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.

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 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.

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.

Genetic engineering of virus resistance: a successful genetical alchemy

1992 ◽  
Vol 99 (3-4) ◽  
pp. 61-77
Author(s):  
B. D. Harrison
Keyword(s):  
Genetic Engineering ◽  
Resistance Genes ◽  
Virus Resistance ◽  
Crop Improvement ◽  
Genetically Engineered ◽  
Satellite Rna ◽  
Virus Diseases ◽  
Naturally Occurring ◽  
Resistance To Infection ◽  
Specific Tolerance

SynopsisSome of the most successful early applications of genetic engineering in crop improvement have been in the production of virus-resistant plants. This has been achieved not by the transfer of naturally occurring resistance genes from one plant species or variety to another but by transformation with novel resistance genes based on nucleotide sequences derived from the viruses themselves or from virus-associated nucleic acids. Transformation of plants with a DNA copy of the particle protein gene of viruses that have positive-sense single-stranded RNA genomes typically confers resistance to infection with the homologous and closely related viruses. Transformation with a gene that is transcribed to produce a benign viral satellite RNA can confer virus-specific tolerance of infection. In addition, recent work with viral poly-merase gene-related sequences offers much promise, and research is active on other strategies such as the use of virus-specific ribozymes.Already the field trialling of plants incorporating transgenic virus resistance has begun, with encouraging results, and effects on virus spread are being studied. Deployment strategies for the resistant plants must now be devised and the conjectural hazards of growing them assessed. Genetically engineered virus resistance promises to make a major contribution to the control of plant virus diseases by non-chemical methods.

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 Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Pengfan Zhang ◽  
Stjin Spaepen ◽  
Yang Bai ◽  
Stephane Hacquard ◽  
Ruben Garrido-Oter
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Polymorphic Variation ◽  
Sequencing Data ◽  
Sequencing Errors ◽  
Extensive Evaluation ◽  
Culture Independent ◽  
Reference Sequences ◽  
Synthetic Microbial Communities

AbstractSynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.

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