Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics

L Li, J Nielsen, Y Chen - Current Opinion in Biotechnology, 2025 - Elsevier
Highlights•GEMs serve as knowledge resources of gut microbiome.•Community-level GEMs
allow to design synthetic microbial community.•Personalized modeling could characterize …

[HTML][HTML] ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models

Z Mao, J Niu, J Zhao, Y Huang, K Wu, L Yun… - Synthetic and systems …, 2024 - Elsevier
Genome-scale metabolic models (GEMs) have been widely employed to predict
microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading …

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

WT Scott Jr, S Benito-Vaquerizo… - PLoS Computational …, 2023 - journals.plos.org
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from
healthcare to biotechnology to environmental remediation. To fully realize this potential, it is …

FROG analysis ensures the reproducibility of genome scale metabolic models

K Raman, M Kratochvil, BG Olivier, M Konig… - bioRxiv, 2024 - biorxiv.org
Genome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a
pivotal role in understanding biological phenotypes and advancing research in areas like …

Deciphering lipid mutant phenotypes with a new genome-scale metabolic model of Microchloropsis gaditana encompassing detailed lipid metabolism

C Dupont-Thibert, S Carneiro, B Pereira, R Carreira… - bioRxiv, 2023 - biorxiv.org
The oleaginous microalga Microchloropsis gaditana (formerly Nannochloropsis gaditana)
has gained large interest due to its potential to produce lipids for a wide range of …

lista-GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi

E Almeida, M Ferreira, W Silveira - bioRxiv, 2023 - biorxiv.org
Oleaginous yeasts cultivation in low-cost substrates is an alternative for more sustainable
production of lipids and oleochemicals. Lipomyces starkeyi accumulates high amounts of …

Modélisation du métabolisme de la microalgue oléagineuse d'intérêt industriel Microchloropsis gaditana

CD Thibert - 2023 - theses.hal.science
Contexte: Les microalgues ont un fort potentiel d'applications dans le domaine des
biotechnologies industrielles. Leur capacité par exemple à produire des lipides à partir de …

Model-driven design of synthetic microbial communities for the upcycling of One-Carbon feedstocks

SB Vaquerizo - 2023 - search.proquest.com
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable
production of commodity chemicals. To date, syngas fermentation focuses mainly on the use …