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Volumn 13, Issue 2, 2017, Pages

Two dynamic regimes in the human gut microbiome

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DYNAMICS; ECONOMICS; PHYLOGENETIC; REGRESSION ANALYSIS;

EID: 85014146143     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005364     Document Type: Article
Times cited : (88)

References (56)
  • 2
    • 84907190237 scopus 로고    scopus 로고
    • Longitudinal analysis of microbial interaction between humans and the indoor environment
    • 517015
    • Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014;345(6200):1048–52. doi: 10.1126/science.125452925170151
    • (2014) Science , vol.345 , Issue.6200 , pp. 1048-1052
    • Lax, S.1    Smith, D.P.2    Hampton-Marcell, J.3    Owens, S.M.4    Handley, K.M.5    Scott, N.M.6
  • 5
  • 6
    • 33845901507 scopus 로고    scopus 로고
    • Microbial ecology: human gut microbes associated with obesity
    • 718330
    • Ley RE, Turnbaugh PJ, Klein S, Gordon JI, Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022–3. doi: 10.1038/4441022a17183309
    • (2006) Nature , vol.444 , Issue.7122 , pp. 1022-1023
    • Ley, R.E.1    Turnbaugh, P.J.2    Klein, S.3    Gordon, J.I.4
  • 7
    • 84858376593 scopus 로고    scopus 로고
    • The impact of the gut microbiota on human health: an integrative view
    • 242423
    • Clemente JC, Ursell LK, Parfrey LW, Knight R, The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148(6):1258–70. doi: 10.1016/j.cell.2012.01.03522424233
    • (2012) Cell , vol.148 , Issue.6 , pp. 1258-1270
    • Clemente, J.C.1    Ursell, L.K.2    Parfrey, L.W.3    Knight, R.4
  • 9
    • 84908341362 scopus 로고    scopus 로고
    • The dynamic microbiome
    • 458307
    • Gerber GK, The dynamic microbiome. FEBS Lett. 2014;588(22):4131–9. doi: 10.1016/j.febslet.2014.02.03724583074
    • (2014) FEBS Lett , vol.588 , Issue.22 , pp. 4131-4139
    • Gerber, G.K.1
  • 14
    • 84900535804 scopus 로고    scopus 로고
    • Dynamics and associations of microbial community types across the human body
    • 473996
    • Ding T, Schloss PD, Dynamics and associations of microbial community types across the human body. Nature. 2014;509(7500):357–60. doi: 10.1038/nature1317824739969
    • (2014) Nature , vol.509 , Issue.7500 , pp. 357-360
    • Ding, T.1    Schloss, P.D.2
  • 15
    • 84892828465 scopus 로고    scopus 로고
    • Diet rapidly and reproducibly alters the human gut microbiome
    • 433621
    • David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63. http://www.nature.com/nature/journal/v505/n7484/abs/nature12820.html—supplementary-information. doi: 10.1038/nature1282024336217
    • (2014) Nature , vol.505 , Issue.7484 , pp. 559-563
    • David, L.A.1    Maurice, C.F.2    Carmody, R.N.3    Gootenberg, D.B.4    Button, J.E.5    Wolfe, B.E.6
  • 16
    • 34247882011 scopus 로고    scopus 로고
    • Interactions and competition within the microbial community of the human colon: links between diet and health
    • 747262
    • Flint HJ, Duncan SH, Scott KP, Louis P, Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol. 2007;9(5):1101–11. doi: 10.1111/j.1462-2920.2007.01281.x17472627
    • (2007) Environ Microbiol , vol.9 , Issue.5 , pp. 1101-1111
    • Flint, H.J.1    Duncan, S.H.2    Scott, K.P.3    Louis, P.4
  • 17
  • 18
    • 35848931007 scopus 로고    scopus 로고
    • IgA response to symbiotic bacteria as a mediator of gut homeostasis
    • 800575
    • Peterson DA, McNulty NP, Guruge JL, Gordon JI, IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007;2(5):328–39. doi: 10.1016/j.chom.2007.09.01318005754
    • (2007) Cell Host Microbe , vol.2 , Issue.5 , pp. 328-339
    • Peterson, D.A.1    McNulty, N.P.2    Guruge, J.L.3    Gordon, J.I.4
  • 19
    • 0141818183 scopus 로고    scopus 로고
    • Biodiversity and species interactions: extending Lotka-Volterra community theory
    • Wilson WG, Lundberg P, Vazquez DP, Shurin JB, Smith MD, Langford W, et al. Biodiversity and species interactions: extending Lotka-Volterra community theory. Ecol Lett. 2003;6(10):944–52.
    • (2003) Ecol Lett , vol.6 , Issue.10 , pp. 944-952
    • Wilson, W.G.1    Lundberg, P.2    Vazquez, D.P.3    Shurin, J.B.4    Smith, M.D.5    Langford, W.6
  • 20
    • 84904687373 scopus 로고    scopus 로고
    • Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression
    • 5054627,.; ():
    • Fisher CK, Mehta P, Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One. 2014;9(7):e102451. doi: 10.1371/journal.pone.010245125054627
    • (2014) PLoS One , vol.9 , Issue.7 , pp. e102451
    • Fisher, C.K.1    Mehta, P.2
  • 21
    • 84892708007 scopus 로고    scopus 로고
    • Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
    • 4348232,..; ():
    • Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol. 2013;9(12):e1003388. doi: 10.1371/journal.pcbi.100338824348232
    • (2013) PLoS Comput Biol , vol.9 , Issue.12 , pp. e1003388
    • Stein, R.R.1    Bucci, V.2    Toussaint, N.C.3    Buffie, C.G.4    Rätsch, G.5    Pamer, E.G.6
  • 22
    • 84975223360 scopus 로고    scopus 로고
    • MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
    • 7259475,..; ():
    • Bucci V, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, et al. MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biol. 2016;17(1):121. doi: 10.1186/s13059-016-0980-627259475
    • (2016) Genome Biol , vol.17 , Issue.1 , pp. 121
    • Bucci, V.1    Tzen, B.2    Li, N.3    Simmons, M.4    Tanoue, T.5    Bogart, E.6
  • 23
    • 84867864222 scopus 로고    scopus 로고
    • Detecting Causality in Complex Ecosystems
    • 299713
    • Sugihara G, May R, Ye H, Hsieh C-h, Deyle E, Fogarty M, et al. Detecting Causality in Complex Ecosystems. Science. 2012;338(6106):496–500. doi: 10.1126/science.122707922997134
    • (2012) Science , vol.338 , Issue.6106 , pp. 496-500
    • Sugihara, G.1    May, R.2    Ye, H.3    Hsieh, C.-H.4    Deyle, E.5    Fogarty, M.6
  • 24
    • 84918535911 scopus 로고    scopus 로고
    • Convergent cross-mapping and pairwise asymmetric inference
    • McCracken JM, Weigel RS, Convergent cross-mapping and pairwise asymmetric inference. Phys Rev E. 2014;90(6):062903.
    • (2014) Phys Rev E , vol.90 , Issue.6 , pp. 062903
    • McCracken, J.M.1    Weigel, R.S.2
  • 26
    • 84931265628 scopus 로고    scopus 로고
    • Metagenomics meets time series analysis: unraveling microbial community dynamics
    • 6005845,.;: –
    • Faust K, Lahti L, Gonze D, de Vos WM, Raes J, Metagenomics meets time series analysis: unraveling microbial community dynamics. Curr Opin Microbiol. 2015;25:56–66. doi: 10.1016/j.mib.2015.04.00426005845
    • (2015) Curr Opin Microbiol , vol.25 , pp. 56-66
    • Faust, K.1    Lahti, L.2    Gonze, D.3    de Vos, W.M.4    Raes, J.5
  • 27
    • 84991010752 scopus 로고    scopus 로고
    • A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
    • Chen EZ, Li H, A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics. 2016.
    • (2016) Bioinformatics
    • Chen, E.Z.1    Li, H.2
  • 28
    • 84962355546 scopus 로고    scopus 로고
    • Wang Y, Hu X, Jiang X, He T, Yuan J, editors. Predicting microbial interactions by using network-constrained regularization incorporating covariate coefficients and connection signs. IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2015.
    • (2015) , vol.10
    • Wang, Y.1    Hu, X.2
  • 29
    • 34250894615 scopus 로고    scopus 로고
    • London Palgrave MacMilla
    • Asteriou D, Hall S, Vector Autoregressive (VAR) Models and Causality Tests. Applied Econometrics. London: Palgrave MacMillan; 2011.
    • (2011) Applied Econometrics
    • Asteriou, D.1    Hall, S.2
  • 30
    • 84933511111 scopus 로고    scopus 로고
    • Regularized estimation in sparse high-dimensional time series models
    • Basu S, Michailidis G, Regularized estimation in sparse high-dimensional time series models. Ann Stat. 2015;43(4):1535–67.
    • (2015) Ann Stat , vol.43 , Issue.4 , pp. 1535-1567
    • Basu, S.1    Michailidis, G.2
  • 32
    • 0000678046 scopus 로고
    • Lotka-Volterra population models
    • Wangersky PJ, Lotka-Volterra population models. Ann Rev Ecol Syst. 1978;9:189–218.
    • (1978) Ann Rev Ecol Syst , vol.9 , pp. 189-218
    • Wangersky, P.J.1
  • 33
    • 0001880021 scopus 로고
    • Variations and fluctuations of the number of individuals in animal species living together
    • Volterra V, Variations and fluctuations of the number of individuals in animal species living together. J Cons Int Explor Mer. 1928;3(1):3–51.
    • (1928) J Cons Int Explor Mer , vol.3 , Issue.1 , pp. 3-51
    • Volterra, V.1
  • 34
    • 84973651887 scopus 로고    scopus 로고
    • Universality of human microbial dynamics
    • 727922
    • Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, et al. Universality of human microbial dynamics. Nature. 2016;534(7606):259–62. http://www.nature.com/nature/journal/v534/n7606/abs/nature18301.html—supplementary-information. doi: 10.1038/nature1830127279224
    • (2016) Nature , vol.534 , Issue.7606 , pp. 259-262
    • Bashan, A.1    Gibson, T.E.2    Friedman, J.3    Carey, V.J.4    Weiss, S.T.5    Hohmann, E.L.6
  • 36
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • 213464
    • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6(3):610–8. doi: 10.1038/ismej.2011.13922134646
    • (2012) ISME J , vol.6 , Issue.3 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    DeSantis, T.Z.5    Probst, A.6
  • 37
    • 84920714710 scopus 로고    scopus 로고
    • Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
    • 5177538,..;:
    • Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014;2:e545. doi: 10.7717/peerj.54525177538
    • (2014) PeerJ , vol.2 , pp. e545
    • Rideout, J.R.1    He, Y.2    Navas-Molina, J.A.3    Walters, W.A.4    Ursell, L.K.5    Gibbons, S.M.6
  • 38
    • 84906829581 scopus 로고    scopus 로고
    • The Earth Microbiome project: successes and aspirations
    • Gilbert JA, Jansson JK, Knight R, The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12(1):69.
    • (2014) BMC Biol , vol.12 , Issue.1 , pp. 69
    • Gilbert, J.A.1    Jansson, J.K.2    Knight, R.3
  • 41
    • 0001476603 scopus 로고
    • Monotone piecewise cubic interpolation
    • Fritsch FN, Carlson RE, Monotone piecewise cubic interpolation. SIAM J. 1980;17(2):238–46.
    • (1980) SIAM J , vol.17 , Issue.2 , pp. 238-246
    • Fritsch, F.N.1    Carlson, R.E.2
  • 42
    • 84856521514 scopus 로고    scopus 로고
    • Dirichlet multinomial mixtures: generative models for microbial metagenomics
    • 2319561,.; ():
    • Holmes I, Harris K, Quince C, Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One. 2012;7(2):e30126. doi: 10.1371/journal.pone.003012622319561
    • (2012) PLoS One , vol.7 , Issue.2 , pp. e30126
    • Holmes, I.1    Harris, K.2    Quince, C.3
  • 43
    • 84930925914 scopus 로고    scopus 로고
    • Temporal patterns of rarity provide a more complete view of microbial diversity
    • Shade A, Gilbert JA, Temporal patterns of rarity provide a more complete view of microbial diversity. Trends Microbiol. 2015.
    • (2015) Trends Microbiol
    • Shade, A.1    Gilbert, J.A.2
  • 46
    • 85014163836 scopus 로고    scopus 로고
    • yczewska EM. Empirical power of the Kwiatkowski-Phillips-Schmidt-Shin test. 2010
    • Syczewska EM. Empirical power of the Kwiatkowski-Phillips-Schmidt-Shin test. 2010.
  • 47
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net
    • Zou H, Hastie T, Regularization and variable selection via the elastic net. J R Stat Soc Series B Statist Methodol. 2005;67(2):301–20.
    • (2005) J R Stat Soc Series B Statist Methodol , vol.67 , Issue.2 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 48
    • 28144459550 scopus 로고
    • Some recent development in a concept of causality
    • Granger CW, Some recent development in a concept of causality. J Econ. 1988;39(1):199–211.
    • (1988) J Econ , vol.39 , Issue.1 , pp. 199-211
    • Granger, C.W.1
  • 49
    • 85014253120 scopus 로고    scopus 로고
    • cKinney W, editor Data structures for statistical computing in Python. Proceedings of the 9th Python in Science Conference; 2010
    • McKinney W, editor Data structures for statistical computing in Python. Proceedings of the 9th Python in Science Conference; 2010.
  • 50
    • 0000122573 scopus 로고
    • PHYLIP-phylogeny inference package (version 3.2)
    • Felsenstein J, PHYLIP-phylogeny inference package (version 3.2). Cladistics. 1989;5:163–6.
    • (1989) Cladistics , vol.5 , pp. 163-166
    • Felsenstein, J.1
  • 51
    • 84865733148 scopus 로고    scopus 로고
    • Inferring correlation networks from genomic survey data
    • 3028285,.; ():
    • Friedman J, Alm EJ, Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9):e1002687. doi: 10.1371/journal.pcbi.100268723028285
    • (2012) PLoS Comput Biol , vol.8 , Issue.9 , pp. e1002687
    • Friedman, J.1    Alm, E.J.2
  • 52
    • 84880924622 scopus 로고    scopus 로고
    • Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis
    • 367700
    • Rigottier-Gois L, Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 2013;7(7):1256–61. doi: 10.1038/ismej.2013.8023677008
    • (2013) ISME J , vol.7 , Issue.7 , pp. 1256-1261
    • Rigottier-Gois, L.1
  • 53
    • 10844275734 scopus 로고    scopus 로고
    • Network ecology: topological constraints on ecosystem dynamics
    • Jordán F, Scheuring I, Network ecology: topological constraints on ecosystem dynamics. Phys Life Rev. 2004;1(3):139–72.
    • (2004) Phys Life Rev , vol.1 , Issue.3 , pp. 139-172
    • Jordán, F.1    Scheuring, I.2
  • 54
    • 84863989287 scopus 로고    scopus 로고
    • The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases
    • 235753
    • Khan MT, Duncan SH, Stams AJM, van Dijl JM, Flint HJ, Harmsen HJM, The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J. 2012;6(8):1578–85. doi: 10.1038/ismej.2012.522357539
    • (2012) ISME J , vol.6 , Issue.8 , pp. 1578-1585
    • Khan, M.T.1    Duncan, S.H.2    Stams, A.J.M.3    van Dijl, J.M.4    Flint, H.J.5    Harmsen, H.J.M.6
  • 55
    • 40549106737 scopus 로고    scopus 로고
    • The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract
    • 808388
    • Derrien M, Collado MC, Ben-Amor K, Salminen S, de Vos WM, The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol. 2008;74(5):1646–8. doi: 10.1128/AEM.01226-0718083887
    • (2008) Appl Environ Microbiol , vol.74 , Issue.5 , pp. 1646-1648
    • Derrien, M.1    Collado, M.C.2    Ben-Amor, K.3    Salminen, S.4    de Vos, W.M.5
  • 56
    • 68249110221 scopus 로고    scopus 로고
    • The role of pH in determining the species composition of the human colonic microbiota
    • Duncan SH, Louis P, Thomson JM, Flint HJ, The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol microbiology. 2009;11(8):2112–22.
    • (2009) Environ Microbiol microbiology , vol.11 , Issue.8 , pp. 2112-2122
    • Duncan, S.H.1    Louis, P.2    Thomson, J.M.3    Flint, H.J.4


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