The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Abstract

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (mmtb.brenda-enzymes.org (accessed on 9 Febraury 2021)), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

Reducing the Bacterial Lag Phase Through Methylated Compounds: Insights from Algal-Bacterial Interactions

“…This assumption is corroborated by the fact that P. inhibens is, like E. coli , a copiotrophic bacterium 95 with a single cell length of 1-2 µm 89 . To estimate ATP costs, we retrieved the growth-associated ATP maintenance costs (GAM) from the metabolic model of P. inhibens , which is given as 85 mmol ATP per gram dry weight 40 . Based on a dry weight of 280 fg per cell 39 , this equals 23,800 amol ATP per P. inhibens cell.…”

“…1C; gene 29). According to the provided growth-associated maintenance cost (GAM) in the metabolic model of P. inhibens 40 , a single P. inhibens cell requires 23,800 amol ATP to conduct one cell duplication during exponential growth with glucose. If a freshly initiated P. inhibens culture (25,000 CFU/mL) were to rely entirely on the dissimilation of DMSP methyl groups during the lag phase to meet its ATP requirements, the bacterial population would need 298 nM of DMSP to fulfill 100% of the ATP costs for one duplication.…”

Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1 T

“…The stoichiometric model was reconstructed bottom-up, based on the genome reannotation presented in this study and on the application of the integrative reaction lookup service of the Metano Modeling Toolbox (MMTB) ( 83 ). The reaction names were manually adjusted to include information on pathways and enzymes, as well as reaction identifiers from public databases.…”