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Volumn 5, Issue MAY, 2014, Pages

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Author keywords

16S rRNA sequencing surveys; Correlation analysis; Habitat filtering; Keystone species; Lotka Volterra models; Microbial competition; Microbial cooperation; Network analysis

Indexed keywords

ARTICLE; CO OCCURRENCE NETWORK; GENETIC HETEROGENEITY; KEYSTONE SPECIES; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; NONBIOLOGICAL MODEL; ORGANISMAL INTERACTION; SAMPLING; SENSITIVITY AND SPECIFICITY; SIMULATION;

EID: 84905030166     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00219     Document Type: Article
Times cited : (1181)

References (65)
  • 1
    • 1942443733 scopus 로고    scopus 로고
    • Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
    • doi: 10.1128/JB.186.9.2629-2635.2004
    • Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V., and Polz, M. F. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186, 2629-2635. doi: 10.1128/JB.186.9.2629-2635.2004
    • (2004) J. Bacteriol , vol.186 , pp. 2629-2635
    • Acinas, S.G.1    Marcelino, L.A.2    Klepac-Ceraj, V.3    Polz, M.F.4
  • 2
    • 84873517188 scopus 로고    scopus 로고
    • A concise guide to compositional data analysis
    • in 2nd Compositional Data Analysis Workshop (Girona)
    • Aitchison, J. (2003). "A concise guide to compositional data analysis," in 2nd Compositional Data Analysis Workshop (Girona).
    • (2003)
    • Aitchison, J.1
  • 3
    • 0037447834 scopus 로고    scopus 로고
    • Microbial communities in acid mine drainage
    • doi: 10.1016/S0168-6496(03)00028-X
    • Baker, B. J., and Banfield, J. F. (2003). Microbial communities in acid mine drainage. FEMS Microbiol. Rev. 44, 139-152. doi: 10.1016/S0168-6496(03)00028-X
    • (2003) FEMS Microbiol. Rev. , vol.44 , pp. 139-152
    • Baker, B.J.1    Banfield, J.F.2
  • 4
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • doi: 10.1126/science.286.5439.509
    • Barabasi, A., and Albert, R. (1999). Emergence of scaling in random networks. Science 286, 509-512. doi: 10.1126/science.286.5439.509
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.1    Albert, R.2
  • 5
    • 84855949949 scopus 로고    scopus 로고
    • Using network analysis to explore co-occurrence patterns in soil microbial communities
    • doi: 10.1038/ismej.2011.119
    • Barberán, A., Bates, S. T., Casamayor, E. O., and Fierer, N. (2012). Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6, 343-351. doi: 10.1038/ismej.2011.119
    • (2012) ISME J , vol.6 , pp. 343-351
    • Barberán, A.1    Bates, S.T.2    Casamayor, E.O.3    Fierer, N.4
  • 6
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • doi: 10.2307/2346101
    • Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. [Ser. B]. 57, 289-300. doi: 10.2307/2346101
    • (1995) J. R. Stat. Soc. [Ser. B]. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 46749150088 scopus 로고    scopus 로고
    • The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity
    • doi: 10.1038/ismej.2008.44
    • Bent, S. J., and Forney, L. J. (2008). The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J. 2, 689-695. doi: 10.1038/ismej.2008.44
    • (2008) ISME J , vol.2 , pp. 689-695
    • Bent, S.J.1    Forney, L.J.2
  • 8
    • 83155178360 scopus 로고    scopus 로고
    • Barcoded primers used in multiplex amplicon pyrosequencing bias amplification
    • doi: 10.1128/AEM.05220-11
    • Berry, D., Ben Mahfoudh, K., Wagner, M., and Loy, A. (2011). Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 77, 7846-7849. doi: 10.1128/AEM.05220-11
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 7846-7849
    • Berry, D.1    Ben Mahfoudh, K.2    Wagner, M.3    Loy, A.4
  • 9
    • 84875246466 scopus 로고    scopus 로고
    • Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing
    • doi: 10.1073/pnas.1219247110
    • Berry, D., Stecher, B., Schintlmeister, A., Reichert, J., Brugiroux, S., Wild, B., et al. (2013). Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing. Proc. Natl. Acad. Sci. U.S.A. 110, 4720-4725. doi: 10.1073/pnas.1219247110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 4720-4725
    • Berry, D.1    Stecher, B.2    Schintlmeister, A.3    Reichert, J.4    Brugiroux, S.5    Wild, B.6
  • 10
    • 67651245379 scopus 로고    scopus 로고
    • Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei
    • doi: 10.1128/AEM.00447-09
    • Bowers, R. M., Lauber, C. L., Wiedinmyer, C., Hamady, M., Hallar, A. G., Fall, R., et al. (2009). Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei. Appl. Environ. Microbiol. 75, 5121-5130. doi: 10.1128/AEM.00447-09
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 5121-5130
    • Bowers, R.M.1    Lauber, C.L.2    Wiedinmyer, C.3    Hamady, M.4    Hallar, A.G.5    Fall, R.6
  • 11
    • 0038482137 scopus 로고    scopus 로고
    • Diversity and dynamics of microbial communities in engineered environments and their implications for process stability
    • doi: 10.1016/S0958-1669(03)00065-X
    • Briones, A., and Raskin, L. (2003). Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr. Opin. Biotechnol. 14, 270-276. doi: 10.1016/S0958-1669(03)00065-X
    • (2003) Curr. Opin. Biotechnol. , vol.14 , pp. 270-276
    • Briones, A.1    Raskin, L.2
  • 12
    • 79952005915 scopus 로고    scopus 로고
    • Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    • doi: 10.1073/pnas.1000080107
    • Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., et al. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl. 1), 4516-4522. doi: 10.1073/pnas.1000080107
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , Issue.SUPPL. 1 , pp. 4516-4522
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Lozupone, C.A.5    Turnbaugh, P.J.6
  • 14
    • 0031149569 scopus 로고    scopus 로고
    • Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries
    • doi: 10.1046/j.1365-294X.1997.00205.x
    • Chandler, D. P., Fredrickson, J. K., and Brockman, F. J. (1997). Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6, 475-482. doi: 10.1046/j.1365-294X.1997.00205.x
    • (1997) Mol. Ecol. , vol.6 , pp. 475-482
    • Chandler, D.P.1    Fredrickson, J.K.2    Brockman, F.J.3
  • 16
    • 84905042117 scopus 로고    scopus 로고
    • The Igraph Software Package for Complex Network Research. Available online at
    • Csardi, G., and Nepusz, T. (2006). The Igraph Software Package for Complex Network Research. Available online at: http://www.necsi.edu/events/iccs6/papers/c1602a3c126ba822d0bc4293371c.pdf
    • (2006)
    • Csardi, G.1    Nepusz, T.2
  • 17
    • 2942566096 scopus 로고    scopus 로고
    • Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology
    • doi: 10.1016/j.mib.2004.04.010
    • Curtis, T. P., and Sloan, W. T. (2004). Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr. Opin. Microbiol. 7, 221-226. doi: 10.1016/j.mib.2004.04.010
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 221-226
    • Curtis, T.P.1    Sloan, W.T.2
  • 18
    • 84855951093 scopus 로고    scopus 로고
    • Coherent dynamics and association networks among lake bacterioplankton taxa
    • doi: 10.1038/ismej.2011.113
    • Eiler, A., Heinrich, F., and Bertilsson, S. (2012). Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J. 6, 330-342. doi: 10.1038/ismej.2011.113
    • (2012) ISME J , vol.6 , pp. 330-342
    • Eiler, A.1    Heinrich, F.2    Bertilsson, S.3
  • 20
    • 79959855078 scopus 로고    scopus 로고
    • Predicting a human gut microbiota's response to diet in gnotobiotic mice
    • doi: 10.1126/science.1206025
    • Faith, J. J., McNulty, N. P., Rey, F. E., and Gordon, J. I. (2011). Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333, 101-104. doi: 10.1126/science.1206025
    • (2011) Science , vol.333 , pp. 101-104
    • Faith, J.J.1    McNulty, N.P.2    Rey, F.E.3    Gordon, J.I.4
  • 21
    • 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, F. A., and 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
  • 22
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: from networks to models
    • doi: 10.1038/nrmicro2832
    • Faust, K., and Raes, J. (2012). Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538-550. doi: 10.1038/nrmicro2832
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 23
    • 79952751932 scopus 로고    scopus 로고
    • The generation and maintenance of diversity in microbial communities
    • doi: 10.3732/ajb.1000498
    • Fierer, N., and Lennon, J. T. (2011). The generation and maintenance of diversity in microbial communities. Am. J. Bot. 98, 439-448. doi: 10.3732/ajb.1000498
    • (2011) Am. J. Bot. , vol.98 , pp. 439-448
    • Fierer, N.1    Lennon, J.T.2
  • 24
    • 84867405105 scopus 로고    scopus 로고
    • Competition, not cooperation, dominates interactions among culturable microbial species
    • doi: 10.1016/j.cub.2012.08.005
    • Foster, K. R., and Bell, T. (2012). Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845-1850. doi: 10.1016/j.cub.2012.08.005
    • (2012) Curr. Biol. , vol.22 , pp. 1845-1850
    • Foster, K.R.1    Bell, T.2
  • 25
    • 84455174807 scopus 로고    scopus 로고
    • Competitive and cooperative metabolic interactions in bacterial communities
    • doi: 10.1038/ncomms1597
    • Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., et al. (2011). Competitive and cooperative metabolic interactions in bacterial communities. Nat. Commun. 2, 589. doi: 10.1038/ncomms1597
    • (2011) Nat. Commun. , vol.2 , pp. 589
    • Freilich, S.1    Zarecki, R.2    Eilam, O.3    Segal, E.S.4    Henry, C.S.5    Kupiec, M.6
  • 26
    • 84865733148 scopus 로고    scopus 로고
    • Inferring correlation networks from genomic survey data
    • doi: 10.1371/journal.pcbi.1002687
    • Friedman, J., and Alm, E. J. (2012). Inferring correlation networks from genomic survey data. PLoS Comp. Biol. 8:e1002687. doi: 10.1371/journal.pcbi.1002687
    • (2012) PLoS Comp. Biol. , vol.8
    • Friedman, J.1    Alm, E.J.2
  • 27
    • 0000052408 scopus 로고    scopus 로고
    • Species co-occurrence: a meta-analysis of J. M. Diamond's assembly rules model
    • doi:10.1890/0012-9658(2002)083[2091:SCOAMA]2.0.CO;
    • Gotelli, N. J., and McCabe, D. J. (2002). Species co-occurrence: a meta-analysis of J. M. Diamond's assembly rules model. Ecology 83, 2091. doi: 10.1890/0012-9658(2002)083[2091:SCOAMA]2.0.CO;2
    • (2002) Ecology 83, 2091 , pp. 2
    • Gotelli, N.J.1    McCabe, D.J.2
  • 28
    • 73949111750 scopus 로고    scopus 로고
    • Bacterial competition: surviving and thriving in the microbial jungle
    • doi: 10.1038/nrmicro2259
    • Hibbing, M. E., Fuqua, C., Parsek, M. R., and Peterson, S. B. (2010). Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15-25. doi: 10.1038/nrmicro2259
    • (2010) Nat. Rev. Microbiol. , vol.8 , pp. 15-25
    • Hibbing, M.E.1    Fuqua, C.2    Parsek, M.R.3    Peterson, S.B.4
  • 29
    • 35148888609 scopus 로고    scopus 로고
    • Microbial population structures in the deep marine biosphere
    • doi: 10.1126/science.1146689
    • Huber, J. A., Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., et al. (2007). Microbial population structures in the deep marine biosphere. Science 318, 97-100. doi: 10.1126/science.1146689
    • (2007) Science , vol.318 , pp. 97-100
    • Huber, J.A.1    Mark Welch, D.B.2    Morrison, H.G.3    Huse, S.M.4    Neal, P.R.5    Butterfield, D.A.6
  • 30
    • 41349116090 scopus 로고    scopus 로고
    • Highly clustered scale-free networks
    • doi: 10.1103/PhysRevE.65.036123
    • Klemm, K., and Eguíluz, V. M. (2002). Highly clustered scale-free networks. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 65:036123. doi: 10.1103/PhysRevE.65.036123
    • (2002) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. , vol.65 , pp. 036123
    • Klemm, K.1    Eguíluz, V.M.2
  • 31
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • doi: 10.1093/nar/gks808
    • Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1. doi: 10.1093/nar/gks808
    • (2013) Nucleic Acids Res , vol.41
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6
  • 32
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • doi: 10.1371/journal.pcbi.1001002
    • Klitgord, N., and Segrè, D. (2010). Environments that induce synthetic microbial ecosystems. PLoS Comput. Biol. 6:e1001002. doi: 10.1371/journal.pcbi.1001002
    • (2010) PLoS Comput. Biol. , vol.6
    • Klitgord, N.1    Segrè, D.2
  • 33
    • 79251567361 scopus 로고    scopus 로고
    • Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
    • doi: 10.1186/1752-0509-5-21
    • Krumsiek, J., Suhre, K., Illig, T., Adamski, J., and Theis, F. J. (2011). Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst. Biol. 5:21. doi: 10.1186/1752-0509-5-21
    • (2011) BMC Syst. Biol. , vol.5 , pp. 21
    • Krumsiek, J.1    Suhre, K.2    Illig, T.3    Adamski, J.4    Theis, F.J.5
  • 34
    • 84865501143 scopus 로고    scopus 로고
    • Low sequencing efforts bias analyses of shared taxa in microbial communities
    • doi: 10.1007/s12223-012-0155-0
    • Lemos, L. N., Fulthorpe, R. R., and Roesch, L. F. W. (2012). Low sequencing efforts bias analyses of shared taxa in microbial communities. Folia Microbiol. 57, 409-413. doi: 10.1007/s12223-012-0155-0
    • (2012) Folia Microbiol , vol.57 , pp. 409-413
    • Lemos, L.N.1    Fulthorpe, R.R.2    Roesch, L.F.W.3
  • 35
    • 33947269742 scopus 로고    scopus 로고
    • Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
    • doi: 10.1128/AEM.01996-06
    • Lozupone, C. A., Hamady, M., Kelley, S. T., and Knight, R. (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576-1585. doi: 10.1128/AEM.01996-06
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 1576-1585
    • Lozupone, C.A.1    Hamady, M.2    Kelley, S.T.3    Knight, R.4
  • 36
    • 84875365733 scopus 로고    scopus 로고
    • Phylogenetic conservatism of functional traits in microorganisms
    • doi: 10.1038/ismej.2012.160
    • Martiny, A. C., Treseder, K., and Pusch, G. (2013). Phylogenetic conservatism of functional traits in microorganisms. ISME J. 7, 830-838. doi: 10.1038/ismej.2012.160
    • (2013) ISME J , vol.7 , pp. 830-838
    • Martiny, A.C.1    Treseder, K.2    Pusch, G.3
  • 37
    • 33746327503 scopus 로고    scopus 로고
    • Ecological networks and their fragility
    • doi: 10.1038/nature04927
    • Montoya, J. M., Pimm, S. L., and Solé, R. V. (2006). Ecological networks and their fragility. Nature 442, 259-264. doi: 10.1038/nature04927
    • (2006) Nature , vol.442 , pp. 259-264
    • Montoya, J.M.1    Pimm, S.L.2    Solé, R.V.3
  • 39
    • 78649448174 scopus 로고    scopus 로고
    • A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland
    • doi: 10.1038/ismej.2010.75
    • Pester, M., Bittner, N., Deevong, P., Wagner, M., and Loy, A. (2010). A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. ISME J. 4, 1591-1602. doi: 10.1038/ismej.2010.75
    • (2010) ISME J , vol.4 , pp. 1591-1602
    • Pester, M.1    Bittner, N.2    Deevong, P.3    Wagner, M.4    Loy, A.5
  • 40
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz, M. F., and Cavanaugh, C. M. (1998). Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64, 3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 41
    • 10244235264 scopus 로고    scopus 로고
    • Challenges in the quest for keystones
    • doi: 10.2307/1312990
    • Power, M., Tilman, D., Estes, J., and Menge, B. (1996). Challenges in the quest for keystones. BioScience 46, 609-620. doi: 10.2307/1312990
    • (1996) BioScience , vol.46 , pp. 609-620
    • Power, M.1    Tilman, D.2    Estes, J.3    Menge, B.4
  • 42
    • 84959529931 scopus 로고    scopus 로고
    • Methods for generating complex networks with selected structural properties for simulations: a review and tutorial for neuroscientists
    • doi: 10.3389/fncom.2011.00011
    • Prettejohn, B. J., Berryman, M. J., and McDonnell, M. D. (2011). Methods for generating complex networks with selected structural properties for simulations: a review and tutorial for neuroscientists. Front. Comput. Neurosci. 5:11. doi: 10.3389/fncom.2011.00011
    • (2011) Front. Comput. Neurosci. , vol.5
    • Prettejohn, B.J.1    Berryman, M.J.2    McDonnell, M.D.3
  • 43
    • 77952670727 scopus 로고    scopus 로고
    • doi: 10.1038/ismej.2010.1
    • Rodriguez-Brito, B., Li, L. L., Wegley, L., and Furlan, M. (2010). Viral and microbial community dynamics in four aquatic environments. ISME J. 4, 739-751. doi: 10.1038/ismej.2010.1
    • (2010) , vol.4 , pp. 739-751
    • Rodriguez-Brito, B.1    Li, L.L.2    Wegley, L.3    Furlan, M.4
  • 44
    • 33749824905 scopus 로고    scopus 로고
    • Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
    • doi: 10.1093/bioinformatics/btl417
    • Ruan, Q., Dutta, D., Schwalbach, M. S., Steele, J. A., Fuhrman, J. A., and Sun, F. (2006). Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22, 2532-2538. doi: 10.1093/bioinformatics/btl417
    • (2006) Bioinformatics , vol.22 , pp. 2532-2538
    • Ruan, Q.1    Dutta, D.2    Schwalbach, M.S.3    Steele, J.A.4    Fuhrman, J.A.5    Sun, F.6
  • 45
    • 80054036798 scopus 로고    scopus 로고
    • Strong contributors to network persistence are the most vulnerable to extinction
    • doi: 10.1038/nature10433
    • Saavedra, S., Stouffer, D. B., Uzzi, B., and Bascompte, J. (2011). Strong contributors to network persistence are the most vulnerable to extinction. Nature 478, 233-235. doi: 10.1038/nature10433
    • (2011) Nature , vol.478 , pp. 233-235
    • Saavedra, S.1    Stouffer, D.B.2    Uzzi, B.3    Bascompte, J.4
  • 46
    • 84899484295 scopus 로고    scopus 로고
    • Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery
    • doi: 10.1038/ismej.2013.223
    • Schwab, C., Berry, D., Rauch, I., Rennisch, I., Ramesmayer, J., Hainzl, E., et al. (2014). Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J. 8, 1101-1114. doi: 10.1038/ismej.2013.223
    • (2014) ISME J , vol.8 , pp. 1101-1114
    • Schwab, C.1    Berry, D.2    Rauch, I.3    Rennisch, I.4    Ramesmayer, J.5    Hainzl, E.6
  • 47
    • 84875883112 scopus 로고    scopus 로고
    • Fundamentals of microbial community resistance and resilience
    • doi: 10.3389/fmicb.2012.00417
    • Shade, A., Peter, H., Allison, S. D., Baho, D. L., Berga, M., Bürgmann, H., et al. (2012). Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3:417. doi: 10.3389/fmicb.2012.00417
    • (2012) Front. Microbiol. , vol.3 , pp. 417
    • Shade, A.1    Peter, H.2    Allison, S.D.3    Baho, D.L.4    Berga, M.5    Bürgmann, H.6
  • 48
    • 84859625932 scopus 로고    scopus 로고
    • Next-generation sequencing technologies for environmental DNA research
    • doi: 10.1111/j.1365-294X.2012.05538.x
    • Shokralla, S., Spall, J. L., Gibson, J. F., and Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Mol. Ecol. 21, 1794-1805. doi: 10.1111/j.1365-294X.2012.05538.x
    • (2012) Mol. Ecol. , vol.21 , pp. 1794-1805
    • Shokralla, S.1    Spall, J.L.2    Gibson, J.F.3    Hajibabaei, M.4
  • 49
    • 72949116371 scopus 로고    scopus 로고
    • Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome
    • doi: 10.1128/AEM.00946-09
    • Simon, C., Wiezer, A., Strittmatter, A. W., and Daniel, R. (2009). Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 75, 7519-7526. doi: 10.1128/AEM.00946-09
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 7519-7526
    • Simon, C.1    Wiezer, A.2    Strittmatter, A.W.3    Daniel, R.4
  • 50
    • 77953162975 scopus 로고    scopus 로고
    • Solving differential equations in R: Package deSolve
    • Available online at
    • Soetaert, K., Petzoldt, T., and Woodrow Setzer, R. (2010). Solving differential equations in R: Package deSolve. J. Stat. Softw. 33, 1-25. Available online at: http://www.jstatsoft.org/v33/i09/paper
    • (2010) J. Stat. Softw. , vol.33 , pp. 1-25
    • Soetaert, K.1    Petzoldt, T.2    Woodrow Setzer, R.3
  • 51
    • 84881249747 scopus 로고    scopus 로고
    • Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle
    • doi: 10.1111/1574-6976.12024
    • Stecher, B., Berry, D., and Loy, A. (2013). Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol. Rev. 37, 793-829. doi: 10.1111/1574-6976.12024
    • (2013) FEMS Microbiol. Rev. , vol.37 , pp. 793-829
    • Stecher, B.1    Berry, D.2    Loy, A.3
  • 52
    • 84892708007 scopus 로고    scopus 로고
    • Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
    • doi: 10.1371/journal.pcbi.1003388
    • Stein, R. R., Bucci, V., Toussaint, N. C., Buffie, C. G., Rätsch, G., Pamer, E. G., et al. (2013). Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9:e1003388. doi: 10.1371/journal.pcbi.1003388
    • (2013) PLoS Comput. Biol. , vol.9
    • Stein, R.R.1    Bucci, V.2    Toussaint, N.C.3    Buffie, C.G.4    Rätsch, G.5    Pamer, E.G.6
  • 53
    • 0027066409 scopus 로고
    • Competitive exclusion
    • doi: 10.1007/BF00317632
    • Stone, L., and Roberts, A. (1992). Competitive exclusion, or species aggregation? Oecologia 91, 419-424. doi: 10.1007/BF00317632
    • (1992) or species aggregation? Oecologia , vol.91 , pp. 419-424
    • Stone, L.1    Roberts, A.2
  • 54
    • 84884193898 scopus 로고    scopus 로고
    • Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity
    • doi: 10.1128/AEM.01282-13
    • Sun, D. L., Jiang, X., Wu, Q. L., and Zhou, N. Y. (2013). Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. Appl. Environ. Microbiol. 79, 5962-5969. doi: 10.1128/AEM.01282-13
    • (2013) Appl. Environ. Microbiol. , vol.79 , pp. 5962-5969
    • Sun, D.L.1    Jiang, X.2    Wu, Q.L.3    Zhou, N.Y.4
  • 55
    • 84888884475 scopus 로고    scopus 로고
    • Metagenomic species profiling using universal phylogenetic marker genes
    • doi: 10.1038/nmeth.2693
    • Sunagawa, S., Mende, D. R., and Zeller, G. (2013). Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196-1199. doi: 10.1038/nmeth.2693
    • (2013) Nat. Methods , vol.10 , pp. 1196-1199
    • Sunagawa, S.1    Mende, D.R.2    Zeller, G.3
  • 56
    • 70349233883 scopus 로고    scopus 로고
    • Towards the human intestinal microbiota phylogenetic core
    • doi: 10.1111/j.1462-2920.2009.01982.x
    • Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J.-P., et al. (2009). Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11, 2574-2584. doi: 10.1111/j.1462-2920.2009.01982.x
    • (2009) Environ. Microbiol. , vol.11 , pp. 2574-2584
    • Tap, J.1    Mondot, S.2    Levenez, F.3    Pelletier, E.4    Caron, C.5    Furet, J.-P.6
  • 57
    • 77955625829 scopus 로고    scopus 로고
    • Stability of ecological communities and the architecture of mutualistic and trophic networks
    • doi: 10.1126/science.1188321
    • Thébault, E., and Fontaine, C. (2010). Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853-856. doi: 10.1126/science.1188321
    • (2010) Science , vol.329 , pp. 853-856
    • Thébault, E.1    Fontaine, C.2
  • 58
    • 20244376755 scopus 로고    scopus 로고
    • Comparative metagenomics of microbial communities
    • doi: 10.1126/science.1107851
    • Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., et al. (2005). Comparative metagenomics of microbial communities. Science 308, 554-557. doi: 10.1126/science.1107851
    • (2005) Science , vol.308 , pp. 554-557
    • Tringe, S.G.1    von Mering, C.2    Kobayashi, A.3    Salamov, A.A.4    Chen, K.5    Chang, H.W.6
  • 59
    • 77956095233 scopus 로고    scopus 로고
    • Web of ecological interactions in an experimental gut microbiota
    • doi: 10.1111/j.1462-2920.2010.02236.x
    • Trosvik, P., Rudi, K., Straetkvern, K. O., Jakobsen, K. S., Naes, T., and Stenseth, N. C. (2010). Web of ecological interactions in an experimental gut microbiota. Environ. Microbiol. 12, 2677-2687. doi: 10.1111/j.1462-2920.2010.02236.x.
    • (2010) Environ. Microbiol. , vol.12 , pp. 2677-2687
    • Trosvik, P.1    Rudi, K.2    Straetkvern, K.O.3    Jakobsen, K.S.4    Naes, T.5    Stenseth, N.C.6
  • 60
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • doi: 10.1038/nature02340
    • Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43. doi: 10.1038/nature02340
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5    Richardson, P.M.6
  • 61
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of "small-world" networks
    • doi: 10.1038/30918
    • Watts, D. J., and Strogatz, S. H. (1998). Collective dynamics of "small-world" networks. Nature 393, 440-442. doi: 10.1038/30918
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 62
    • 0031031474 scopus 로고    scopus 로고
    • A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models
    • doi: 10.1111/j.1574-6941.1997.tb00351.x
    • Wimpenny, J. W. T., and Colasanti, R. (1997). A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models. FEMS Microbiol. Rev. 22, 1-16. doi: 10.1111/j.1574-6941.1997.tb00351.x
    • (1997) FEMS Microbiol. Rev. , vol.22 , pp. 1-16
    • Wimpenny, J.W.T.1    Colasanti, R.2
  • 63
    • 33745282930 scopus 로고    scopus 로고
    • Sex and virulence in Escherichia coli: an evolutionary perspective
    • doi: 10.1111/j.1365-2958.2006.05172.x
    • Wirth, T., Falush, D., Lan, R., Colles, F., Mensa, P., Wieler, L. H., et al. (2006). Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60, 1136-1151. doi: 10.1111/j.1365-2958.2006.05172.x
    • (2006) Mol. Microbiol. , vol.60 , pp. 1136-1151
    • Wirth, T.1    Falush, D.2    Lan, R.3    Colles, F.4    Mensa, P.5    Wieler, L.H.6
  • 64
    • 84863990011 scopus 로고    scopus 로고
    • Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon
    • doi: 10.1038/ismej.2012.4
    • Ze, X., Duncan, S. H., Louis, P., and Flint, H. J. (2012). Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535-1543. doi: 10.1038/ismej.2012.4
    • (2012) ISME J , vol.6 , pp. 1535-1543
    • Ze, X.1    Duncan, S.H.2    Louis, P.3    Flint, H.J.4
  • 65
    • 80052540333 scopus 로고    scopus 로고
    • Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems
    • doi: 10.1371/journal.pone.0024570
    • Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., et al. (2011). Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6:e24570. doi: 10.1371/journal.pone.0024570
    • (2011) PLoS ONE , vol.6
    • Zinger, L.1    Amaral-Zettler, L.A.2    Fuhrman, J.A.3    Horner-Devine, M.C.4    Huse, S.M.5    Welch, D.B.M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.