Microbial Metabolic Engineering and Bioproduction

Kinbiont: From time series to ecological and evolutionary responses in microbial systems

Kinbiont provides a model-based analysis pipeline for microbial kinetics data, enabling ecological and evolutionary insights through numerical methods and machine learning.

Quantitative, temporal dynamics of the cellular amino acid economy reveals public vs private goods and enables syntrophic yeast community design.

The paper quantifies amino acid dynamics in yeast to identify public and private goods, enabling the design of syntrophic yeast communities.

A shotgun approach for highly multiplexed mammalian metabolic engineering

This paper introduces SGE, a method for screening metabolic pathways in mammalian cells, and finds that mitochondrial localization and large synthetic DNA constructs are key for successful pathway engineering.

Sequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization

This study sequences and annotates the genome of Kluyveromyces marxianus Y-1190, identifies genetic factors for lactose metabolism, and develops tools for genetic manipulation to enhance its use in industrial biotechnology.

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation

This study engineers synthetic serine cycles in Pseudomonas putida to improve methanol assimilation, revealing novel metabolic topologies for C1 compound utilization.

Comparative genomic assessment of the Cupriavidus necator species for one-carbon based biomanufacturing

This paper curates and analyzes 22 genomes of Cupriavidus necator to assess genomic diversity and metabolic potential for one-carbon biomanufacturing, identifying three strains with promising traits.

Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

The paper shows that bacteria minimize proteome reallocation during metabolic transitions and introduces dMORP to simulate this process using omics data.

Biosynthesis of lavandulol and lavandulyl acetate in Escherichia coli

This paper reports the de novo microbial biosynthesis of lavandulol and lavandulyl acetate in Escherichia coli using pathway engineering, achieving production levels of 24.9 mg/L and 42.4 mg/L respectively.

Directed evolution of L-DOPA sensing and production enables efficient incorporation of an expanded genetic code into proteins

This paper develops a L-DOPA sensing system and improves biosynthesis via directed evolution, achieving high-efficiency incorporation into proteins.

Sustained Isobutene Production by Synechocystis sp. PCC 6803 Entrapped in Polyvinyl Alcohol Hydrogel Beads

This paper enhances isobutene production in Synechocystis sp. PCC 6803 by optimizing culture conditions and using PVA-SA hydrogel entrapment, achieving a 60-80% increase in yield.

Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production

The paper uses kinetic models to guide metabolic engineering of S. cerevisiae strains, resulting in improved p-coumaric acid production with minimal impact on growth rate.

Modelling dynamic host-pathway interactions at the genome scale with machine learning

The paper develops a method integrating kinetic pathway models with genome-scale metabolic models to simulate dynamic host-pathway interactions in Escherichia coli, enabling faster predictions of metabolite dynamics under genetic perturbations.

Acetate as a metabolic booster for glucose-based bioproduction in Escherichia coli

This study shows acetate can boost bioproduction in glucose-grown E. coli by reducing carbon loss, increasing acetyl-CoA levels, and improving biomass accumulation, validated for mevalonate and 3-hydroxypropionate.

Synthetic autotrophic yeast enables high itaconic acid production from CO2 via integrated pathway and process design

This study develops a synthetic autotrophic yeast strain that produces itaconic acid from CO2, achieving high titers through integrated pathway and process design.

Machine Learning-Assisted Pathway Optimization in Large Combinatorial Design Spaces: a p-Coumaric Acid Case Study

This paper applies a machine learning-assisted recommendation strategy with exploration-exploitation balance to optimize p-coumaric acid production in yeast, achieving a 137% increase over parent strains.

Systems-level analysis provides insights on methanol-based production of L-glutamate and its decarboxylation product γ-aminobutyric acid by Bacillus methanolicus

The paper describes the engineering of Bacillus methanolicus to enhance L-glutamate and GABA production through systems-level analysis and metabolic engineering.

Simulating Iron Deficiency in Plant Plastidial Metabolism With a Flexible Neural-Mechanistic Hybrid Approach

The paper uses a neural-mechanistic hybrid model to simulate iron deficiency effects on plastid metabolism in Poplar and Sorghum, revealing species-specific metabolic responses.

A robust synthetic biology toolkit to advance carboxysome study and design

This paper introduces a plasmid toolkit for expressing and purifying functional carboxysomes, showing that modifying specific genes affects their size and uniformity.

Thermodynamics of unicellular life: Entropy production rate as function of the balanced growth rate

The paper investigates whether microbial cells can reduce entropy production rate by shifting to less thermodynamically driven metabolism at faster growth rates, using yeast models and experimental data.

Asymmetric co-substrate usage at a metabolic branch point as a minimal network motif that can drive overflow metabolism

The paper identifies asymmetric co-substrate usage at a metabolic branch point as a mechanism that enables flux switching and drives overflow metabolism, validated through modeling and experimental data in yeast.

Biotin-Independent Saccharomyces cerevisiae with Enhanced Growth: Engineering an Acetyl-CoA Carboxylase Bypass

This paper engineers a biotin-independent Saccharomyces cerevisiae strain by bypassing acetyl-CoA carboxylase, enabling growth without biotin and improved malonate utilization.

A consortium-based approach to adaptive laboratory evolution of Acinetobacter baylyi ADP1 for lignin valorization

This study evolves a unique Acinetobacter baylyi strain through a two-step adaptive laboratory evolution process to improve lignin valorization capabilities.

Multi-Step Pathway Engineering in Probiotic Saccharomyces boulardii for Abscisic Acid Production in the Gut

This study genetically engineers a probiotic yeast to produce abscisic acid (ABA) in the gut, but finds low serum ABA levels due to temperature-dependent production challenges.

De novo production of prenylnaringenin compounds by a metabolically engineered Escherichia coli

This paper reports the de novo production of prenylnaringenin compounds in Escherichia coli using metabolic engineering and CRISPR-Cas12a to boost DMAPP availability.

Engineering the key central metabolic enzyme to utilize a non-canonical redox cofactor

This paper engineers Escherichia coli GapA to use NMN+ instead of NAD+, achieving a high cofactor specificity switch through rational design and mutagenesis.

Prediction of metabolic dynamics through deep learning and high-throughput multiomics data

This paper trains a deep learning model on multiomics data to predict metabolic dynamics in synthetic biology, achieving high accuracy in predicting product and metabolite levels.

Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

This paper introduces SubNetX, a computational algorithm that extracts and assembles balanced reaction subnetworks for producing target biochemicals, and demonstrates its application to eight secondary metabolites and one non-natural chemical.

COSMOS: COmmunity and Single Microbe Optimisation System

COSMOS compares microbial monocultures and communities to identify optimal systems for specific carbon sources and environments, finding Shewanella oneidensis-Klebsiella pneumoniae community most efficient for 1,3-propanediol production under anaerobic conditions.

Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

This paper develops a genome-scale metabolic model of S. epidermidis that accurately predicts growth and carbon source utilization under in vitro conditions.

Genome-Scale Metabolic Modeling Identifies Causal Reactions Mediated by SNP-SNP Interactions Influencing Yeast Sporulation

The paper uses genome-scale metabolic models to identify causal reactions influenced by SNP-SNP interactions affecting yeast sporulation efficiency.