Adam M. Feist

Adaptive laboratory evolution rewires Pseudomonas putida for resource-efficient acetate assimilation

This study improves acetate tolerance in Pseudomonas putida through adaptive laboratory evolution and identifies gacA and fabB as key targets for efficient acetate assimilation.

Improving acetate metabolism of Pseudomonas putida KT2440 by evolutionary and rational engineering

This paper improves acetate metabolism in P. putida KT2440 through rational and evolutionary engineering, enhancing growth rate and HAA production.

Evolved microbial diversity enables combinatoric biosensing in complex environments

The paper develops a framework using evolved microbial diversity and machine learning to enable combinatoric biosensing of multiple analytes in complex environments.

Seven mutations unlock strict synthetic methylotrophy in engineered Pseudomonas putida

The paper engineers Pseudomonas putida to strictly metabolize methanol through seven mutations, enabling growth on methanol as the sole carbon source.

Spore-Based Biocomposite Thermoplastic Polyesters with Enhanced Toughness and Programmable Disintegration

This paper develops spore-based biocomposite thermoplastic polyesters with enhanced toughness and programmable disintegration through integration of heat-shock-tolerized Bacillus subtilis spores.

Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.

This study analyzes 164 Pseudomonas putida strains to reveal metabolic and genetic diversity, curating GEMs and identifying strain-specific adaptations for biotechnology applications.

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.

Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants

The paper identifies an aerobicity stimulon in E. coli through computational analysis of evolved respiratory variants, showing gene groups co-regulated with aerobic capacity and proteome reallocation.

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.

Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of Escherichia coli

This study uses adaptive laboratory evolution to identify five transcriptional mechanisms enabling Escherichia coli to grow at high temperatures.

Host evolution improves genetic circuit function in complex growth environments

This study improves genetic circuit function in E. coli by evolving strains in complex environments using adaptive laboratory evolution.

Evolution guided tolerance engineering of Pseudomonas putida KT2440 for production of the sustainable aviation fuel precursor isoprenol

This study uses adaptive laboratory evolution and rational engineering to improve Pseudomonas putida's tolerance to isoprenol, enhancing its production of a sustainable aviation fuel precursor.

Metabolic growth coupling strategies for in vivo enzyme selection systems

The paper presents a computational workflow to design enzyme selection systems (ESSs) that couple enzyme activity to microbial metabolism, creating a database of 25,505 ESS designs for Escherichia coli.

Scalable Fabrication of a Tough and Recyclable Spore-Bearing Biocomposite Thermoplastic Polyurethane

This paper develops a scalable method to create recyclable and tougher biocomposite TPUs by embedding spore-based living fillers, showing improved toughness and recyclability.

Using the E. coli Alleleome in Strain Design

This study combines ALE and WT variants to explore sequence solutions for industrial tolerance in E. coli, finding that WT variants can provide greater benefits and help identify feasible genome design variables.

Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

The paper uses adaptive laboratory evolution and transcriptomic analysis to identify six mechanisms of paraquat tolerance in E. coli.

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

The paper evolves ETS variants in E. coli and finds they all optimize growth rate and proteome allocation, with conserved aero-type strategies except for ETS-4H.

Machine-learning from Pseudomonas putida transcriptomes reveals its transcriptional regulatory network

This study uses machine learning to uncover the genome-scale transcriptional regulatory network in Pseudomonas putida using gene expression data.

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

The paper estimates in vivo enzyme turnover numbers (kcats) in E. coli using metabolic specialist strains and shows their stability and predictive power over in vitro kcats.

Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes

This study uses multi-omics data from evolving E. coli strains to identify convergent and divergent adaptation principles at metabolic, transcriptomic, and genetic levels.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

This study uses adaptive laboratory evolution to generate E. coli strains with increased superoxide stress tolerance and identifies genetic and transcriptomic mechanisms underlying this adaptation.

Model-driven design and evolution of non-trivial synthetic syntrophic pairs

This paper designs and evolves synthetic syntrophic E. coli pairs using a novel algorithm, revealing metabolic changes that enhance community fitness and guide co-culture optimization.

ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution

ALEdb 1.0 is a database of mutations from adaptive laboratory evolution experiments, providing structured access to over 11,000 mutations across multiple organisms.

Growth adaptation of gnd and sdhCB Escherichia coli deletion strains diverges from a similar initial perturbation of the transcriptome

This study uses adaptive laboratory evolution to reveal divergent transcriptomic and metabolomic adaptations in E. coli knockout strains with similar initial perturbations.

Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions

The paper shows how multiple optimal phenotypes emerge in Escherichia coli pgi knockout strains through adaptive evolution, overcoming redox and metabolite imbalances.

Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms

The paper develops a quantitative framework to predict ROS stress responses in E. coli across molecular, network, and genetic levels.

Enzyme promiscuity shapes evolutionary innovation and optimization

This study shows that enzyme promiscuity enables E. coli to adapt to novel substrates through computational modeling and lab evolution experiments.

BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

BOFdat generates biomass objective function stoichiometric coefficients from omic data and calculates maintenance costs.