A Preliminary Assessment of Three Strategies for the Agent-Based Modeling of Bacterial Conjugation

  • Antonio Prestes GarcíaEmail author
  • Alfonso Rodríguez-Patón
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 375)


Bacterial conjugation is a cell-cell communication by which neighbor cells transmit circular DNA strands called plasmids. The transmission of these plasmids has been traditionally modeled using differential equations. Recently agent-based systems with spatial resolution have emerged as a promising tool that we use in this work to assess three different schemes for modeling the bacterial conjugation. The three schemes differ basically in which point of cell cycle the conjugation is most prone to happen. One alternative is to allow a conjugative event occurs as soon a suitable recipient is found, the second alternative is to make conjugation equally like to happen throughout the cell cycle and finally, the third one technique to assume that conjugation is more likely to occur in a specific point late in the cell cycle.


Agent-based modeling Individual-based modeling Plasmids Bacterial conjugation Synthetic biology 



This work was supported by the European FP7-ICT-FET EU research project 612146 (PLASWIRES “Plasmids as Wires” project) and by Spanish Government (MINECO) research grant TIN2012-36992.


  1. 1.
    Arutyunov, D., Frost, L.S.: F conjugation: back to the beginning. Plasmid 70(1), 18–32 (Jul 2013)Google Scholar
  2. 2.
    Berec, L.: Techniques of spatially explicit individual-based models:construction, simulation, and mean-field analysis. Ecol. Model. 150(1–2), 55–81 (April 2002)Google Scholar
  3. 3.
    del Campo, I., Ruiz, R., Cuevas, A., Revilla, C., Vielva, L., de la Cruz, F.: Determination of conjugation rates on solid surfaces. Plasmid 67(2), 174–182 (March 2012)Google Scholar
  4. 4.
    Fox, R.E., Zhong, X., Krone, S.M., Top, E.M.: Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. ISME J. 2(10), 1024–1039 (June 2008)Google Scholar
  5. 5.
    Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., Goss-Custard, J., Grand, T., Heinz, S.K., Huse, G., Huth, A., Jepsen, J.U., Jørgensen, C., Mooij, W.M., Müller, B., Pe’er, G., Piou, C., Railsback, S.F., Robbins, A.M., Robbins, M.M., Rossmanith, E., Rüger, N., Strand, E., Souissi, S., Stillman, R.A., Vabø R., Visser, U., DeAngelis, D.L.: A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198(1–2), 115–126 (Sept 2006)Google Scholar
  6. 6.
    Grimm, V., Berger, U., DeAngelis, D.L., Polhill, J.G., Giske, J., Railsback, S.F.: The ODD protocol: a review and first update. Ecol. Model. 221(23), 2760–2768 (Nov 2010)Google Scholar
  7. 7.
    Hellweger, F.L., Bucci, V.: A bunch of tiny individuals—individual-based modeling for microbes. Ecol. Model. 220(1), 8–22 (Jan 2009)Google Scholar
  8. 8.
    Kreft, J.U., Booth, G., Wimpenny, J.W.T.: BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144(12), 3275–3287 (Dec 1998)Google Scholar
  9. 9.
    Krone, S.M., Lu, R., Fox, R., Suzuki, H., Top, E.M.: Modelling the spatial dynamics of plasmid transfer and persistence. Microbiology (Reading, England) 153(Pt 8), 2803–2816 (Aug 2007)Google Scholar
  10. 10.
    Merkey, B.V., Lardon, L.A., Seoane, J.M., Kreft, J.U., Smets, B.F.: Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environ. Microbiol. 13(9), 2435–2452 (2011)Google Scholar
  11. 11.
    North, M., Collier, N., Ozik, J., Tatara, E., Macal, C., Bragen, M., Sydelko, P.: Complex adaptive systems modeling with Repast Simphony. Complex Adapt. Syst. Model. 1(1), 1–26 (2013)Google Scholar
  12. 12.
    Simonsen, L., Gordon, D.M., Stewart, F.M., Levin, B.R.: Estimating the rate of plasmid transfer: an end-point method. J. Gen. Microbiol. 136(11), 2319–2325 (Nov 1990)Google Scholar
  13. 13.
    Zhong, X., Droesch, J., Fox, R., Top, E.M., Krone, S.M.: On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations. J. Theor. Biol. 294, 144–152 (Feb 2012)Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Antonio Prestes García
    • 1
    Email author
  • Alfonso Rodríguez-Patón
    • 1
  1. 1.Departamento de Inteligencia ArtificialUniversidad Politécnica de Madrid, Campus de Montegancedo s/nMadridSpain

Personalised recommendations