Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution

Growth of E. coli on formate and methanol via the reductive glycine pathway

(2020) Seohyoung Kim et al.   Nature Chemical Biology

Adaptive Laboratory Evolution of Ale and Lager Yeasts for Improved Brewing Efficiency and Beer Quality

(2020) B. Gibson et al.   Annual Review of Food Science and Technology

Enhanced astaxanthin production in yeast via combined mutagenesis and evolution

(2020) Guozhen Jiang et al.   BIOCHEMICAL ENGINEERING JOURNAL

Microbial microdroplet culture system (MMC): An integrated platform for automated, high‐throughput microbial cultivation and adaptive evolution

(2020) Xingjin Jian et al.   BIOTECHNOLOGY AND BIOENGINEERING

Methanol-Essential Growth of Corynebacterium glutamicum: Adaptive Laboratory Evolution Overcomes Limitation due to Methanethiol Assimilation Pathway

(2020) Guido Hennig et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

In vivo evolutionary engineering of riboswitch with high-threshold for N-acetylneuraminic acid production

(2020) Qingxiao Pang et al.   METABOLIC ENGINEERING

The developing toolkit of continuous directed evolution

(2020) Mary S. Morrison et al.   Nature Chemical Biology

The omnistat: a flexible continuous‐culture system for prolonged experimental evolution

(2020) David M. Ekkers et al.   Methods in Ecology and Evolution

Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide

(2020) Seulgi Kang et al.   Frontiers in Microbiology

Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol

(2020) Frederic Y.-H. Chen et al.   CELL

Improvement and Metabolomics-Based Analysis of d-Lactic Acid Production from Agro-Industrial Wastes by Lactobacillus delbrueckii Submitted to Adaptive Laboratory Evolution

(2020) Shaoxiong Liang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms

(2020) SuRin Lee et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production

(2020) R. Kyle Bennett et al.   METABOLIC ENGINEERING

Directed Evolution of Ornithine Cyclodeaminase Using an EvolvR-Based Growth-Coupling Strategy for Efficient Biosynthesis of l-Proline

(2020) Mengfei Long et al.   ACS Synthetic Biology

Empowering a Methanol-Dependent Escherichia coli via Adaptive Evolution Using a High-Throughput Microbial Microdroplet Culture System

(2020) Jia Wang et al.   Frontiers in Bioengineering and Biotechnology

Adaptive laboratory evolution for growth coupled microbial production

(2020) Avinash Godara et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway

(2020) Chad W. Johnston et al.   Nature Communications

The Era of Big Data: Genome-scale Modelling meets Machine Learning

(2020) Athanasios Antonakoudis et al.   Computational and Structural Biotechnology Journal

Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo

(2020) Hyojin Park et al.   NUCLEIC ACIDS RESEARCH

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli

(2020) Tomoya Maeda et al.   Nature Communications

Construction of Mini-Chemostats for High-throughput Strain Characterization

(2019) David Bergenholm et al.   BIOTECHNOLOGY AND BIOENGINEERING

Coupling S-adenosylmethionine–dependent methylation to growth: Design and uses

(2019) Hao Luo et al.   PLOS BIOLOGY

Adaptive laboratory evolution of a genome-reduced Escherichia coli

(2019) Donghui Choe et al.   Nature Communications

Tools and systems for evolutionary engineering of biomolecules and microorganisms

(2019) Sungho Jang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

In vivo continuous evolution of metabolic pathways for chemical production

(2019) Zheng Lin Tan et al.   Microbial Cell Factories

Genetic compatibility and extensibility of orthogonal replication

(2019) Alex Arash Javanpour et al.   ACS Synthetic Biology

Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries

(2019) Tatyana E. Saleski et al.   METABOLIC ENGINEERING

GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli

(2019) Xiaowei Wang et al.   Microbial Cell Factories

Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations

(2019) Sophia Belkhelfa et al.   Frontiers in Microbiology

Efficient production of d-lactate from methane in a lactate-tolerant strain of Methylomonas sp. DH-1 generated by adaptive laboratory evolution

(2019) Jong Kwan Lee et al.   Biotechnology for Biofuels

Determination of growth-coupling strategies and their underlying principles

(2019) Tobias B. Alter et al.   BMC BIOINFORMATICS

Continuous Adaptive Evolution of a Fast-Growing Corynebacterium glutamicum Strain Independent of Protocatechuate

(2019) Michaela Graf et al.   Frontiers in Microbiology

Laboratory evolution strategies for improving lipid accumulation in Yarrowia lipolytica

(2019) Alexandra Daskalaki et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Conversion of Escherichia coli to Generate All Biomass Carbon from CO2

(2019) Shmuel Gleizer et al.   CELL

Synthetic Biology Enables Programmable Cell‐Based Biosensors

(2019) Maggie Hicks et al.   CHEMPHYSCHEM

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

(2019) Rui Pereira et al.   METABOLIC ENGINEERING

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

Dynamics of transcription–translation coordination tune bacterial indole signaling

(2019) Tianmin Wang et al.   Nature Chemical Biology

Evolutionary engineering of industrial microorganisms-strategies and applications

(2018) Zhengming Zhu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Construction of Halomonas bluephagenesis capable of high cell density growth for efficient PHA production

(2018) Yilin Ren et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain

(2018) Kento Tokuyama et al.   BIOTECHNOLOGY AND BIOENGINEERING

Development of a cooperative two-factor adaptive-evolution method to enhance lipid production and prevent lipid peroxidation in Schizochytrium sp.

(2018) Xiao-Man Sun et al.   Biotechnology for Biofuels

Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production

(2018) Robert Mans et al.   CURRENT OPINION IN BIOTECHNOLOGY

Design and optimization of genetically encoded biosensors for high-throughput screening of chemicals

(2018) Hyun Gyu Lim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Strategies for directed and adapted evolution as part of microbial strain engineering

(2018) Shenghu Zhou et al.   JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY

A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo

(2018) Christopher L. Moore et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Methanol assimilation in Escherichia coli is improved by co-utilization of threonine and deletion of leucine-responsive regulatory protein

(2018) Jacqueline E. Gonzalez et al.   METABOLIC ENGINEERING

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

(2018) Tomas Strucko et al.   METABOLIC ENGINEERING

Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device

(2018) Joo Yeon Seok et al.   METABOLIC ENGINEERING

A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: Riboflavin overproduction in Yarrowia lipolytica

(2018) James M. Wagner et al.   METABOLIC ENGINEERING

CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

(2018) Tadas Jakočiūnas et al.   METABOLIC ENGINEERING

Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER

(2018) Brandon G Wong et al.   NATURE BIOTECHNOLOGY

Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion

(2018) Diane Plouchart et al.   PLoS One

Adaptive evolution of genomically recodedEscherichia coli

(2018) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction and evolution of anEscherichia colistrain relying on nonoxidative glycolysis for sugar catabolism

(2018) Paul P. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic addiction extends the productive life time of engineeredEscherichia colipopulations

(2018) Peter Rugbjerg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methanol-essential growth of Escherichia coli

(2018) Fabian Meyer et al.   Nature Communications

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

(2018) Tianmin Wang et al.   Nature Communications

An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast

(2018) Tim Snoek et al.   ACS Synthetic Biology

High mutation rates limit evolutionary adaptation in Escherichia coli

(2018) Kathleen Sprouffske et al.   PLoS Genetics

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes

(2018) Denis Shepelin et al.   Genes

Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

(2018) Tao Yu et al.   CELL

Rationally designed perturbation factor drives evolution in Saccharomyces cerevisiae for industrial application

(2018) Xin Xu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Engineering Corynebacterium glutamicum for methanol-dependent growth and glutamate production

(2018) Philibert Tuyishime et al.   METABOLIC ENGINEERING

Directed strain evolution restructures metabolism for 1-butanol production in minimal media

(2018) Sammy Pontrelli et al.   METABOLIC ENGINEERING

Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production

(2018) Chang-Ting Chen et al.   METABOLIC ENGINEERING

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators

(2018) Javier F. Juárez et al.   Nature Communications

Utilization of rare codon-rich markers for screening amino acid overproducers

(2018) Bo Zheng et al.   Nature Communications

Retroelement-based genome editing and evolution

(2018) Anna J. Simon et al.   ACS Synthetic Biology

Enhancing Production of Pinene in Escherichia coli by Using a Combination of Tolerance, Evolution, and Modular Co-culture Engineering

(2018) Fu-Xing Niu et al.   Frontiers in Microbiology

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

Rewiring metabolic network by chemical modulator based laboratory evolution doubles lipid production in Crypthecodinium cohnii

(2018) Jinjin Diao et al.   METABOLIC ENGINEERING

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation

(2018) Patrick V Phaneuf et al.   NUCLEIC ACIDS RESEARCH

Understanding and engineering alcohol-tolerant bacteria using OMICS technology

(2018) Takaaki Horinouchi et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Development of Freeze-Thaw Tolerant Lactobacillus rhamnosus GG by Adaptive Laboratory Evolution

(2018) Ye Won Kwon et al.   Frontiers in Microbiology

Deletion of four genes in Escherichia coli enables preferential consumption of xylose and secretion of glucose

(2018) Camil A.C. Diaz et al.   METABOLIC ENGINEERING

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

(2017) Hemanshu Mundhada et al.   METABOLIC ENGINEERING

Biosensor-assisted transcriptional regulator engineering for Methylobacterium extorquens AM1 to improve mevalonate synthesis by increasing the acetyl-CoA supply

(2017) Wei-Fan Liang et al.   METABOLIC ENGINEERING

Pathway optimization and key enzyme evolution of N -acetylneuraminate biosynthesis using an in vivo aptazyme-based biosensor

(2017) Peng Yang et al.   METABOLIC ENGINEERING

Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli

(2017) W. Brian Whitaker et al.   METABOLIC ENGINEERING

Specificity of genome evolution in experimental populations ofEscherichia colievolved at different temperatures

(2017) Daniel E. Deatherage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

(2017) Axel von Kamp et al.   Nature Communications

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

(2017) Jiazhang Lian et al.   Nature Communications

Automated multiplex genome-scale engineering in yeast

(2017) Tong Si et al.   Nature Communications

RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes

(2017) Joseph Abatemarco et al.   Nature Communications

Maltose Utilization as a Novel Selection Strategy for Continuous Evolution of Microbes with Enhanced Metabolite Production

(2017) Shu-De Liu et al.   ACS Synthetic Biology

Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production

(2017) Solvej Siedler et al.   ACS Synthetic Biology

Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae

(2017) John M. Leavitt et al.   Biotechnology Journal

Computational design of environmental sensors for the potent opioid fentanyl

(2017) Matthew J Bick et al.   eLife

Design and application of a lactulose biosensor

(2017) Jieyuan Wu et al.   Scientific Reports

Directional regulation of the metabolic heterogeneity in anaerobic mixed culture to enhance fermentative hydrogen production by adaptive laboratory evolution

(2016) Zhenxing Huang et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Increased acid resistance of the archaeon, Metallosphaera sedula by adaptive laboratory evolution

(2016) Chenbing Ai et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Intermediate-sensor assisted push–pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli

(2016) Mingyue Fang et al.   METABOLIC ENGINEERING

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Functional mining of transporters using synthetic selections

(2016) Hans J Genee et al.   Nature Chemical Biology

Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast

(2016) Mette L Skjoedt et al.   Nature Chemical Biology

Engineering nonphosphorylative metabolism to generate lignocellulose-derived products

(2016) Yi-Shu Tai et al.   Nature Chemical Biology

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

(2016) D. Dar et al.   SCIENCE

In vivo continuous evolution of genes and pathways in yeast

(2016) Nathan Crook et al.   Nature Communications

Metabolic Engineering of Corynebacterium glutamicum for Methanol Metabolism

(2015) Sabrina Witthoff et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acid-Adapted Strains of Escherichia coli K-12 Obtained by Experimental Evolution

(2015) Mark M. Harden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Design and engineering of intracellular-metabolite-sensing/regulation gene circuits inSaccharomyces cerevisiae

(2015) Meng Wang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Evolutionary engineering to enhance starter culture performance in food fermentations

(2015) Herwig Bachmann et al.   CURRENT OPINION IN BIOTECHNOLOGY

On the feasibility of growth-coupled product synthesis in microbial strains

(2015) Steffen Klamt et al.   METABOLIC ENGINEERING

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

(2015) Sang-Woo Lee et al.   METABOLIC ENGINEERING

Applications and advances of metabolite biosensors for metabolic engineering

(2015) Di Liu et al.   METABOLIC ENGINEERING

Engineering Escherichia coli for methanol conversion

(2015) Jonas E.N. Müller et al.   METABOLIC ENGINEERING

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

(2015) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals

(2015) Aindrila Mukhopadhyay   TRENDS IN MICROBIOLOGY

Development of potent in vivo mutagenesis plasmids with broad mutational spectra

(2015) Ahmed H. Badran et al.   Nature Communications

A Small-Volume, Low-Cost, and Versatile Continuous Culture Device

(2015) Dominick Matteau et al.   PLoS One

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

(2014) Ryan A. LaCroix et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Use of Nonionic Surfactants for Improvement of Terpene Production in Saccharomyces cerevisiae

(2014) James Kirby et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recent advances in the evolutionary engineering of industrial biocatalysts

(2014) James D. Winkler et al.   GENOMICS

Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption

(2014) Benjamin L Wang et al.   NATURE BIOTECHNOLOGY

An orthogonal DNA replication system in yeast

(2014) Arjun Ravikumar et al.   Nature Chemical Biology

Evolution-guided optimization of biosynthetic pathways

(2014) Srivatsan Raman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production

(2013) Guodong Luan et al.   Biotechnology for Biofuels

Improving carotenoids production in yeast via adaptive laboratory evolution

(2013) Luis H. Reyes et al.   METABOLIC ENGINEERING

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM

(2013) Shawn P. Finney-Manchester et al.   NUCLEIC ACIDS RESEARCH

Programming adaptive control to evolve increased metabolite production

(2013) Howard H. Chou et al.   Nature Communications

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes

(2013) Jina Yang et al.   Nature Communications

Synthetic Gene Circuit-Mediated Monitoring of Endogenous Metabolites: Identification of GAL11 as a Novel Multicopy Enhancer of S-Adenosylmethionine Level in Yeast

(2013) Taichi Umeyama et al.   ACS Synthetic Biology

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering

(2011) Vasiliy A Portnoy et al.   CURRENT OPINION IN BIOTECHNOLOGY

An evolutionary strategy for isobutanol production strain development in Escherichia coli

(2011) Kevin M. Smith et al.   METABOLIC ENGINEERING

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

Design and Application of a Mevalonate-Responsive Regulatory Protein

(2010) Shuang-Yan Tang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection

(2010) Jeffrey A. Dietrich et al.   Annual Review of Biochemistry

Microbial experimental evolution

(2009) Albert F. Bennett et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA