Synthetic Ecology of Microbes: Mathematical Models and Applications. Issue 5 (27th February 2016)

• Record Type: Journal Article
• Authors: Zomorrodi, Ali R.; Segrè, Daniel
• Is Part Of: Journal of molecular biology. Volume 428:Issue 5 Part B(2016:Mar. 01)
• Page Start: 837
• Page End: 861
• Publication Date: 2016-02-27
• Subjects: RRT resource ratio theory -- MPP maximum power principle -- BQH Black Queen Hypothesis -- LV Lotka–Volterra -- ODE ordinary differential equation -- PDE partial deferential equation -- IbM individual-based model -- FBA flux balance analysis -- dFBA dynamic FBA -- DMMM dynamic multispecies metabolic modeling; Microbial communities -- Synthetic Biology -- Systems Biology -- Metabolic network modeling -- Metabolic engineering; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2015.10.019
• Languages: English
• ISSNs: 0022-2836

Abstract

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. Finally, 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. Graphical abstract: Highlights: Synthetic microbial consortia are implicated in environmental sustainability and biomedicine Mathematical models are an essential tool for the rational design of synthetic ecosystems A main goal is to infer community outputs and interactions based on genomes Faster computation, data/model integration and standardization needed for progress