Microbial Metabolic Engineering and Bioproduction

MicroGrowAgents: An Agentic AI System for Microbial Cultivation Engineering

MicroGrowAgents is an agentic AI system that designs microbial growth media using structured knowledge and experimental design, identifying optimal conditions for Methylorubrum extorquens AM1.

Statistical learning of bacterial growth in combinatorially constructed environments

The paper measures bacterial growth in combinatorial nutrient environments to estimate resource interactions and shows that simple models can predict growth in novel conditions.

Curating MitoCore: A Standardized Small-Scale Human Metabolic Model as Platform for Proteomics Integration and Disease Modeling

Re-annotated MitoCore (SBML3, UniProt, EC, Human-GEM gene rules) supports sMOMENT proteomics integration, reducing thrombocyte ATP prediction error by 89% relative to the original model.

Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities

The paper introduces minimal metabolic pathways to enable scalable analysis of metabolic subnetworks in organisms and communities.

CarveMe-GutMicrobes: Automated Metabolic Model Reconstruction for Gut Microbial Species and Communities

CarveMe-GutMicrobes reconstructs genome-scale metabolic models for gut microbes from genomic data, showing high accuracy in predicting gene essentiality and metabolite secretion.

From plasmid sequence to process design: A computational analysis of metabolism in the context of plasmid DNA manufacturing

The paper uses computational analysis to link plasmid design features to metabolic changes in E. coli, revealing correlations between promoter strength, copy number, and pDNA productivity.

Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles

This study uses in-silico DBTL cycles to evaluate how process parameters affect strain optimization outcomes in metabolic engineering.

Comp2GPR: A Sequence-Driven Framework for Gene.Protein-Reaction Rule Reconstruction

Comp2GPR improves gene-protein-reaction rules by integrating curated protein complex data with sequence-based validation, enhancing metabolic model accuracy.

High-Yield Recovery of Reactive Nitrogen as Cyanophycin by Engineering Acinetobacter baylyi ADP1 under Wastewater-Relevant Conditions

This study engineers Acinetobacter baylyi to produce cyanophycin from wastewater nutrients, achieving high yields without arginine supplementation and expanding temperature tolerance.

On the conditions for shifts in metabolic strategies

The paper derives conditions under which microorganisms shift to an inefficient overflow metabolism above a critical growth rate, using a core metabolic model and validating it with yeast data.

Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy.

The paper develops a theory linking cell geometry, membrane protein crowding, and metabolic traits in E. coli, validated through experimental data.

Expanding the Promoter Toolbox for Metabolic Engineering in the Lignocellulolytic Thermophile Anaerocellum bescii

This study identifies and characterizes new promoters in Anaerocellum bescii to enhance metabolic engineering capabilities for ethanol production.

Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes

This study investigates how Pseudomonas putida uses two transhydrogenases to maintain redox balance across different metabolic conditions, revealing their essential roles in growth and stress tolerance.

Dynamic balance of sparse flux vectors for efficient simulation of culture dynamics and metabolic network reduction

This paper introduces DFVB, a method that reduces computational costs of DFBA by using sparse flux vectors, achieving faster simulations and better pathway identification.

SIMOFF: Discovering the metabolic objective of the cell

SIMOFF infers metabolic objectives from flux data, improving gene essentiality predictions in yeast and CHO cells.

13C flux ratio analysis with FRAPPPE reveals differences in metabolic fluxes between gut Bacteroidota and Escherichia coli

This study uses FRAPPPE to analyze metabolic flux differences between gut Bacteroidota and E. coli, revealing distinct metabolic patterns under anaerobic conditions and in co-metabolism of nucleosides.

Enzyme-Constrained Metabolic Modeling of the Tripartite Synapse Links Astrocyte-Neuron Lactate Shuttle to Lipid Trafficking and Redox Homeostasis

This paper develops an enzyme-constrained metabolic model of the tripartite synapse to show that lactate shuttling between astrocytes and neurons arises from protein limitations and that FABP7 is critical for lipid-redox homeostasis.

Genome-scale metabolic model atlas of the zoonotic pathogen Streptococcus suis

This study creates a genome-scale metabolic model atlas for Streptococcus suis, revealing lineage-specific metabolic differences and identifying potential antimicrobial targets.

Stress-Related Transcriptional Regulators Dominate the Conserved Core GRN for Three Cyanobacteria: Network Topology Maps the Highest-Influence Nodes as Promising Engineering Targets

The paper constructs gene regulatory networks for three cyanobacteria, identifies stress-related regulators as high-influence nodes, and highlights their importance for bioproduction engineering.

Machine learning-guided olivetolic acid cyclase engineering enables tailored cannabinoid biosynthesis in yeast

This paper uses machine learning to engineer olivetolic acid cyclase in yeast, enhancing cannabinoid production and selectivity.

First Genome-Scale Metabolic Model for Understanding HMPV-Host Interaction

The paper constructs the first genome-scale metabolic model for HMPV, identifies antiviral targets, and highlights UDP-GlcNAc as a critical metabolic hub for viral replication.

Amino acid auxotrophy is a feature of a distinct bacterial lifestyle across environments

This study shows auxotrophy is a conserved genomic lifestyle feature, not a transient response to nutrients, challenging the Black Queen Hypothesis.

Mapping metabolic phases through online pressure and backscatter rates

This study maps microbial metabolic phases using online pressure and backscatter measurements in closed batch vials, identifying distinct catabolic and anabolic phases in yeast and syngas fermentation.

Measure Catabolism: Real-time shifts in microbial metabolism through online pressure measurements

This paper introduces a method to measure microbial catabolism in real-time using pressure measurements, distinguishing metabolic shifts not detectable by biomass alone.

A Low-Cost, High-Throughput Design-Build-Test Pipeline for Engineering Genetic Systems: Stress Testing with Complex Structural Proteins

The paper develops a low-cost, high-throughput pipeline for genetic systems engineering, achieving high success rates in plasmid assembly and identifying factors affecting protein expression.

Clostridial acidogenesis product profiles are discontinuous: a thermodynamic hypothesis

The paper identifies three thermodynamically distinct product profiles in Clostridial fermentation and shows that intermediate ratios require less efficient pathways due to conflicting redox demands.

Comprehensive evaluation of LLM capabilities for interpretation and analysis of genome-scale metabolic models in metabolic engineering

This paper evaluates LLM capabilities for analyzing genome-scale metabolic models, identifying strengths and limitations across domain knowledge, flux prediction, pathway construction, and optimization tasks.

Small but Mighty: The Surprising Metabolic Range of a Bacterial Microcompartment

This paper demonstrates that heterologous Pdu BMCs in E. coli can metabolize a broader range of diols and triols than previously known, including glycerol and up to 1,2-pentanediol, and shows their potential for biotechnological applications.

CytoGem-XAI:A Hypergraph Neural Network Framework for Genome-Scale Metabolic Modeling and Interpretable Analysis

CytoGem-XAI combines hypergraph neural networks with interpretable analysis to improve metabolic modeling and prediction in E. coli, outperforming existing methods and revealing new essential nutrients.

On the Distribution of Free-Energy in Metabolism

The paper investigates how half-site reactivity in enzymes allows metabolic reactions to redistribute chemical potential, enhancing catalytic efficiency and pathway flexibility.