8
    • 0036624813 scopus 로고    scopus 로고
    • Molecular community analysis of microbial diversity
    • Dahllof I. (2002). Molecular community analysis of microbial diversity. Curr Opin Biotechnol 13: 213-217.
    • (2002) Curr Opin Biotechnol , vol.13 , pp. 213-217
    • Dahllof, I.1
  • 9
    • 0035527414 scopus 로고    scopus 로고
    • Environmental diversity of bacteria and archaea
    • DeLong EF, Pace NR. (2001). Environmental diversity of bacteria and archaea. Syst Biol 50: 470-478.
    • (2001) Syst Biol , vol.50 , pp. 470-478
    • DeLong, E.F.1    Pace, N.R.2
  • 10
    • 0036269049 scopus 로고    scopus 로고
    • Empirical and theoretical bacterial diversity in four Arizona soils
    • Dunbar J, Barns SM, Ticknor LO, Kuske CR. (2002). Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68: 3035-3045.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 3035-3045
    • Dunbar, J.1    Barns, S.M.2    Ticknor, L.O.3    Kuske, C.R.4
  • 11
    • 0032914126 scopus 로고    scopus 로고
    • Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning
    • Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR. (1999). Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65: 1662-1669.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1662-1669
    • Dunbar, J.1    Takala, S.2    Barns, S.M.3    Davis, J.A.4    Kuske, C.R.5
  • 12
    • 0031981808 scopus 로고    scopus 로고
    • Santa Rosalia revisited: Why are there so many species of bacteria?
    • Dykhuizen DE. (1998). Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73: 25-33.
    • (1998) Antonie Van Leeuwenhoek , vol.73 , pp. 25-33
    • Dykhuizen, D.E.1
  • 13
    • 0029032318 scopus 로고
    • Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
    • Farrelly V, Rainey FA, Stackebrandt E. (1995). Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61: 2798-2801.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 2798-2801
    • Farrelly, V.1    Rainey, F.A.2    Stackebrandt, E.3
  • 15
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans J, Wolinsky M, Dunbar J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
    • (2005) Science , vol.309 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 16
    • 0031842162 scopus 로고    scopus 로고
    • Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region
    • Hansen MC, Tolker-Nielsen T, Givskov M, Molin S. (1998). Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol Ecol 26: 141-149.
    • (1998) FEMS Microbiol Ecol , vol.26 , pp. 141-149
    • Hansen, M.C.1    Tolker-Nielsen, T.2    Givskov, M.3    Molin, S.4
  • 17
    • 33845521652 scopus 로고    scopus 로고
    • Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices
    • Hartmann M, Widmer F. (2006). Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72: 7804-7812.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 7804-7812
    • Hartmann, M.1    Widmer, F.2
  • 18
    • 2942556578 scopus 로고    scopus 로고
    • Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia
    • Hewson I, Fuhrman J. (2004). Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70: 3425-3433.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 3425-3433
    • Hewson, I.1    Fuhrman, J.2
  • 19
    • 0000006498 scopus 로고
    • Diversity and evenness: A unifying notation and its consequences
    • Hill MO. (1973). Diversity and evenness: a unifying notation and its consequences. Ecology 54: 427-432.
    • (1973) Ecology , vol.54 , pp. 427-432
    • Hill, M.O.1
  • 21
    • 0035487318 scopus 로고    scopus 로고
    • Counting the uncountable: Statistical approaches to estimating microbial diversity
    • Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ. (2001). Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 4399-4406
    • Hughes, J.B.1    Hellmann, J.J.2    Ricketts, T.H.3    Bohannan, B.J.4
  • 22
    • 0022849288 scopus 로고
    • Theories and models of species abundance
    • Hughes RG. (1986). Theories and models of species abundance. Am Nat 128: 897-899.
    • (1986) Am Nat , vol.128 , pp. 897-899
    • Hughes, R.G.1
  • 23
    • 33646876613 scopus 로고    scopus 로고
    • Entropy and diversity
    • Jost L. (2006). Entropy and diversity. Oikos 113: 363-375.
    • (2006) Oikos , vol.113 , pp. 363-375
    • Jost, L.1
  • 24
    • 0343618412 scopus 로고    scopus 로고
    • When species accumulation curves intersect: Implications for ranking diversity using small samples
    • Lande R, DeVries PJ, Walla TR. (2000). When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos 89: 601-605.
    • (2000) Oikos , vol.89 , pp. 601-605
    • Lande, R.1    DeVries, P.J.2    Walla, T.R.3
  • 25
    • 0030661563 scopus 로고    scopus 로고
    • Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
    • Liu WT, Marsh TL, Cheng H, Forney LJ. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 4516-4522
    • Liu, W.T.1    Marsh, T.L.2    Cheng, H.3    Forney, L.J.4
  • 26
    • 33644838781 scopus 로고    scopus 로고
    • Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
    • Loisel P, Harmand J, Zemb O, Latrille E, Lobry C, Delgenes J-P et al. (2006). Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8: 720-731.
    • (2006) Environ Microbiol , vol.8 , pp. 720-731
    • Loisel, P.1    Harmand, J.2    Zemb, O.3    Latrille, E.4    Lobry, C.5    Delgenes, J.-P.6
  • 27
    • 18844436544 scopus 로고    scopus 로고
    • Native Thistles: Expendable or integral to ecosystem resistance to invasion?
    • Kareiva P and Levin SA eds, Princeton University Press: Princeton NJ. pp
    • Louda SM, Rand TA. (2002). Native Thistles: expendable or integral to ecosystem resistance to invasion?. In: Kareiva P and Levin SA (eds). The Importance of Species: Perspectives on Expendability and Triage. Princeton University Press: Princeton NJ. pp 5-15.
    • (2002) The Importance of Species: Perspectives on Expendability and Triage , pp. 5-15
    • Louda, S.M.1    Rand, T.A.2
  • 28
    • 0035018373 scopus 로고    scopus 로고
    • Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia
    • Maarit Niemi R, Heiskanen I, Wallenius K, Lindstrom K. (2001). Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45: 155-165.
    • (2001) J Microbiol Methods , vol.45 , pp. 155-165
    • Maarit Niemi, R.1    Heiskanen, I.2    Wallenius, K.3    Lindstrom, K.4
  • 29
    • 0003071920 scopus 로고
    • On the relative abundance of species
    • MacArthur RH. (1960). On the relative abundance of species. Am Nat 94: 25-36.
    • (1960) Am Nat , vol.94 , pp. 25-36
    • MacArthur, R.H.1
  • 30
    • 0002970941 scopus 로고
    • Patterns of species abundance and diversity
    • Diamond JM, Cody ML eds, Belknap Press: Cambridge, MA. pp
    • May RM. (1975). Patterns of species abundance and diversity. In: Diamond JM, Cody ML (eds). Ecology and Evolution of Communities. Belknap Press: Cambridge, MA. pp 81-120.
    • (1975) Ecology and Evolution of Communities , pp. 81-120
    • May, R.M.1
  • 31
    • 2342449125 scopus 로고    scopus 로고
    • Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter
    • Nandi S, Maurer JJ, Hofacre C, Summers AO. (2004). Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. Proc Natl Acad Sci USA 101: 7118-7122.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7118-7122
    • Nandi, S.1    Maurer, J.J.2    Hofacre, C.3    Summers, A.O.4
  • 32
    • 3042723492 scopus 로고    scopus 로고
    • Modeling bacterial species abundance from small community surveys
    • Narang R, Dunbar J. (2004). Modeling bacterial species abundance from small community surveys. Microb Ecol 47: 396-406.
    • (2004) Microb Ecol , vol.47 , pp. 396-406
    • Narang, R.1    Dunbar, J.2
  • 33
    • 21344431639 scopus 로고    scopus 로고
    • Whither or wither geomicrobiology in the era of 'community metagenomics'
    • Oremland RS, Capone DG, Stolz JF, Fuhrman J. (2005). Whither or wither geomicrobiology in the era of 'community metagenomics'. Nat Rev Microbiol 3: 572-578.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 572-578
    • Oremland, R.S.1    Capone, D.G.2    Stolz, J.F.3    Fuhrman, J.4
  • 34
    • 33144466522 scopus 로고    scopus 로고
    • New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities
    • Osborne CA, Rees GN, Bernstein Y, Janssen PH. (2006). New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72: 1270-1278.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1270-1278
    • Osborne, C.A.1    Rees, G.N.2    Bernstein, Y.3    Janssen, P.H.4
  • 35
    • 0346816538 scopus 로고    scopus 로고
    • Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP)
    • Ovreas L, Daae FL, Torsvik V, Rodriguez-Valera F. (2003). Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 46: 291-301.
    • (2003) Microb Ecol , vol.46 , pp. 291-301
    • Ovreas, L.1    Daae, F.L.2    Torsvik, V.3    Rodriguez-Valera, F.4
  • 37
    • 0001572401 scopus 로고
    • The commonness, and rarity, of species
    • Preston FW. (1948). The commonness, and rarity, of species. Ecology 29: 254-283.
    • (1948) Ecology , vol.29 , pp. 254-283
    • Preston, F.W.1
  • 38
    • 0035145056 scopus 로고    scopus 로고
    • Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning
    • Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM et al. (2001). Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67: 880-887.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 880-887
    • Qiu, X.1    Wu, L.2    Huang, H.3    McDonel, P.E.4    Palumbo, A.V.5    Tiedje, J.M.6
  • 41
    • 33344464667 scopus 로고
    • Measurement of diversity
    • Simpson EH. (1949). Measurement of diversity. Nature 163: 688.
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.H.1
  • 42
    • 0027842316 scopus 로고
    • The use of species accumulation functions for the prediction of species richness
    • Soberon J, Llorente J. (1993). The use of species accumulation functions for the prediction of species richness. Conserv Biol 7: 480-488.
    • (1993) Conserv Biol , vol.7 , pp. 480-488
    • Soberon, J.1    Llorente, J.2
  • 44
    • 33751258603 scopus 로고    scopus 로고
    • The bacterial species dilemma and the genomic-phylogenetic species concept
    • Staley JT. (2006). The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361: 1899-1909.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , pp. 1899-1909
    • Staley, J.T.1
  • 45
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki MT, Giovannoni SJ. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 47
    • 77956844644 scopus 로고
    • Species abundance patterns and community structure
    • Begon M, Fitter AH eds, Academic Press: London, UK. pp
    • Tokeshi M. (1993). Species abundance patterns and community structure. In: Begon M, Fitter AH (eds). Advances in Ecological Research. Academic Press: London, UK. pp 112-186.
    • (1993) Advances in Ecological Research , pp. 112-186
    • Tokeshi, M.1
  • 48
    • 0032219204 scopus 로고    scopus 로고
    • Novel techniques for analysing microbial diversity in natural and perturbed environments
    • Torsvik V, Daae FL, Sandaa RA, Ovreas L. (1998). Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64: 53-62.
    • (1998) J Biotechnol , vol.64 , pp. 53-62
    • Torsvik, V.1    Daae, F.L.2    Sandaa, R.A.3    Ovreas, L.4
  • 49
    • 0036679334 scopus 로고    scopus 로고
    • How many species of prokaryotes are there?
    • Ward BB. (2002). How many species of prokaryotes are there? Proc Natl Acad Sci USA 99: 10234-10236.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10234-10236
    • Ward, B.B.1
  • 50
    • 0038265142 scopus 로고    scopus 로고
    • Resolving functional diversity in relation to microbial community structure in soil: Exploiting genomics and stable isotope probing
    • Wellington EM, Berry A, Krsek M. (2003). Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6: 295-301.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 295-301
    • Wellington, E.M.1    Berry, A.2    Krsek, M.3
  • 52
    • 84986765232 scopus 로고
    • Methods for fitting dominance/diversity curves
    • Wilson JB. (1991). Methods for fitting dominance/diversity curves. J Veg Sci 2: 35-46.
    • (1991) J Veg Sci , vol.2 , pp. 35-46
    • Wilson, J.B.1
  • 53
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese CR. (1987). Bacterial evolution. Microbiol Rev 51: 221-271.
    • (1987) Microbiol Rev , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 54
    • 0033574013 scopus 로고    scopus 로고
    • Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis
    • Yachi S, Loreau M. (1999). Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci USA 96: 1463-1468.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 1463-1468
    • Yachi, S.1    Loreau, M.2
  • 55
    • 0037772204 scopus 로고    scopus 로고
    • Microarrays for bacterial detection and microbial community analysis
    • Zhou J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 288-294
    • Zhou, J.1
  • 56
    • 34249945020 scopus 로고    scopus 로고
    • Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women
    • Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P et al. (2007). Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J 1: 121-133.
    • (2007) ISME J , vol.1 , pp. 121-133
    • Zhou, X.1    Brown, C.J.2    Abdo, Z.3    Davis, C.C.4    Hansmann, M.A.5    Joyce, P.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.