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Systems Biology of Microbial Communities

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Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 500))

Summary

Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

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References

  1. Ram, R. J., Verberkmoes, N. C., Thelen, M. P., Tyson, G. W., Baker, B. J., Blake, R. C., 2nd, Shah, M., Hettich, R. L., and Banfield, J. F. (2005) Community proteomics of a natural microbial biofilm. Science 308, 1915–1920.

    Article  Google Scholar 

  2. Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F., and Rohwer, F. (2002) Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 99, 14250–14255.

    Article  Google Scholar 

  3. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. H., and Smith, H. O. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74.

    Article  Google Scholar 

  4. Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., and Banfield, J. F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43.

    Article  Google Scholar 

  5. Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., and Gordon, J. I. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031.

    Article  Google Scholar 

  6. Colwell, R. R., Huq, A., Islam, M. S., Aziz, K. M., Yunus, M., Khan, N. H., Mahmud, A., Sack, R. B., Nair, G. B., Chakraborty, J., Sack, D. A., and Russek-Cohen, E. (2003) Reduction of cholera in Bangladeshi villages by simple filtration. Proc. Natl Acad. Sci. USA 100, 1051–1055.

    Article  Google Scholar 

  7. Lotka, A. J. (1925) Elements of Physical Biology. Williams & Wilkins, Baltimore, MD.

    Google Scholar 

  8. Volterra, V. (1926) Fluctuations in the abundance of a species considered mathematically. Nature 118, 558–560.

    Article  Google Scholar 

  9. Chassagnole, C., Noisommit-Rizzi, N., Schmid, J. W., Mauch, K., and Reuss, M. (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79, 53–73.

    Article  Google Scholar 

  10. Maher, A. D., Kuchel, P. W., Ortega, F., de Atauri, P., Centelles, J., and Cascante, M. (2003) Mathematical modelling of the urea cycle. A numerical investigation into substrate channelling. Eur. J. Biochem. 270, 3953–3961.

    Article  Google Scholar 

  11. Teusink, B., Passarge, J., Reijenga, C. A., Esgalhado, E., van der Weijden, C. C., Schepper, M., Walsh, M. C., Bakker, B. M., van Dam, K., Westerhoff, H. V., and Snoep, J. L. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem. 267, 5313–5329.

    Article  Google Scholar 

  12. Hynne, F., Dano, S., and Sorensen, P. G. (2001) Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. 94, 121–163.

    Article  Google Scholar 

  13. Zhdanov, V. P. and Kasemo, B. (2001) Simulations of oscillatory glycolytic patterns in cells. Phys. Chem. Chem. Phys. 3, 3786–3791.

    Article  Google Scholar 

  14. Klipp, E. (2007) Modelling dynamic processes in yeast. Yeast 24, 943–959.

    Article  Google Scholar 

  15. Bakker, B. M., Westerhoff, H. V., Opperdoes, F. R., and Michels, P. A. (2000) Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol. Biochem. Parasitol. 106, 1–10.

    Article  Google Scholar 

  16. Navid, A. and Ortoleva, P. J. (2004) Simulated complex dynamics of glycolysis in protozoan parasite Trypanosoma brucei. J. Theor. Biol. 228, 449–458.

    Article  Google Scholar 

  17. Smolen, P. (1995) A model for glycolylic oscillations based on skeletal muscle phosphotructokinase kinetics. J. Theor. Biol. 174, 137–148.

    Article  Google Scholar 

  18. Westermark, P. O. and Lansner, A. (2003) A model of phosphofructokinase and glycolytic oscillations in the pancreatic β-cell. Biophys. J. 85, 126–139.

    Article  Google Scholar 

  19. Dano, S., Madsen, M. F., Schmidt, H., and Cedersund, G. (2006) Reduction of a biochemical model with preservation of its basic dynamic properties. FEBS J. 273, 4862–4877.

    Article  Google Scholar 

  20. Chance, B., Hess, B., and Betz, A. (1964) DPNH oscillations in a cell-free extract of S. carlsbergensis. Biochem. Biophys. Res. Commun. 16, 182–187.

    Article  Google Scholar 

  21. Chance, B., Schoener, B., and Elsaesser, S. (1964) Control of the waveform of oscillations of the reduced pyridine nucleotide level in a cell-free extract. Proc. Natl Acad. Sci. USA 52, 337–341.

    Article  Google Scholar 

  22. Ghosh, A. and Chance, B. (1964) Oscillations of glycolytic intermediates in yeast cells. Biochem. Biophys. Res. Commun. 16, 174–181.

    Article  Google Scholar 

  23. Markus, M. and Hess, B. (1984) Transitions between oscillatory modes in a glycolytic model system. Proc. Natl Acad. Sci. USA 81, 4394–4398.

    Article  Google Scholar 

  24. Wolf, J. and Heinrich, R. (1997) Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states. Biosystems 43, 1–24.

    Article  Google Scholar 

  25. Markus, M. and Hess, B. (1985) Input–response relationships in the dynamics of glycolysis. Arch. Biol. Med. Exp. (Santiago) 18, 261–271.

    Google Scholar 

  26. Markus, M., Kuschmitz, D., and Hess, B. (1984) Chaotic dynamics in yeast. Glycolysis under periodic substrate input flux. FEBS Lett. 172, 235–238.

    Article  Google Scholar 

  27. Markus, M., Mueller, S. C., and Hess, B. (1985) Observation of entrainment, quasiperiodicity and chaos in glycolysing yeast extracts under periodic glucose input. Ber. Bunsenges. Phys. Chem. 89, 651–654.

    Google Scholar 

  28. Patnaik, P. R. (2003) Oscillatory metabolism of Saccharomyces cerevisiae: An overview of mechanisms and models. Biotechnol. Adv. 21, 183–192.

    Article  Google Scholar 

  29. Wolf, J. and Heinrich, R. (1997) Dynamics of biochemical oscillators in a large number of interacting cells. Nonlinear Anal. 30, 1835–1845.

    Article  Google Scholar 

  30. Zhdanov, V. P. and Kasemo, B. (2001) Synchronization of metabolic oscillations: Two cells and ensembles of adsorbed cells. J. Biol. Phys. 27, 295–311.

    Article  Google Scholar 

  31. Richard, P., Bakker, B. M., Teusink, B., Van Dam, K., and Westerhoff, H. V. (1996) Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells. Eur. J. Biochem. 235, 238–241.

    Article  Google Scholar 

  32. Wolf, J., Passarge, J., Somsen, O. J., Snoep, J. L., Heinrich, R., and Westerhoff, H. V. (2000) Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys. J. 78, 1145–1153.

    Article  Google Scholar 

  33. Richard, P., Teusink, B., Hemker, M. B., Van Dam, K., and Westerhoff, H. V. (1996) Sustained oscillations in free-energy state and hexose phosphates in yeast. Yeast 12, 731–740.

    Article  Google Scholar 

  34. Bergmeyer, H. U. (1974) Methods of Enzymatic Analysis. Verlag Chemie, Weinheim.

    Google Scholar 

  35. Fuqua, W. C., Winans, S. C., and Greenberg, E. P. (1994) Quorum sensing in bacteria: The LuxR–LuxI family of cell density-responsive transcriptional regulators. J. Bacteriol. 176, 269–275.

    Google Scholar 

  36. Fuqua, C., Winans, S. C., and Greenberg, E. P. (1996) Census and consensus in bacterial ecosystems: The LuxR–LuxI family of quorum-sensing transcriptional regulators. Annu. Rev. Microbiol. 50, 727–751.

    Article  Google Scholar 

  37. McFall-Ngai, M. J. and Ruby, E. G. (2000) Developmental biology in marine invertebrate symbioses. Curr. Opin. Microbiol. 3, 603–607.

    Article  Google Scholar 

  38. Miller, M. B. and Bassler, B. L. (2001) Quorum sensing in bacteria. Annu. Rev. Microbiol. 55, 165–199.

    Article  Google Scholar 

  39. Hammer, B. K. and Bassler, B. L. (2003) Quorum sensing controls biofilm formation in Vibrio cholerae. Mol. Microbiol. 50, 101–104.

    Article  Google Scholar 

  40. Henke, J. M. and Bassler, B. L. (2004) Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. J. Bacteriol. 186, 3794–3805.

    Article  Google Scholar 

  41. Waters, C. M. and Bassler, B. L. (2005) Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319–346.

    Article  Google Scholar 

  42. Freeman, J. A., Lilley, B. N., and Bassler, B. L. (2000) A genetic analysis of the functions of LuxN: A two-component hybrid sensor kinase that regulates quorum sensing in Vibrio harveyi. Mol. Microbiol. 35, 139–149.

    Article  Google Scholar 

  43. Miller, M. B., Skorupski, K., Lenz, D. H., Taylor, R. K., and Bassler, B. L. (2002) Parallel quorum sensing systems converge to regulate virulence in Vibrio cholerae. Cell 110, 303–314.

    Article  Google Scholar 

  44. Mok, K. C., Wingreen, N. S., and Bassler, B. L. (2003) Vibrio harveyi quorum sensing: A coincidence detector for two autoinducers controls gene expression. EMBO J. 22, 870–881.

    Article  Google Scholar 

  45. Henke, J. M. and Bassler, B. L. (2004) Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J. Bacteriol. 186, 6902–6914.

    Article  Google Scholar 

  46. Fuqua, C. and Greenberg, E. P. (2002) Listening in on bacteria: Acyl-homoserine lactone signalling. Nat. Rev. Mol. Cell Biol. 3, 685–695.

    Article  Google Scholar 

  47. Pesci, E. C., Milbank, J. B., Pearson, J. P., McKnight, S., Kende, A. S., Greenberg, E. P., and Iglewski, B. H. (1999) Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 96, 11229–11234.

    Article  Google Scholar 

  48. McKnight, S. L., Iglewski, B. H., and Pesci, E. C. (2000) The Pseudomonas quinolone signal regulates rhl quorum sensing in Pseudomonas aeruginosa. J. Bacteriol. 182, 2702–2708.

    Article  Google Scholar 

  49. Pearson, J. P., Van Delden, C., and Iglewski, B. H. (1999) Active eflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals. J. Bacteriol. 181, 1203–1210.

    Google Scholar 

  50. James, S., Nilsson, P., James, G., Kjelleberg, S., and Fagerstrom, T. (2000) Luminescence control in the marine bacterium Vibrio fischeri: An analysis of the dynamics of lux regulation. J. Mol. Biol. 296, 1127–1137.

    Article  Google Scholar 

  51. Eberhard, A., Burlingame, A. L., Eberhard, C., Kenyon, G. L., Nealson, K. H., and Oppenheimer, N. J. (1981) Structural identification of autoinducer of Photobacterium fischeri luciferase. Biochemistry 20, 2444–2449.

    Article  Google Scholar 

  52. Engebrecht, J., Nealson, K., and Silverman, M. (1983) Bacterial bioluminescence: Isolation and genetic analysis of functions from Vibrio fischeri. Cell 32, 773–781.

    Article  Google Scholar 

  53. Engebrecht, J. and Silverman, M. (1984) Identification of genes and gene products necessary for bacterial bioluminescence. Proc. Natl Acad. Sci. USA 81, 4154–4158.

    Article  Google Scholar 

  54. Fuqua, C., Parsek, M. R., and Greenberg, E. P. (2001) Regulation of gene expression by cell-to-cell communication: Acyl-homoserine lactone quorum sensing. Annu. Rev. Genet. 35, 439–468.

    Article  Google Scholar 

  55. Mueller, J., Kuttler, C., Hense, B. A., Rothballer, M., and Hartmann, A. (2006) Cell-cell communication by quorum sensing and dimension-reduction. J. Math. Biol. 53, 672–702.

    Article  Google Scholar 

  56. Kuttler, C. and Hense, B. A. (2008) The interplay of two quorum sensing regulation systems of Vibrio fischeri. J. Theor. Biol. 251, 167–180.

    Article  Google Scholar 

  57. Ward, J. P., King, J. R., Koerber, A. J., Williams, P., Croft, J. M., and Sockett, R. E. (2001) Mathematical modelling of quorum sensing in bacteria. IMA J. Math. Appl. Med. Biol. 18, 263–292.

    Article  Google Scholar 

  58. Dockery, J. D. and Keener, J. P. (2001) A mathematical model for quorum sensing in Pseudomonas aeruginosa. Bull. Math. Biol. 63, 95–116.

    Article  Google Scholar 

  59. Kreft, J. U., Picioreanu, C., Wimpenny, J. W., and van Loosdrecht, M. C. (2001) Individual-based modelling of biofilms. Microbiology 147, 2897–2912.

    Google Scholar 

  60. Wimpenny, J. W. T. and Colasanti, R. (1997) A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models. FEMS Microbiol. Ecol. 22, 1–16.

    Article  Google Scholar 

  61. Pizarro, G., Griffeath, D., and Noguera, D. R. (2001) Quantitative cellular automaton model for biofilms. J. Environ. Eng. 127, 782–789.

    Article  Google Scholar 

  62. Xavier, J. B. and Foster, K. R. (2007) Cooperation and conflict in microbial biofilms. Proc. Natl Acad. Sci. USA 104, 876–881.

    Article  Google Scholar 

  63. West, S. A., Griffin, A. S., Gardner, A., and Diggle, S. P. (2006) Social evolution theory for microorganisms. Nat. Rev. Microbiol. 4, 597–607.

    Article  Google Scholar 

  64. Kreft, J. U. (2004) Biofilms promote altruism. Microbiology 150, 2751–2760.

    Article  Google Scholar 

  65. Chambless, J. D., Hunt, S. M., and Stewart, P. S. (2006) A three-dimensional computer model of four hypothetical mechanisms protecting biofilms from antimicrobials. Appl. Environ. Microbiol. 72, 2005–2013.

    Article  Google Scholar 

  66. Hunt, S. M., Hamilton, M. A., Sears, J. T., Harkin, G., and Reno, J. (2003) A computer investigation of chemically mediated detachment in bacterial biofilms. Microbiology 149, 1155–1163.

    Article  Google Scholar 

  67. Mobilia, M., Georgiev, I. T., and Täuber, U. C. (2007) Phase transitions and spatio-temporal fluctuations in stochastic lattice Lotka–Volterra models. J. Stat. Phys. 128, 447–483.

    Article  Google Scholar 

  68. May, R. M. (1976) Simple mathematical models with very complicated dynamics. Nature 261, 459–467.

    Article  Google Scholar 

  69. May, R. M. (1973) Stability and Complexity in Model Ecosystems. Princeton University Press, Princeton, NJ.

    Google Scholar 

  70. Kondoh, M. (2003) Foraging adaptation and the relationship between food-web complexity and stability. Science 299, 1388–1391.

    Article  Google Scholar 

  71. Ackland, G. J. and Gallagher, I. D. (2004) Stabilization of large generalized Lotka–Volterra foodwebs by evolutionary feedback. Phys. Rev. Lett. 93, 158701.

    Article  Google Scholar 

  72. Murray, J. D. (2002) Mathematical Biology. Springer, New York, NY.

    Google Scholar 

  73. Collet, P. and Eckmann, J. P. (1990) Instabilities and Fronts in Extended Systems. Princeton University Press, Princeton, NJ.

    Google Scholar 

  74. Kussell, E. and Leibler, S. (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075–2078.

    Article  Google Scholar 

  75. Thattai, M. and van Oudenaarden, A. (2004) Stochastic gene expression in fluctuating environments. Genetics 167, 523–530.

    Article  Google Scholar 

  76. Hoffmann, K. H., Rodriguez-Brito, B., Breitbart, M., Bangor, D., Angly, F., Felts, B., Nulton, J., Rohwer, F., and Salamon, P. (2007) Power law rank-abundance models for marine phage communities. FEMS Microbiol. Lett. 273, 224–228.

    Article  Google Scholar 

  77. Thingstad, T. F. (2000) Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceanogr. 45, 1320–1328.

    Article  Google Scholar 

  78. Mounier, J., Monnet, C., Vallaeys, T., Arditi, R., Sarthou, A. S., Helias, A., and Irlinger, F. (2008) Microbial interactions within a cheese microbial community. Appl. Environ. Microbiol. 74, 172–181.

    Article  Google Scholar 

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Acknowledgments

This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344, and supported by the LLNL Laboratory Directed Research and Development program on grant 06-ERD-061.

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Authors and Affiliations

  1. Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, P.O. Box 808,L-452, Livermore, CA, 94550, USA

    Eivind Almaas

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  1. Ali Navid
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  2. Cheol-Min Ghim
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  3. Andrew T. Fenley
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  4. Sooyeon Yoon
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  5. Sungmin Lee
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  6. Eivind Almaas
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Correspondence to Eivind Almaas .

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    © 2009 Humana Press

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    Navid, A., Ghim, CM., Fenley, A., Yoon, S., Lee, S., Almaas, E. (2009). Systems Biology of Microbial Communities. In: Maly, I. (eds) Systems Biology. Methods in Molecular Biology, vol 500. Humana Press. https://doi.org/10.1007/978-1-59745-525-1_16

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    • DOI: https://doi.org/10.1007/978-1-59745-525-1_16

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