Microbial Metabolic Engineering and Bioproduction

GALLANT: A Scalable Computational Platform for Microbial Consortium Interaction and Population Heterogeneity Analysis

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

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports co-existence of diverse lineages

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

EMBER: A Genome-Scale Approach for a Systematic Characterization of Bacterial Metabolic Heterogeneity through the Growth-Adaptation Trade-Off

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

Gempipe: a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models.

Gempipe improves multi-strain genome-scale metabolic model reconstruction by combining reference and reference-free methods, enhancing accuracy and enabling strain-specific metabolic analysis.

Model-driven exploration of underground metabolism reveals drivers of metabolic innovation in Pseudomonas putida

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.

Programmable cell differentiation in budding yeast uncouples reproductive and metabolic tasks

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.

Valine overproduction with metabolically engineered Methanothermobacter marburgensis

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

Synthetic Modular Cyanobacterial Consortium Enables Carbon-Negative Production of Glycerol and Derivatives

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

Generative design and construction of functional plasmids with a DNA language model

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

Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis

The paper identifies genomic targets for improving anaerobic chemical tolerance in Zymomonas mobilis using orthogonal gene perturbation screens and validates findings through gene deletions.

Acetate metabolism during xylose fermentation enhances 3-hydroxypropionic acid production in engineered acid-tolerant Issatchenkia orientalis

This paper engineers an acid-tolerant Issatchenkia orientalis strain to produce 3-hydroxypropionic acid from acetate-rich biomass, achieving 8.7 g/L via separate hydrolysis and fermentation.

XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models

XomicsToModel integrates multi-omics data with a generic metabolic model to generate context-specific, thermodynamically consistent metabolic models.

Isolation of bacteria that catabolize abiotically synthesized tetroses via the formose reaction

This study isolates bacteria capable of catabolizing abiotically synthesized tetroses, which are not metabolized by common microorganisms.

Integration of strain and process optimization to increase autotrophic growth of engineered Komagataella phaffii

This study improves autotrophic growth of engineered Komagataella phaffii through strain optimization and process parameter adjustment, achieving up to 50% faster growth.

MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

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

Cellulase secretion by engineered Pseudomonas putida enables growth on cellulose oligomers.

This study engineers Pseudomonas putida to secrete cellulase enzymes, enabling growth on cellulose oligomers.

Tri-Functional CRISPR Screen Reveals Overexpression of QDR2 and QDR3 Transporters Increase Fumaric Acid Production in Kluyveromyces marxianus

The paper uses a trifunctional CRISPR screen to identify gene perturbations that enhance fumaric acid tolerance and production in Kluyveromyces marxianus.

Creating an energy efficient central metabolism for boosting biosynthesis without compromising cell growth of yeast

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.

Parameterization of cell-free systems with time-series data using KETCHUP

The paper extends the KETCHUP tool to parameterize kinetic models using time-course data from cell-free systems, demonstrating accurate simulation of multi-enzyme systems.

Design and analysis of synthetic carbon fixation pathways based on novel enzymatic reactions

This paper identifies novel carbon fixation pathways using bioretrosynthetic analysis and expert knowledge, finding several that could outperform the Calvin cycle in biomass yield and do not require vitamin B12.

Development and characterisation of a promoter library for Sulfolobus acidocaldarius

The paper develops and characterises a promoter library for Sulfolobus acidocaldarius, showing a 5-fold range of expression levels in the organism.

Engineering amino acid-derived malonyl-CoA pathways to boost polyketide production in Yarrowia lipolytica

The paper engineers two malonyl-CoA pathways in Yarrowia lipolytica using amino acids to boost polyketide production, achieving 6.4 g/L of a new polyketide.

BiosInt: Biosensor-based smart design of pathway dynamic regulation for industrial biomanufacturing

The paper introduces BiosInt, a genetic circuit for dynamic pathway regulation in biomanufacturing, validated through synthetic datasets and applied to flavonoid production.

Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

The paper presents a genome-scale metabolic model of Escherichia coli Nissle 1917 that includes cryptic plasmids, improving predictive accuracy and revealing its unique probiotic metabolic traits.

Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation

This paper designs and tests synthetic CO2 fixation pathways in E. coli, demonstrating their potential to outperform natural pathways.

An Ehrlich-inspired retrobiosynthesis of pharmaceutical scaffolds

The paper repurposes the yeast Ehrlich pathway to synthesize pharmaceutical alkaloids using retrobiosynthetic analysis and enzyme screening.

Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis

The paper engineering Pseudomonas putida KT2440 to produce 3-hydroxy fatty acids (3-HFAs) with controlled chain lengths, achieving titers up to 0.73 g/L using a direct route and demonstrating scalability.

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

The paper predicts neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases using a systems biology approach and integrates metabolic networks with single nucleus RNA sequencing data.

StrainOptimizer empowers rational cell factory design through multi-scale metabolic models with expression and proteome constraints

StrainOptimizer improves microbial cell factory design by integrating multi-scale metabolic models with expression and proteome constraints, achieving higher bioproduction in yeast.

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin

This paper introduces a growth-coupled biosynthesis strategy (GrowBio) for producing xanthommatin, demonstrating its effectiveness in microbial production through engineered Pseudomonas putida.