Article
Biotechnology & Applied Microbiology
Hao Luo, Peishun Li, Boyang Ji, Jens Nielsen
Summary: The hybrid cybernetic model (HCM) approach is a dynamic modeling framework that integrates enzyme synthesis and activity regulation. It has been widely used in bioreaction engineering, especially for simulating microbial growth in different carbon source mixtures. The HCM strategy presented in this study introduces an optimized yield analysis algorithm (opt-yield-FBA) to simulate metabolic dynamics at the genome scale without the need for elementary flux modes (EFMs) calculation. The opt-yield-FBA algorithm can calculate optimal yield solutions and yield space for genome-scale metabolic models (GEMs).
METABOLIC ENGINEERING
(2023)
Review
Microbiology
Jack Jansma, Sahar El Aidy
Summary: Through in silico simulation methods based on flux balance analysis, interactions within the complex microbiota community in the human gut can be better investigated, aiding in understanding the intricate relationship between microbiota and the host. This approach can help researchers study the effects of various perturbations on different bacterial species in a shared metabolic environment, ultimately leading to improvements in human health.
Article
Multidisciplinary Sciences
Angelo Lucia, Emily Ferrarese, Korkut Uygun
Summary: In this article, a Nash Equilibrium approach is used to model and simulate the static cold storage and warm ischemia of a proposed model of liver cells. The results show that the Nash Equilibrium approach provides a good match to experimental data for energy depletion and that the uncertainty in model parameters is very small.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Ilija Dukovski, Djordje Bajic, Jeremy M. Chacon, Michael Quintin, Jean C. C. Vila, Snorre Sulheim, Alan R. Pacheco, David B. Bernstein, William J. Riehl, Kirill S. Korolev, Alvaro Sanchez, William R. Harcombe, Daniel Segre
Summary: The genome-scale stoichiometric modeling of metabolism is a standard systems biology tool, with extensions like COMETS providing simulations of multiple microbial species in complex environments. The new version of COMETS incorporates a more accurate biophysical model and user-friendly interfaces for compatibility with COBRA models, making it a valuable tool for studying microbial communities.
Article
Food Science & Technology
Omer Sabach, Keren Buhnik-Rosenblau, Inbar Kesten, Shay Freilich, Shiri Freilich, Yechezkel Kashi
Summary: This study demonstrates the potential of genome-scale metabolic modeling (GEMs) in studying sourdough microbial communities. In-silico modeling was used to investigate the relationship between bacterial compositions and sourdough phenotypes. The results show that Pediococcus spp. - Lb. sakei group is associated with increased yeast cell counts and fermentation rates, providing a novel strategy for designing sourdough starter communities.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Microbiology
Muberra Fatma Cesur, Tunahan Cakir, Pinar Pir
Summary: Saccharomyces cerevisiae undergoes robust oscillations and metabolic alterations to adapt and survive under nutrient-limited conditions. This study used ATAC-seq data to enhance the predictive capability of metabolic modeling for the yeast metabolic cycle. Epigenetic information can contribute to accurate metabolic simulations.
Editorial Material
Plant Sciences
Nicholas J. Kruger, R. George Ratcliffe
Summary: Stable isotope labeling experiments provide opportunities for probing metabolic pathways, and metabolic flux analysis (MFA) is commonly used in prokaryotes but more challenging in plants. Constrains-based modeling for simulating network fluxes offers a versatile approach for exploring network capabilities, while MFA can be best utilized to probe interesting features revealed by simulation.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Maciek R. Antoniewicz
Summary: Metabolic engineering aims to improve biological production by designing and optimizing metabolic pathways, quantifying metabolic fluxes, and analyzing metabolic network models; essential concepts include metabolic network models and metabolic fluxes; in recent years, advancements in technology and methods have allowed for a deeper understanding of the capabilities of biological systems.
METABOLIC ENGINEERING
(2021)
Review
Microbiology
Christian Diener, Sean M. Gibbons
Summary: Microbial consortia play a crucial role in various essential processes, but it is challenging to understand their functional capacities based on their composition alone. Community-scale metabolic models have the potential to simulate complex microbial communities, but there is no consensus on the fitness function and community-wide growth. Transitioning from single-taxon models to multitaxon models poses challenges as well. Dynamic approaches are a solution but are computationally expensive, while two steady-state approaches provide ecologically relevant solutions with improved scalability.
Article
Biochemistry & Molecular Biology
Blas Blazquez, David San Leon, Antonia Rojas, Marta Tortajada, Juan Nogales
Summary: In this study, a high-quality genome-scale model (iBB1018) was constructed for accurate prediction of metabolic capabilities in B. subtilis. The model showed great accuracy in predicting carbon source utilization and identified potential novel carbon sources. Furthermore, the model was used for constructing the panphenome of B. subtilis, revealing the large metabolic versatility of the species and the importance of accessory metabolism at a species level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Juan C. Villada, Maria F. Duran, Chee Kent Lim, Lisa Y. Stein, Patrick K. H. Lee
Summary: The study constructed a genome-scale metabolic model for Methylomicrobium album BG8, highlighting the importance of the ratio between oxygen and methane uptake for optimal growth. The results revealed a coupling between biomass production and carbon dioxide excretion, as well as a trade-off between biomass and acetate production. The integrative model developed in this study will aid in metabolic engineering and the development of a methane bioconversion platform.
Review
Engineering, Chemical
Philippe Bogaerts, Alain Vande Wouwer
Summary: Metabolic flux analysis is often faced with system underdeterminacy, with various methods proposed to tackle this issue, including flux pathway analysis, flux balance analysis, flux variability analysis, and sampling.
Article
Biochemical Research Methods
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loic Pauleve, Anne Siegel
Summary: This study presents a novel approach to infer Boolean rules for metabolic regulation from time-series data and a prior knowledge network (PKN). By combining answer set programming and linear programming, candidate Boolean regulations that can reproduce the given data are generated. The quality of predictions depends on the available time-series data, such as kinetic, fluxomics or transcriptomics data.
Review
Biotechnology & Applied Microbiology
Varshit Dusad, Denise Thiel, Mauricio Barahona, Hector C. Keun, Diego A. Oyarzun
Summary: Metabolism is crucial for cell growth, composed of thousands of reactions at the genome-scale. Flux Balance Analysis and network science are two complementary strategies for analyzing genome-scale metabolic models, offering insights into the structure and function of metabolic systems. Integration of both approaches can deliver comprehensive understanding with implications in discovery science, precision medicine, and industrial biotechnology.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Daniel J. Lugar, Sean G. Mack, Ganesh Sriram
Summary: Flux balance analysis (FBA) is a powerful method for predicting cell-wide metabolic activity, but interpreting the resulting flux vector can be challenging. The NetRed algorithm systematically reduces a stoichiometric matrix and flux vector to a more easily interpretable form, providing transparent and lossless simplification for metabolic networks. This reduction allows users to quickly identify metabolites and reaction pathways of interest with simplified presentation.
METABOLIC ENGINEERING
(2021)