Which games are growing bacterial populations playing?

Journal of the Royal Society Interface

Volumn 12, Issue 108, 2015, Pages

  Li, Xiang Yi ^a   Pietschke, Cleo ^a,b   Fraune, Sebastian ^b   Altrock, Philipp M ^c,d,e   Bosch, Thomas C G ^b   Traulsen, Arne ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b UNIVERSITY OF KIEL   (Germany)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^e HARVARD UNIVERSITY   (United States)

Author keywords

Bacterial interactions; Frequency dependent selection; Lotka Volterra equations; Nonlinear dynamics; Population dynamics

Indexed keywords

BACTERIA; DYNAMICS; INTEGRAL EQUATIONS; MICROORGANISMS; NONLINEAR EQUATIONS; POPULATION DYNAMICS; POPULATION STATISTICS; PREDATOR PREY SYSTEMS;

BACTERIAL INTERACTIONS; EVOLUTIONARY GAME THEORY; FREQUENCY-DEPENDENT SELECTION; LOTKA-VOLTERRA EQUATIONS; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY DYNAMICS; MICROBIAL POPULATIONS; NONLINEAR GROWTH RATES;

GAME THEORY;

ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; BACTERIUM; COCULTURE; COMMENSAL; CURVIBACTER; DUGANELLA; GROWTH RATE; HYDRA VULGARIS; IN VITRO STUDY; MASS EXTINCTION; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; MICROBIAL POPULATION DYNAMICS; MYCOSIS; NONHUMAN; POPULATION GROWTH; POPULATION SIZE; ANIMAL; BACTERIAL PHENOMENA AND FUNCTIONS; BIOLOGICAL MODEL; GAME; HYDRA; METABOLISM; MICROBIAL CONSORTIUM; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); CURVIBACTER; DUGANELLA; HYDRA VULGARIS; METAZOA;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; GAME THEORY; HYDRA; MICROBIAL CONSORTIA; MODELS, BIOLOGICAL;

EID: 84936748692     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2015.0121     Document Type: Article

References (74)

1. McFall-Ngai M et al. 2013 Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. USA 110, 3229-3236. (doi:10.1073/pnas.1218525110)
2. Sommer F, Bäckhed F. 2013 The gut microbiota-masters of host development and physiology. Nat. Rev. Microbiol. 11, 227-238. (doi:10.1038/nrmicro2974)
3. Zilber-Rosenberg I, Rosenberg E. 2008 Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723-735. (doi:10.1111/j.1574-6976.2008.00123.x)
4. Brucker RM, Bordenstein SR. 2013 The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science 341, 667-669. (doi:10.1126/science.1240659)
5. Gustafsson BE, Laurell CB. 1959 Gamma globulin production in germfree rats after bacterial contamination. J. Exp. Med. 110, 675-684. (doi:10. 1084/jem.110.5.675)
6. Douglas A, Minto L, Wilkinson T. 2001 Quantifying nutrient production by the microbial symbionts in an aphid. J. Exp. Biol. 204, 349-358.
7. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. 2012 Host-gut microbiota metabolic interactions. Science 336, 1262-1267. (doi:10.1126/science.1223813)
8. Yatsunenko T et al. 2012 Human gut microbiome viewed across age and geography. Nature 486, 222-227. (doi:10.1038/nature11053)
9. Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda C, Xavier J, Pamer EG. 2012 Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect. Immunity 80, 62-73. (doi:10.1128/IAI.05496-11)
10. Kamada N, Seo SU, Chen GY, Nún?ez G. 2013 Role of the gut microbiota in immunity and inflammatory disease. Nat. Rev. Immunol. 13, 321-335. (doi:10. 1038/nri3430)
11. Fraune S, Anton-Erxleben F, Augustin R, Franzenburg S, Knop M, Schröder K, Willoweit-Ohl D, Bosch TCG. 2014 Bacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. ISME J. (doi:10.1038/ismej.2014.239)
12. Jones RM et al. 2013 Symbiotic lactobacilli stimulate gut epithelial proliferation via Noxmediated generation of reactive oxygen species. EMBO J. 32, 3017-3028. (doi:10.1038/emboj.2013. 224)
13. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. 2005 An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107-118. (doi:10.1016/j.cell. 2005.05.007)
14. Weiss BL, Maltz M, Aksoy S. 2012 Obligate symbionts activate immune system development in the tsetse fly. J. Immunol. 188, 3395-3403. (doi:10.4049/jimmunol.1103691)
15. Montgomery MK, McFall-Ngai M. 1994 Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes. Development 120, 1719-1729.
16. Rawls JF, Samuel BS, Gordon JI. 2004 Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl Acad. Sci. USA 101, 4596-4601. (doi:10.1073/pnas.0400706101)
17. Prosser JI et al. 2007 The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5, 384-392. (doi:10.1038/nrmicro1643)
18. Blaser MJ, Kirschner D. 2007 The equilibria that allow bacterial persistence in human hosts. Nature 449, 843-849. (doi:10.1038/nature06198)
19. Schluter J, Foster KR. 2012 The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol. 10, e1001424. (doi:10.1371/journal.pbio.1001424)
20. Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB. 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)
21. Bucci V, Xavier JB. 2014 Towards predictive models of the human gut microbiome. J. Mol. Biol. 426, 3907-3916. (doi:10.1016/j.jmb.2014.03.017)
22. Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD. 2014 Mathematical modeling of primary succession of murine intestinal microbiota. Proc. Natl Acad. Sci. USA 111, 439-444. (doi:10.1073/pnas.1311322111)
23. Hallatschek O, Hersen P, Ramanathan S, Nelson DR. 2007 Genetic drift at expanding frontiers promotes gene segregation. Proc. Natl Acad. Sci. USA 104, 19 926-19 930. (doi:10.1073/pnas.0710150104)
24. Melbinger A, Cremer J, Frey E. 2010 Evolutionary game theory in growing populations. Phys. Rev. Lett. 105, 178101. (doi:10.1103/PhysRevLett.105.178101)
25. Franzenburg S, Fraune S, Altrock PM, Kuenzel S, Baines JF, Traulsen A, Bosch TCG. 2013 Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. ISME J. 7, 781-790. (doi:10. 1038/ismej.2012.156)
26. Palmer C, Bik EM, Diguilio DB, Relman DA, Brown PO. 2007 Development of the human infant intestinal microbiota. PLoS Biol. 5, e177. (doi:10. 1371/journal.pbio.0050177)
27. Nowak MA, Sigmund K. 2004 Evolutionary dynamics of biological games. Science 303, 793-799. (doi:10. 1126/science.1093411)
28. Frey E, Reichenbach T. 2011 Bacterial games. In Principles of evolution: from the Planck epoch to complex multicellular life (eds H Meyer-Ortmanns, S Thurner), pp. 297-330. Berlin, Germany: Springer.
29. Kerr B, Riley MA, Feldman MW, Bohannan BJM. 2002 Local dispersal promotes biodiversity in a reallife game of rock-paper-scissors. Nature 418, 171-174. (doi:10.1038/nature00823)
30. Rainey PB, Rainey K. 2003 Evolution of cooperation and conflict in experimental bacterial populations. Nature 425, 72-74. (doi:10.1038/nature01906)
31. Hofbauer J, Sigmund K. 1998 Evolutionary games and population dynamics. Cambridge, UK: Cambridge University Press.
32. Murray JD. 2007 Mathematical biology I: an introduction, 3rd edn. Berlin, Germany: Springer.
33. May RM, McLean AR (eds). 2007 Theoretical ecology. Oxford, UK: Oxford University Press.
34. Ellner SP, Guckenheimer J. 2011 Dynamics models in biology. Princeton, NJ: Princeton University Press.
35. Fraune S, Bosch TC. 2007 Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc. Natl Acad. Sci. USA 104, 13 146-13 151. (doi:10.1073/pnas. 0703375104)
36. Bosch TCG. 2013 Cnidarian-microbe interactions and the origin of innate immunity in metazoans. Annu. Rev. Microbiol. 67, 499-518. (doi:10.1146/annurev-micro-092412-155626)
37. Fraune S, Bosch TC. 2010 Why bacteria matter in animal development and evolution. Bioessays 32, 571-580. (doi:10.1002/bies.200900192)
38. Kvalseth TO. 1985 Cautionary note about R 2. Amer. Stat. 39, 279-285
39. Draper NR, Smith H. 1998 Applied regression analysis (Wiley Series in Probability and Statistics), 3rd edn. New York, NY: Wiley-Interscience.
40. Bozdogan H. 1987 Model selection and Akaike's information criterion (AIC): the general theory and its analytical extensions. Psychometrika 52, 345-370. (doi:10.1007/BF02294361)
41. Burnham KP, Anderson DR. 2004 Multimodel inference understanding AIC and BIC in model selection. Sociol. Methods Res. 33, 261-304. (doi:10.1177/0049124104268644)
42. Posada D, Buckley TR. 2004 Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53, 793-808. (doi:10.1080/10635150490522304)
43. Nowak MA. 2006 Evolutionary dynamics. Cambridge, MA: Harvard University Press.
44. Wiggins S. 2003 Invariant manifolds: linear and nonlinear systems. In Introduction to applied nonlinear dynamical systems and chaos, pp. 28-70. New York, NY: Springer Science & Business Media.
45. Strogatz S. 2000 Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering (studies in nonlinearity). Boulder, CO: Westview Press.
46. Paine RT. 1995 A conversation on refining the concept of keystone species. Conserv. Biol. 9, 962-964. (doi:10.1046/j.1523-1739.1995. 09040962.x)
47. Mills LS, Soulé ME, Doak DF. 1993 The keystonespecies concept in ecology and conservation. BioScience 43, 219-224. (doi:10.2307/1312122)
48. Alain K, Zbinden M, Le Bris N, Lesongeur F, Quérellou J, Gaill F, Cambon-Bonavita M-A. 2004 Early steps in microbial colonization processes at deep-sea hydrothermal vents. Environ. Microbiol. 6, 227-241. (doi:10.1111/j.1462-2920.2003.00557.x)
49. Guezennec J, Ortega-Morales O, Raguenes G, Geesey G. 1998 Bacterial colonization of artificial substrate in the vicinity of deep-sea hydrothermal vents. FEMS Microbiol. Ecol. 26, 89-99. (doi:10.1111/j. 1574-6941.1998.tb00495.x)
50. Goldmann DA, Leclair J, Macone A. 1978 Bacterial colonization of neonates admitted to an intensive care environment. J. Pediatrics 93, 288-293. (doi:10.1016/S0022-3476(78)80523-X)
51. Baty AM, Eastburn CC, Techkarnjanaruk S, Goodman AE, Geesey GG. 2000 Spatial and temporal variations in chitinolytic gene expression and bacterial biomass production during chitin degradation. Appl. Environ. Microbiol. 66, 3574-3585. (doi:10.1128/AEM.66.8.3574-3585.2000)
52. Sauer K, Camper AK, Ehrlich GD, Costerton JW, Davies DG. 2002 Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184, 1140-1154. (doi:10.1128/jb.184.4.1140-1154.2002)
53. Poltak SR, Cooper VS. 2011 Ecological succession in long-term experimentally evolved biofilms produces synergistic communities. ISME J. 5, 369-378. (doi:10.1038/ismej.2010.136)
54. Hall-Stoodley L, Costerton JW, Stoodley P. 2004 Bacterial biofilms: from the natural environment to infectious diseases. Nat. Rev. Microbiol. 2, 95-108. (doi:10.1038/nrmicro821)
55. Buchanan R, Whiting R, Damert W. 1997 When is simple good enough: a comparison of the Gompertz, Baranyi, and three-phase linear models for fitting bacterial growth curves. Food Microbiol. 14, 313-326. (doi:10.1006/fmic.1997.0125)
56. Koch AL. 1982 Multistep kinetics: choice of models for the growth of bacteria. J. Theor. Biol. 98, 401-417. (doi:10.1016/0022-5193(82)90127-8)
57. Kompala DS, Ramkrishna D, Jansen NB, Tsao GT. 1986 Investigation of bacterial growth on mixed substrates: experimental evaluation of cybernetic models. Biotechnol. Bioeng. 28, 1044-1055. (doi:10.1002/bit.260280715)
58. Berryman AA. 1992 The origins and evolution of predator-prey theory. Ecology 73, 1530-1535. (doi:10.2307/1940005)
59. Hanson FB, Tuckwell HC. 1981 Logistic growth with random density independent disasters. Theor. Popul. Biol. 19, 1-18. (doi:10.1016/0040-5809(81)90032-0)
60. Tsoularis A, Wallace J. 2002 Analysis of logistic growth models. Math. Biosci. 179, 21-55. (doi:10. 1016/S0025-5564(02)00096-2)
61. Verhulst PF. 1838 Notice sur la loi que la population suit dans son accroissement. Correspondance Mathématique et Physique Publiée par A Quetelet 10, 113-121.
62. Novak S, Chatterjee K, Nowak MA. 2013 Density games. J. Theor. Biol. 334, 26-34. (doi:10.1016/j. jtbi.2013.05.029)
63. Hibbing ME, Fuqua C, Parsek MR, Peterson SB. 2009 Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15-25. (doi:10.1038/nrmicro2259)
64. Bucci V, Bradde S, Biroli G, Xavier JB. 2012 Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput. Biol. 8, e1002497. (doi:10.1371/journal.pcbi. 1002497)
65. Wolf D, Vazirani V, Arkin A. 2005 A microbial modified prisoner's dilemma game: how frequencydependent selection can lead to random phase variation. J. Theor. Biol. 234, 255-262. (doi:10. 1016/j.jtbi.2004.11.021)
66. Trosvik P, Rudi K, N?s T, Kohler A, Chan KS, Jakobsen KS, Stenseth NC. 2008 Characterizing mixed microbial population dynamics using timeseries analysis. ISME J. 2, 707-715. (doi:10.1038/ismej.2008.36)
67. Hagen J, Wood W, Hashimoto T. 1982 In vitro stimulation of Bacteroides fragilis growth by Escherichia coli. Eur. J. Clin. Microbiol. 1, 338-343. (doi:10.1007/BF02019931)
68. Kurokawa S, Ihara Y. 2009 Emergence of cooperation in public goods games. Proc. R. Soc. B 276, 1379-1384. (doi:10.1098/rspb.2008.1546)
69. Gokhale CS, Traulsen A. 2010 Evolutionary games in the multiverse. Proc. Natl Acad. Sci. USA 107, 5500-5504. (doi:10.1073/pnas. 0912214107)
70. Gokhale CS, Traulsen A. 2014 Evolutionary multiplayer games. Dyn. Games Appl. 4, 468-488. (doi:10.1007/s13235-014-0106-2)
71. Sanchez C. 2011 Cellular microbiology: bacterial networking. Nat. Rev. Microbiol. 9, 229. (doi:10. 1038/nrmicro2543)
72. Dubey GP, Ben-Yehuda S. 2011 Intercellular nanotubes mediate bacterial communication. Cell 144, 590-600. (doi:10.1016/j.cell.2011.01.015)
73. Ohtsuki H. 2014 Evolutionary dynamics of nplayer games played by relatives. Phil. Trans. R. Soc. B 369, 20130359. (doi:10.1098/rstb. 2013.0359)
74. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006 Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc. Natl Acad. Sci. USA 103, 12 115-12 120. (doi:10.1073/pnas.0605127103)