Synthetic biology tools to engineer microbial communities for biotechnology

NS McCarty, R Ledesma-Amaro - Trends in biotechnology, 2019 - cell.com
Microbial consortia have been used in biotechnology processes, including fermentation,
waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly …

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

NE Lewis, H Nagarajan, BO Palsson - Nature Reviews Microbiology, 2012 - nature.com
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

AR Zomorrodi, CD Maranas - PLoS computational biology, 2012 - journals.plos.org
Microorganisms rarely live isolated in their natural environments but rather function in
consolidated and socializing communities. Despite the growing availability of high …

Engineering microbial consortia for controllable outputs

SR Lindemann, HC Bernstein, HS Song… - The ISME …, 2016 - academic.oup.com
Much research has been invested into engineering microorganisms to perform desired
biotransformations; nonetheless, these efforts frequently fall short of expected results due to …

Environments that induce synthetic microbial ecosystems

N Klitgord, D Segrè - PLoS computational biology, 2010 - journals.plos.org
Interactions between microbial species are sometimes mediated by the exchange of small
molecules, secreted by one species and metabolized by another. Both one-way …

Synthetic ecology of microbes: mathematical models and applications

AR Zomorrodi, D Segrè - Journal of molecular biology, 2016 - Elsevier
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 …

Trait-based modelling in ecology: a review of two decades of research

L Zakharova, KM Meyer, M Seifan - Ecological Modelling, 2019 - Elsevier
Trait-based approaches are an alternative to species-based approaches for functionally
linking individual organisms with community structure and dynamics. In the trait-based …

Challenges and perspectives of polyhydroxyalkanoate production from microalgae/cyanobacteria and bacteria as microbial factories: an assessment of hybrid …

R Afreen, S Tyagi, GP Singh, M Singh - Frontiers in Bioengineering …, 2021 - frontiersin.org
Polyhydroxyalkanoates (PHAs) are the biopolymer of choice if we look for a substitute of
petroleum-based non-biodegradable plastics. Microbial production of PHAs as carbon …

Towards synthetic microbial consortia for bioprocessing

J Shong, MRJ Diaz, CH Collins - Current Opinion in Biotechnology, 2012 - Elsevier
The use of microbial consortia for bioprocessing has been limited by our ability to reliably
control community composition and function simultaneously. Recent advances in synthetic …

Machine learning for the advancement of genome-scale metabolic modeling

P Kundu, S Beura, S Mondal, AK Das, A Ghosh - Biotechnology Advances, 2024 - Elsevier
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
interrelations between genotype, phenotype, and external environment. The recent …