scholarly journals Chaos in small microbial communities

2021 ◽  
Author(s):  
Behzad D Karkaria ◽  
Angelika Manhart ◽  
Alex J H Fedorec ◽  
Chris P Barnes
Keyword(s):  
Microbial Communities ◽  
Chaotic Dynamics ◽  
Resource Competition ◽  
Chaotic Behaviour ◽  
Design Consideration ◽  
Biological Engineering ◽  
Microbial Systems ◽  
Important Design ◽  
Synthetic Microbial Communities ◽  
Fundamental Requirement

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. We show 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.

scholarly journals Automated design of synthetic microbial communities

2020 ◽  
Author(s):  
Behzad D. Karkaria ◽  
Alex J. H. Fedorec ◽  
Chris P. Barnes
Keyword(s):  
Microbial Communities ◽  
Bayesian Methods ◽  
Stable Steady State ◽  
Naturally Occurring ◽  
Important Interaction ◽  
Model Spaces ◽  
Functional Complexity ◽  
Microbial Systems ◽  
Synthetic Microbial Communities ◽  
Functional Output

AbstractIn naturally occurring microbial systems, species rarely exist in isolation. There is strong ecological evidence for a positive relationship between species diversity and the functional output of communities. The pervasiveness of these communities in nature highlights that there may be advantages for engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigates issues often found in engineering a monoculture, especially when functional complexity is increasing. Here, we demonstrate a methodology for designing robust synthetic communities that use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We explore model spaces for two and three strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and tuning the community composition.

scholarly journals Automated design of synthetic microbial communities

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Behzad D. Karkaria ◽  
Alex J. H. Fedorec ◽  
Chris P. Barnes
Keyword(s):  
Microbial Communities ◽  
Bayesian Methods ◽  
Positive Relationship ◽  
Genetically Engineered ◽  
Stable Steady State ◽  
Naturally Occurring ◽  
Important Interaction ◽  
Functional Complexity ◽  
Microbial Systems ◽  
Synthetic Microbial Communities

AbstractMicrobial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between species diversity and productivity of communities. The pervasiveness of these communities in nature highlights possible advantages for genetically engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially as functional complexity increases. Here, we demonstrate a methodology for designing robust synthetic communities that include competition for nutrients, and use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We computationally explore all two- and three- strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and further tuning the community composition.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

scholarly journals Sabot Front Borerider Stiffness vs. Dispersion: Finding the Knee in the Curve

2001 ◽  
Vol 8 (3-4) ◽  
pp. 193-201 ◽  
Author(s):  
Alan F. Hathaway ◽  
John R. Burnett Jr.
Keyword(s):  
Dispersion Curve ◽  
Analytical Approach ◽  
Design Consideration ◽  
Dispersion Characteristics ◽  
Radial Stiffness ◽  
The Subject ◽  
Important Design

In the design of armor piercing, fin-stabilized, discarding sabot projectiles, the radial stiffness of the sabot front borerider has a significant impact on the projectile's dispersion and is, therefore, an important design consideration. Whether designing a new projectile or trying to improve an existing design, projectile designers can achieve front borerider stiffness without understanding its affect on dispersion characteristics. There is a knee in the stiffness vs. dispersion curve at which a change in the sabot front borerider stiffness will have a significant impact on dispersion or no impact at all depending on whether the stiffness is increased or decreased. The subject of this paper is an analytical approach to quantitatively determine the knee in the curve. Results from using this approach on the M865 APFSDS projectile are also presented.

scholarly journals Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristal Zuñiga ◽  
Tingting Li ◽  
Michael T. Guarnieri ◽  
Jackson P. Jenkins ◽  
Chien-Ting Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sustainable Growth ◽  
Synthetic Microbial Communities

scholarly journals Massively parallel screening of synthetic microbial communities

2019 ◽  
Vol 116 (26) ◽  
pp. 12804-12809 ◽  
Author(s):  
Jared Kehe ◽  
Anthony Kulesa ◽  
Anthony Ortiz ◽  
Cheri M. Ackerman ◽  
Sri Gowtham Thakku ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Massively Parallel ◽  
Phenotypic Characterization ◽  
Interspecies Interactions ◽  
Additional Species ◽  
Plant Symbiont ◽  
Complementary Approach ◽  
Potential Applications ◽  
Synthetic Microbial Communities

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiontHerbaspirillum frisingensein a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.

scholarly journals Metabolic dependencies drive species co-occurrence in diverse microbial communities

2015 ◽  
Vol 112 (20) ◽  
pp. 6449-6454 ◽  
Author(s):  
Aleksej Zelezniak ◽  
Sergej Andrejev ◽  
Olga Ponomarova ◽  
Daniel R. Mende ◽  
Peer Bork ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Resource Competition ◽  
Critical Role ◽  
Metabolic Modeling ◽  
Cooperative Groups ◽  
Cooperative Interactions ◽  
A Genome ◽  
Group Survival ◽  
Metabolic Interactions ◽  
Genome Scale

Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated in community assembly. The prevalence of metabolic interactions in microbial communities, however, has remained largely unknown. Here, we systematically survey, by using a genome-scale metabolic modeling approach, the extent of resource competition and metabolic exchanges in over 800 communities. We find that, despite marked resource competition at the level of whole assemblies, microbial communities harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced metabolic exchanges in these co-occurring subcommunities we also predict the likely exchanged metabolites, such as amino acids and sugars, that can promote group survival under nutritionally challenging conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence and hint at cooperative groups as recurring modules of microbial community architecture.

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