Synthetic Ecology of Microbes: Mathematical Models and Applications

Zomorrodi, Ali R.; Segrè, Daniel

doi:10.1016/j.jmb.2015.10.019

Title: Synthetic Ecology of Microbes: Mathematical Models and Applications

Abstract

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

Authors:: Zomorrodi, Ali R.; Segrè, Daniel

Publication Date:: Mon Feb 01 00:00:00 EST 2016

Research Org.:: Boston Univ., MA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1251757

Alternate Identifier(s):: OSTI ID: 1436508

Grant/Contract Number:: SC0012627

Resource Type:: Published Article

Journal Name:: Journal of Molecular Biology

Additional Journal Information:: Journal Name: Journal of Molecular Biology Journal Volume: 428 Journal Issue: 5 PB; Journal ID: ISSN 0022-2836

Publisher:: Elsevier

Country of Publication:: United Kingdom

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Microbial communities; Synthetic Biology; Systems Biology; Metabolic network modeling; Metabolic engineering

Citation Formats


                    Zomorrodi, Ali R., and Segrè, Daniel. Synthetic Ecology of Microbes: Mathematical Models and Applications.  United Kingdom: N. p., 2016. 
Web.  doi:10.1016/j.jmb.2015.10.019.

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                    Zomorrodi, Ali R., & Segrè, Daniel. Synthetic Ecology of Microbes: Mathematical Models and Applications.  United Kingdom.  https://doi.org/10.1016/j.jmb.2015.10.019

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                    Zomorrodi, Ali R., and Segrè, Daniel. Mon .  
"Synthetic Ecology of Microbes: Mathematical Models and Applications".  United Kingdom.  https://doi.org/10.1016/j.jmb.2015.10.019.

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@article{osti_1251757,

  title        = {Synthetic Ecology of Microbes: Mathematical Models and Applications},

  author       = {Zomorrodi, Ali R. and Segrè, Daniel},

  abstractNote = {As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.},

  doi          = {10.1016/j.jmb.2015.10.019},

  journal      = {Journal of Molecular Biology},

  number       = 5 PB,

  volume       = 428,

  place        = {United Kingdom},

  year         = {Mon Feb 01 00:00:00 EST 2016},

  month        = {Mon Feb 01 00:00:00 EST 2016}

}

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Title: Synthetic Ecology of Microbes: Mathematical Models and Applications

Abstract

Citation Formats

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