Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications

PT van Leeuwen, S Brul, J Zhang… - FEMS Microbiology …, 2023‏ - academic.oup.com
The human gut harbors native microbial communities, forming a highly complex ecosystem.
Synthetic microbial communities (SynComs) of the human gut are an assembly of …

[HTML][HTML] 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 …

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 …

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

A Heinken, DA Ravcheev, F Baldini, L Heirendt… - Microbiome, 2019‏ - Springer
Background The human gut microbiome performs important functions in human health and
disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of …

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 …

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 …

[HTML][HTML] Optimization and scale-up of fermentation processes driven by models

YH Du, MY Wang, LH Yang, LL Tong, DS Guo, XJ Ji - Bioengineering, 2022‏ - mdpi.com
In the era of sustainable development, the use of cell factories to produce various
compounds by fermentation has attracted extensive attention; however, industrial …

[HTML][HTML] Metabolic modelling approaches for describing and engineering microbial communities

B García-Jiménez, J Torres-Bacete… - Computational and …, 2021‏ - Elsevier
Microbes do not live in isolation but in microbial communities. The relevance of microbial
communities is increasing due to growing awareness of their influence on a huge number of …

[HTML][HTML] Metabolic engineering of human gut microbiome: recent developments and future perspectives

P Li, S Roos, H Luo, B Ji, J Nielsen - Metabolic Engineering, 2023‏ - Elsevier
Many studies have demonstrated that the gut microbiota is associated with human health
and disease. Manipulation of the gut microbiota, eg supplementation of probiotics, has been …

Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion

L Lin - Biotechnology for Biofuels and Bioproducts, 2022‏ - Springer
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition
and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for …