Microbial Metabolic Engineering and Bioproduction

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.

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.

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

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

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.

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.

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.

This study demonstrates that Ustilago maydis can efficiently produce itaconic acid from acetate, achieving high titers and yields comparable to glucose-based processes, supporting acetate as a sustainable feedstock for land-free biotechnology.

METEOR integrates enzyme prediction with genome-scale metabolic model reconstruction to improve functional annotations and network viability.

This paper combines adaptive laboratory evolution and machine learning to engineer a methylsuccinate module for synthetic C1 metabolism in E. coli, achieving growth in three weeks versus six months with evolution alone.

The paper uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

MetaNetMap automates mapping of metabolomic annotations onto genome-scale metabolic networks through direct, conversion-table-bridged and partial identifier matching, reproducing 311 mappings from a Parkinson's disease study.

The paper introduces a geometric framework to analyze microbial community metabolism, linking interaction types to the structure of metabolic spaces and identifying isotypic and anisotypic mutualism.

This paper introduces a Gluconate-Bypass in E. coli to decouple central metabolism from catabolite repression, enabling robust co-consumption of multiple lignocellulosic sugars.

The paper develops a structure-annotated genome-scale metabolic model for Bacillus subtilis to include levan biosynthesis, using AlphaFold2 for structural information.

This paper introduces a gluconate-bypass platform to enhance stationary-phase biomanufacturing in E. coli by decoupling glucose uptake from pyruvate inhibition and co-generating NADPH, achieving high product titers.

This study identifies a metabolic hierarchy in Caulobacter crescentus that coordinates cell cycle transitions and morphogenesis through redox dynamics.

This paper develops a genome-scale metabolic model for Nannochloropsis oceanica to study lipid production under light acclimation conditions.

The paper identifies genome-wide protein-RNA interactions in Clostridium autoethanogenum that contribute to autotrophy using a combination of experimental and computational methods.

The paper introduces tdFBA, a novel method for simulating circadian metabolism across organs, and shows it can recapitulate metabolic oscillations and perturbations in mice and humans.

GALLANT automates genome-scale metabolic model generation and contextualization, enabling analysis of microbial consortia and population heterogeneity using multi-omics data.

EMBER identifies adaptive metabolic reactions in bacteria by integrating transcriptomics and flux analysis, revealing differences in resource allocation strategies across species.

This study explores underground metabolism in Pseudomonas putida to identify novel metabolic traits through adaptive laboratory evolution, revealing how promiscuous enzymatic activities contribute to metabolic innovation.

The paper introduces MiSTY, a genetic platform in budding yeast that separates reproductive and metabolic tasks into distinct cell types, enabling high-yield biomanufacturing by uncoupling cell growth from product synthesis.

This paper demonstrates enhanced valine production in Methanothermobacter marburgensis using genetic engineering and promoter systems, achieving high specific productivity.

This paper describes a synthetic modular cyanobacterial consortium that enables carbon-negative production of glycerol and derivatives by linking carbon fixation with downstream bioconversion.

This paper develops a pipeline to generate functional E. coli plasmids using a DNA language model, resulting in three validated synthetic plasmids.

MIMEco predicts pairwise microbial interactions using multi-objective metabolic modeling without requiring abundance data, validated by replicating experimental results with Escherichia coli.

This paper engineers an energy-efficient pentose phosphate pathway in yeast to boost fatty acid production without compromising cell growth, achieving a record 41.7 g/L titer.