Microbial Metabolic Engineering and Bioproduction

A nitrogen assimilation bottleneck can limit Bacillus subtilis growth in plant culture media

This study identifies a nitrogen assimilation bottleneck in Bacillus subtilis growth in plant culture media under shaking conditions.

Metabolic imbalance limits fermentation in microbes engineered for high-titer ethanol production

The paper identifies thermodynamic limitations in engineered microbial strains that prevent high-titer ethanol production by analyzing metabolite profiles and thermodynamic driving forces.

A comprehensive reference database to support untargeted metabolomics in Pseuudomonas putida

The paper develops a comprehensive metabolomics database for Pseudomonas putida to support untargeted metabolomics studies and enable molecular-level analysis.

OpenMebius2: GUI-based software for 13C-metabolic flux analysis with tracer labeling pattern suggestions for accurate flux predictions

OpenMebius2 is a GUI-based software for 13C-metabolic flux analysis that suggests tracer labeling patterns to improve flux prediction accuracy.

FASTERCC: Accelerating Flux Consistency Testing and Context-Specific Reconstruction for Large-Scale Metabolic Network Models

FASTERCC improves metabolic network analysis by accelerating flux consistency testing and reconstruction, reducing runtime by 20-fold for large networks.

Transcriptome-Driven Constraint-Based Modelling Reveals Metabolic Targets for Ovarian Cancer

This study uses transcriptome-driven constraint-based modeling to identify metabolic targets in ovarian cancer, revealing TPI1 as a potential therapeutic target supported by experimental validation.

Enabling Plasmid-based Expression in Clostridium kluyveri using a Biparental Methylation-Conjugation System

This paper develops a methylation-conjugation system for Clostridium kluyveri to enable plasmid-based genetic modification and demonstrates its use for expressing a fluorescent reporter.

Metabolic engineering of Methanothermobacter thermautotrophicus ΔH for recombinant acetoin production

This paper demonstrates the production of acetoin from H2 and CO2 in Methanothermobacter thermautotrophicus using an inducible promoter system, achieving stable acetoin yields in continuous cultivation.

GeNETop: Context-Specific Genome-Scale Constrained Models Using Network Topology, Flux Variability, and Transcriptomics

GeNETop improves context-specific metabolic models by integrating flux variability, network topology, and transcriptomics to enable dynamic simulations.

Production of the anticancer drug intermediate strictosidinic acid in engineered yeast

This paper engineers yeast to produce strictosidinic acid, a key anticancer drug intermediate, achieving 548 mg/L through metabolic pathway optimization and strain engineering.

Carbon-negative biosynthesis of pyrone and pyridine dicarboxylic acids from terephthalic acid via continuous mixotrophic gas fermentation in Cupriavidus necator H16

This paper describes a carbon-negative bioprocess using Cupriavidus necator H16 to convert terephthalic acid into value-added chemicals, achieving complete conversion to 2-pyrone-4,6-dicarboxylic acid.

Rhodo-Box: a Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides

The paper introduces Rhodo-Box, a toolkit for R. sphaeroides that provides standardized genetic parts and cloning workflows to enhance metabolic engineering.

Genetic modification of Clostridium kluyveri for heterologous n-butanol and n-hexanol production

This paper develops a genetic system for Clostridium kluyveri to enable heterologous production of n-butanol and n-hexanol through modified alcohol dehydrogenases.

Demonstrating and engineering the de novo synthesis of two aromatic chemicals estragole and anethole in Escherichia coli

This study engineers Escherichia coli to de novo synthesize estragole and anethole, achieving 246.88% and 202.44% increases in production compared to initial strains.

Enabling supratheoretical isopropanol yields from carbon-negative glucose fermentations with Clostridium acetobutylicum-Clostridium ljungdahlii cocultures

This study shows that high cell density cocultures of genetically modified Clostridium acetobutylicum and wild-type Clostridium ljungdahlii enable supratheoretical isopropanol yields from glucose fermentation.

Optimization of the glucosinolate core pathway for production of simple glucosinolates in Escherichia coli

This paper optimizes the glucosinolate biosynthesis pathway in E. coli to produce simple glucosinolates with high titers, achieving a 500-fold increase over yeast production.

A Required Sensitivity Analysis for Predictive Reliability of Genome-Scale Metabolic Networks: Probing Biomass, Nutrient Conditions, and Specialised Metabolism with Penicillium rubens as a Case Study

Bioconversion of p-coumaric acid to cis,cis-muconic acid using an engineered A. baylyi ADP1 - E. coli co-culture

This study engineers a co-culture of A. baylyi and E. coli to convert p-coumaric acid to cis,cis-muconic acid, achieving 18.55 mM ccMA with improved titres but highlighting metabolic pathway bottlenecks.

MuSHIN: A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction

MuSHIN improves genome-scale metabolic models by predicting missing reactions using a deep hypergraph learning method, enhancing their predictive accuracy and phenotypic predictions.

Comparison of different computational frameworks for metabolic modeling from single-cell transcriptomics data in glioblastoma

The paper compares three computational methods to infer metabolism from single-cell transcriptomics data in glioblastoma, finding tumor-associated macrophages as metabolically dominant.

Predicting strain-specific metabolic capabilities in the Genus Pseudomonas using a Flux-to-AI approach unravels hidden cell envelope properties.

Multiobjective design of growth media with genome-scale metabolic models and Bayesian optimization

This paper introduces gsMOBO, a computational method that uses genome-scale metabolic models and Bayesian optimization to design cost-effective and productive culture media by optimizing nutrient combinations across high-dimensional spaces.

Development of autotrophy in Escherichia coli through adaptive laboratory evolution

This study achieves autotrophy in E. coli through adaptive laboratory evolution, identifying mutations and gene expression changes that enable CO2 fixation.

Metabolic engineering of Escherichia coli strains for the in vivo synthesis of GP-mediated oligosaccharides

This paper describes the metabolic engineering of E. coli to produce β-mannobiose and laminaribiose from mannose, achieving high product titers and yields through pathway optimization.

Systematic Analysis of Human Tissue- and Cell-Specific Metabolic Models Identifies High-Sugar, High Fat Diet Induced Liver Dysregulation

The paper constructs tissue- and cell-type-specific metabolic models to study the effects of a high-sugar, high-fat diet on liver metabolism, revealing metabolic reprogramming and dysfunction.

M9 Medium Composition Alters E. coli Metabolism During Recombinant Expression

This study examines how different M9-based media compositions affect E. coli metabolism during recombinant protein expression, finding that M9++ reduces overflow metabolites and promotes biosynthesis.

Vibrio natriegens is sensitive to its acidic fermentation products

This study compares the fermentative physiology of Vibrio natriegens and Escherichia coli, finding that V. natriegens is more sensitive to its acidic fermentation products due to lacking acid resistance genes.

Design-Build-Test-Learn guided engineering of a whole-cell pyruvate biosensor based on transcription factor

The paper develops a pyruvate biosensor in E. coli using Design-Build-Test-Learn cycles, achieving improved dynamic range and reduced leaky expression.

Simultaneous optimization of lignocellulosic sugar catabolism via systematic laboratory evolution in dynamic conditions

This study evolves a microbial strain under dynamic conditions to optimize sugar catabolism, finding that mixed-sugar environments promote stable retention and coordinated optimization of multiple pathways.

Evaluating Transcriptomic Integration for Cyanobacterial Constraint-based Metabolic Modelling

The paper evaluates transcriptomic integration methods for cyanobacterial metabolic models, finding that method selection depends on model configuration and that certain approaches improve flux predictions.