메뉴 건너뛰기




Volumn 2013, Issue 1, 2013, Pages

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

Author keywords

Alpha diversity; Diversity indices; Human microbiome; Microbial ecology; Phylogenetic diversity

Indexed keywords

RNA 16S;

EID: 84885148679     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.157     Document Type: Article
Times cited : (55)

References (44)
  • 2
    • 70149113478 scopus 로고    scopus 로고
    • A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats
    • DOI 10.1086/600101.
    • Allen B, Kon M, Bar-Yam Y. 2009. A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. The American Naturalist 174(2):236-243 DOI 10.1086/600101.
    • (2009) The American Naturalist , vol.174 , Issue.2 , pp. 236-243
    • Allen, B.1    Kon, M.2    Bar-Yam, Y.3
  • 3
    • 0020665888 scopus 로고
    • Nonspecific vaginitis: diagnostic criteria and microbial and epidemiologic associations
    • DOI 10.1016/0002-9343(83)91112-9.
    • Amsel R, Totten PA, Spiegel CA, Chen K, Eschenbach D, Holmes KK. 1983. Nonspecific vaginitis: diagnostic criteria and microbial and epidemiologic associations. The American Journal of Medicine 74(1):14-22 DOI 10.1016/0002-9343(83)91112-9.
    • (1983) The American Journal of Medicine , vol.74 , Issue.1 , pp. 14-22
    • Amsel, R.1    Totten, P.A.2    Spiegel, C.A.3    Chen, K.4    Eschenbach, D.5    Holmes, K.K.6
  • 4
    • 0036619726 scopus 로고    scopus 로고
    • Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation
    • DOI 10.1111/j.1095-8312.2002.tb02081.x.
    • Barker GM. 2002. Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biological Journal of the Linnean Society 76(2):165-194 DOI 10.1111/j.1095-8312.2002.tb02081.x.
    • (2002) Biological Journal of the Linnean Society , vol.76 , Issue.2 , pp. 165-194
    • Barker, G.M.1
  • 7
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao A. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11(4):265-270.
    • (1984) Scandinavian Journal of Statistics , vol.11 , Issue.4 , pp. 265-270
    • Chao, A.1
  • 10
    • 84865082160 scopus 로고    scopus 로고
    • Associating microbiome composition with environmental covariates using generalized UniFrac distances
    • DOI 10.1093/bioinformatics/bts342.
    • Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J,Wu GD, Collman RG, Bushman FD, Li H. 2012. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28(16):2106-2113 DOI 10.1093/bioinformatics/bts342.
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2106-2113
    • Chen, J.1    Bittinger, K.2    Charlson, E.S.3    Hoffmann, C.4    Lewis, J.5    Wu, G.D.6    Collman, R.G.7    Bushman, F.D.8    Li, H.9
  • 12
    • 79952756960 scopus 로고    scopus 로고
    • Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
    • DOI 10.1073/pnas.1000087107.
    • Dethlefsen L, Relman DA. 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences of the United States of America 108(Supplement 1):4554 DOI 10.1073/pnas.1000087107.
    • (2011) Proceedings of the National Academy of Sciences of the United States of America , vol.108 , Issue.SUPPL. 1 , pp. 4554
    • Dethlefsen, L.1    Relman, D.A.2
  • 14
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • DOI 10.1093/bioinformatics/btq461.
    • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460-2461 DOI 10.1093/bioinformatics/btq461.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 15
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • DOI 10.1016/0006-3207(92)91201-3.
    • Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61(1):1-10 DOI 10.1016/0006-3207(92)91201-3.
    • (1992) Biological Conservation , vol.61 , Issue.1 , pp. 1-10
    • Faith, D.P.1
  • 17
    • 79960643348 scopus 로고    scopus 로고
    • Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities
    • DOI 10.1111/j.1600-0587.2010.06548.x.
    • Fine PVA, Kembel SW. 2011. Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography 34(4):552-565 DOI 10.1111/j.1600-0587.2010.06548.x.
    • (2011) Ecography , vol.34 , Issue.4 , pp. 552-565
    • Fine, P.V.A.1    Kembel, S.W.2
  • 18
    • 27644443333 scopus 로고    scopus 로고
    • Molecular identification of bacteria associated with bacterial vaginosis
    • DOI 10.1056/NEJMoa043802.
    • Fredricks DN, Fiedler TL,Marrazzo JM. 2005. Molecular identification of bacteria associated with bacterial vaginosis. New England Journal of Medicine 353(18):1899-1911 DOI 10.1056/NEJMoa043802.
    • (2005) New England Journal of Medicine , vol.353 , Issue.18 , pp. 1899-1911
    • Fredricks, D.N.1    Fiedler, T.L.2    Marrazzo, J.M.3
  • 19
    • 84856563821 scopus 로고    scopus 로고
    • Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
    • DOI 10.1111/j.1462-2920.2011.02550.x.
    • Gihring TM, Green SJ, Schadt CW. 2012. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environmental Microbiology 14(2):285-290 DOI 10.1111/j.1462-2920.2011.02550.x.
    • (2012) Environmental Microbiology , vol.14 , Issue.2 , pp. 285-290
    • Gihring, T.M.1    Green, S.J.2    Schadt, C.W.3
  • 21
    • 84861342868 scopus 로고    scopus 로고
    • Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing
    • DOI 10.1038/ismej.2011.191
    • Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, Podar M, Leys EJ. 2011a. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. The ISME Journal 6:1176-1185 DOI 10.1038/ismej.2011.191.
    • (2011) The ISME Journal , vol.6 , pp. 1176-1185
    • Griffen, A.L.1    Beall, C.J.2    Campbell, J.H.3    Firestone, N.D.4    Kumar, P.S.5    Yang, Z.K.6    Podar, M.7    Leys, E.J.8
  • 23
    • 84885099280 scopus 로고    scopus 로고
    • Hmisc: Harrell Miscellaneous
    • Available at (accessed 3 September 2013).
    • Harrell FE Jr. 2012. Hmisc: Harrell Miscellaneous. R package version 3.9-3. Available at http:// CRAN.R-project.org/package=Hmisc (accessed 3 September 2013).
    • (2012) R package version 3.9-3.
    • Harrell Jr., F.E.1
  • 24
    • 0037314132 scopus 로고    scopus 로고
    • Using ecological diversity measures with bacterial communities
    • DOI 10.1111/j.1574- 6941.2003.tb01040.x.
    • Hill TCJ,Walsh KA, Harris JA,Moffett BF. 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiology Ecology 43(1):1-11 DOI 10.1111/j.1574- 6941.2003.tb01040.x.
    • (2003) FEMS Microbiology Ecology , vol.43 , Issue.1 , pp. 1-11
    • Hill, T.C.J.1    Walsh, K.A.2    Harris, J.A.3    Moffett, B.F.4
  • 26
    • 84860253102 scopus 로고    scopus 로고
    • Measuring diversity: the importance of species similarity
    • DOI 10.1890/10-2402.1.
    • Leinster T, Cobbold CA. 2012. Measuring diversity: the importance of species similarity. Ecology 93(3):477-489 DOI 10.1890/10-2402.1.
    • (2012) Ecology , vol.93 , Issue.3 , pp. 477-489
    • Leinster, T.1    Cobbold, C.A.2
  • 27
    • 84860334363 scopus 로고    scopus 로고
    • Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
    • DOI:10.1186/1748-7188-7-8.
    • Matsen FA, Gallagher A. 2012. Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Algorithms for Molecular Biology 7(1):8 DOI 10.1186/1748-7188-7-8.
    • (2012) Algorithms for Molecular Biology , vol.7 , Issue.1 , pp. 8
    • Matsen, F.A.1    Gallagher, A.2
  • 28
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • DOI:10.1186/1471-2105-11-538.
    • Matsen FA, Kodner RB, Armbrust E. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11(1):538 DOI 10.1186/1471-2105-11-538.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.3
  • 30
    • 0026088584 scopus 로고
    • Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation
    • Nugent RP, Krohn MA, Hillier SL. 1991. Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. Journal of Clinical Microbiology 29(2):297-301.
    • (1991) Journal of Clinical Microbiology , vol.29 , Issue.2 , pp. 297-301
    • Nugent, R.P.1    Krohn, M.A.2    Hillier, S.L.3
  • 31
    • 84867220740 scopus 로고    scopus 로고
    • Shifts in human skin and nares microbiota of healthy children and adults
    • DOI 10.1186/gm378.
    • Oh J, Conlan S, Polley E, Segre JA, Kong HH. 2012. Shifts in human skin and nares microbiota of healthy children and adults. Genome Medicine 4(10):1-11 DOI 10.1186/gm378.
    • (2012) Genome Medicine , vol.4 , Issue.10 , pp. 1-11
    • Oh, J.1    Conlan, S.2    Polley, E.3    Segre, J.A.4    Kong, H.H.5
  • 33
    • 34548546830 scopus 로고    scopus 로고
    • Resource-aware taxon selection for maximizing phylogenetic diversity
    • DOI 10.1080/10635150701411279.
    • Pardi F, Goldman N. 2007. Resource-aware taxon selection for maximizing phylogenetic diversity. Systematic Biology 56(3):431-444 DOI 10.1080/10635150701411279.
    • (2007) Systematic Biology , vol.56 , Issue.3 , pp. 431-444
    • Pardi, F.1    Goldman, N.2
  • 34
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • DOI 10.1371/journal.pone.0009490.
    • Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490 DOI 10.1371/journal.pone.0009490.
    • (2010) PLoS ONE , vol.5 , Issue.3
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 35
    • 84888782821 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team. Available at
    • R Development Core Team. 2013. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Version 3.0.1. Available at http://www. R-project.org/.
    • (2013) R Foundation for Statistical Computing, Vienna, Austria. Version 3.0.1.
  • 36
    • 0003143622 scopus 로고
    • Diversity and dissimilarity coefficients: a unified approach
    • DOI 10.1016/0040-5809(82)90004-1.
    • Rao CR. 1982. Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology 21(1):24-43 DOI 10.1016/0040-5809(82)90004-1.
    • (1982) Theoretical Population Biology , vol.21 , Issue.1 , pp. 24-43
    • Rao, C.R.1
  • 38
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • DOI 10.1002/j.1538-7305.1948.tb01338.x.
    • Shannon CE. 1948. A mathematical theory of communication. Bell System Technical Journal 27(1):379-423 DOI 10.1002/j.1538-7305.1948.tb01338.x.
    • (1948) Bell System Technical Journal , vol.27 , Issue.1 , pp. 379-423
    • Shannon, C.E.1
  • 39
    • 33344464667 scopus 로고
    • Measurement of diversity
    • DOI:10.1038/163688a0.
    • Simpson EH. 1949. Measurement of diversity. Nature 163(4148):688 DOI 10.1038/163688a0.
    • (1949) Nature , vol.163 , Issue.4148 , pp. 688
    • Simpson, E.H.1
  • 41
    • 0017261757 scopus 로고
    • Clinical longitudinal standards for height, weight, height velocity, weight velocity, and stages of puberty
    • DOI 10.1136/adc.51.3.170.
    • Tanner JM,Whitehouse RH. 1976. Clinical longitudinal standards for height, weight, height velocity, weight velocity, and stages of puberty. Archives of Disease in Childhood 51(3):170-179 DOI 10.1136/adc.51.3.170.
    • (1976) Archives of Disease in Childhood , vol.51 , Issue.3 , pp. 170-179
    • Tanner, J.M.1    Whitehouse, R.H.2
  • 43
    • 34548293679 scopus 로고    scopus 로고
    • Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • DOI 10.1128/AEM.00062-07.
    • Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73(16):5261-5267 DOI 10.1128/AEM.00062-07.
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 44
    • 0029477712 scopus 로고
    • New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress
    • DOI 10.3354/meps129301.
    • Warwick RM, Clarke KR. 1995. New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Marine Ecology Progress Series 129(1):301-305 DOI 10.3354/meps129301.
    • (1995) Marine Ecology Progress Series , vol.129 , Issue.1 , pp. 301-305
    • Warwick, R.M.1    Clarke, K.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.