Literature DB >> 36215322

Chaos in synthetic microbial communities.

Behzad D Karkaria1, Angelika Manhart2, Alex J H Fedorec1, Chris P Barnes1.   

Abstract

Predictability is a fundamental requirement in biological engineering. As we move to building coordinated multicellular systems, the potential for such systems to display chaotic behaviour becomes a concern. Therefore understanding which systems show chaos is an important design consideration. We developed a methodology to explore the potential for chaotic dynamics in small microbial communities governed by resource competition, intercellular communication and competitive bacteriocin interactions. Our model selection pipeline uses Approximate Bayesian Computation to first identify oscillatory behaviours as a route to finding chaotic behaviour. We have shown that we can expect to find chaotic states in relatively small synthetic microbial systems, understand the governing dynamics and provide insights into how to control such systems. This work is the first to query the existence of chaotic behaviour in synthetic microbial communities and has important ramifications for the fields of biotechnology, bioprocessing and synthetic biology.

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Year:  2022        PMID: 36215322      PMCID: PMC9584520          DOI: 10.1371/journal.pcbi.1010548

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.779


  36 in total

1.  Experimental demonstration of chaos in a microbial food web.

Authors:  Lutz Becks; Frank M Hilker; Horst Malchow; Klaus Jürgens; Hartmut Arndt
Journal:  Nature       Date:  2005-06-30       Impact factor: 49.962

2.  Chaos in a long-term experiment with a plankton community.

Authors:  Elisa Benincà; Jef Huisman; Reinhard Heerkloss; Klaus D Jöhnk; Pedro Branco; Egbert H Van Nes; Marten Scheffer; Stephen P Ellner
Journal:  Nature       Date:  2008-02-14       Impact factor: 49.962

3.  Designing microbial consortia with defined social interactions.

Authors:  Wentao Kong; David R Meldgin; James J Collins; Ting Lu
Journal:  Nat Chem Biol       Date:  2018-06-25       Impact factor: 15.040

4.  Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions.

Authors:  Babak Momeni; Li Xie; Wenying Shou
Journal:  Elife       Date:  2017-03-28       Impact factor: 8.140

5.  Bayesian design of synthetic biological systems.

Authors:  Chris P Barnes; Daniel Silk; Xia Sheng; Michael P H Stumpf
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-29       Impact factor: 11.205

6.  Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production.

Authors:  Chao Ye; Wei Zou; Nan Xu; Liming Liu
Journal:  J Biotechnol       Date:  2014-05-09       Impact factor: 3.307

7.  A comparative analysis of industrial Escherichia coli K-12 and B strains in high-glucose batch cultivations on process-, transcriptome- and proteome level.

Authors:  Karoline Marisch; Karl Bayer; Theresa Scharl; Juergen Mairhofer; Peter M Krempl; Karin Hummel; Ebrahim Razzazi-Fazeli; Gerald Striedner
Journal:  PLoS One       Date:  2013-08-08       Impact factor: 3.240

8.  Automated design of synthetic microbial communities.

Authors:  Behzad D Karkaria; Alex J H Fedorec; Chris P Barnes
Journal:  Nat Commun       Date:  2021-01-28       Impact factor: 14.919

9.  Chaos in high-dimensional dissipative dynamical systems.

Authors:  Iaroslav Ispolatov; Vaibhav Madhok; Sebastian Allende; Michael Doebeli
Journal:  Sci Rep       Date:  2015-07-30       Impact factor: 4.379

Review 10.  SciPy 1.0: fundamental algorithms for scientific computing in Python.

Authors:  Pauli Virtanen; Ralf Gommers; Travis E Oliphant; Matt Haberland; Tyler Reddy; David Cournapeau; Evgeni Burovski; Pearu Peterson; Warren Weckesser; Jonathan Bright; Stéfan J van der Walt; Matthew Brett; Joshua Wilson; K Jarrod Millman; Nikolay Mayorov; Andrew R J Nelson; Eric Jones; Robert Kern; Eric Larson; C J Carey; İlhan Polat; Yu Feng; Eric W Moore; Jake VanderPlas; Denis Laxalde; Josef Perktold; Robert Cimrman; Ian Henriksen; E A Quintero; Charles R Harris; Anne M Archibald; Antônio H Ribeiro; Fabian Pedregosa; Paul van Mulbregt
Journal:  Nat Methods       Date:  2020-02-03       Impact factor: 28.547

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