A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

I Dukovski, D Bajić, JM Chacón, M Quintin, JCC Vila… - Nature protocols, 2021 - nature.com
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Strategies for tailoring functional microbial synthetic communities

J **g, P Garbeva, JM Raaijmakers… - The ISME …, 2024 - academic.oup.com
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are
important for plant growth and health. The vast diversity of soil microorganisms and their …

Engineering agricultural soil microbiomes and predicting plant phenotypes

CA Berruto, GS Demirer - Trends in Microbiology, 2024 - cell.com
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use
efficiency, plant tolerance to stressors, and confer benefits to future generations of crops …

Bioengineered microbial strains for detoxification of toxic environmental pollutants

Q Maqsood, A Sumrin, R Waseem, M Hussain… - Environmental …, 2023 - Elsevier
Industrialization and other anthropogenic human activities pose significant environmental
risks. As a result of the hazardous pollution, numerous living organisms may suffer from …

Microplastic accumulation and degradation in environment via biotechnological approaches

S Thakur, S Mathur, S Patel, B Paital - Water, 2022 - mdpi.com
The extensive use of plastics in daily life has led to the generation of huge amounts of plastic
waste, which causes an enormous burden on the environment. More than half of the plastic …

Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates

MP Mezzina, MT Manoli, MA Prieto… - Biotechnology …, 2021 - Wiley Online Library
Growing environmental concern sparks renewed interest in the sustainable production of
(bio) materials that can replace oil‐derived goods. Polyhydroxyalkanoates (PHAs) are …

[HTML][HTML] Toward merging bottom–up and top–down model-based designing of synthetic microbial communities

D San León, J Nogales - Current Opinion in Microbiology, 2022 - Elsevier
Highlights•Analysis and designing of microbiomes have become a new paradigm in
microbiology.•Understanding and rational engineering of microbiomes require model-based …

[HTML][HTML] Computational modeling of metabolism in microbial communities on a genome-scale

AV Colarusso, I Goodchild-Michelman, M Rayle… - Current Opinion in …, 2021 - Elsevier
Computational modeling of microbial communities using GEnome-scale Models (GEMs) of
metabolism is a new frontier in systems biology. Here, we discuss recent developments in …

[HTML][HTML] Advances in constraint-based modelling of microbial communities

A Heinken, A Basile, I Thiele - Current Opinion in Systems Biology, 2021 - Elsevier
Microbial communities are near universally present in nature. A wealth of meta-omics data
has been gathered from numerous ecosystems, such as the human gut, ocean or soil …

Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform

Y Liu, B Xue, H Liu, S Wang, H Su - Biotechnology Advances, 2024 - Elsevier
The rapid development of synthetic biology has significantly improved the capabilities of
mono-culture systems in converting different substrates into various value-added bio …