Exploiting unconventional prokaryotic hosts for industrial biotechnology

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

(2021) Pablo I. Nikel et al.   ISME Journal

Developing a Sustainable and Circular Bio-Based Economy in EU: By Partnering Across Sectors, Upscaling and Using New Knowledge Faster, and For the Benefit of Climate, Environment & Biodiversity, and People & Business

(2021) Lene Lange et al.   Frontiers in Bioengineering and Biotechnology

Recent advances of Cas12a applications in bacteria

(2021) Meliawati Meliawati et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metabolic engineering of Vibrio natriegens

(2021) Felix Thoma et al.   Essays in Biochemistry

Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways

(2021) Nora Lisa Bitzenhofer et al.   Essays in Biochemistry

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

(2020) Seohyoung Kim et al.   Nature Chemical Biology

Chemical Production from Methanol Using Natural and Synthetic Methylotrophs

(2020) Arvin Y. Chen et al.   Biotechnology Journal

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Meltome atlas—thermal proteome stability across the tree of life

(2020) Anna Jarzab et al.   NATURE METHODS

Genetic Engineering of Oligotropha carboxidovorans Strain OM5—A Promising Candidate for the Aerobic Utilization of Synthesis Gas

(2020) Daniel Siebert et al.   ACS Synthetic Biology

Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440

(2020) Wing-Jin Li et al.   Frontiers in Microbiology

Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions

(2020) Andreas Ankenbauer et al.   Microbial Biotechnology

A hybrid extracellular electron transfer pathway enhances survival of Vibrio natriegens

(2020) Bridget E. Conley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pseudomonas as Versatile Aromatics Cell Factory

(2020) Tobias Schwanemann et al.   Biotechnology Journal

CRISPR‐Cas9 mediated engineering of Bacillus licheniformis for industrial production of ( 2R , 3S )‐butanediol

(2020) Chan Woo Song et al.   BIOTECHNOLOGY PROGRESS

Pollution to products: recycling of ‘above ground’ carbon by gas fermentation

(2020) Michael Köpke et al.   CURRENT OPINION IN BIOTECHNOLOGY

Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere

(2020) Olga V. Karnachuk et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering of the 2,3-butanediol pathway of Paenibacillus polymyxa DSM 365

(2020) Christoph Schilling et al.   METABOLIC ENGINEERING

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

(2020) Samuel M D Seaver et al.   NUCLEIC ACIDS RESEARCH

From Acetate to Bio-Based Products: Underexploited Potential for Industrial Biotechnology

(2020) Dirk Kiefer et al.   TRENDS IN BIOTECHNOLOGY

Charting the Metabolic Landscape of the Facultative Methylotroph Bacillus methanolicus

(2020) Baudoin Delépine et al.   mSystems

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

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

Novel Prokaryotic CRISPR-Cas12a-Based Tool for Programmable Transcriptional Activation and Repression

(2020) Christoph Schilling et al.   ACS Synthetic Biology

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

(2020) Daniel Craig Zielinski et al.   Microorganisms

Constitutively solvent-tolerant Pseudomonas taiwanensis VLB120∆C ∆ttgV supports particularly high styrene epoxidation activities when grown under glucose excess conditions

(2019) Jan Volmer et al.   BIOTECHNOLOGY AND BIOENGINEERING

Chronicle of a Soil Bacterium: Paenibacillus polymyxa E681 as a Tiny Guardian of Plant and Human Health

(2019) Haeyoung Jeong et al.   Frontiers in Microbiology

Establishment and application of CRISPR interference to affect sporulation, hydrogen peroxide detoxification, and mannitol catabolism in the methylotrophic thermophile Bacillus methanolicus

(2019) Kerstin Schultenkämper et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Systems Metabolic Engineering Meets Machine Learning: A New Era for Data‐Driven Metabolic Engineering

(2019) Kristin V. Presnell et al.   Biotechnology Journal

Grand Research Challenges for Sustainable Industrial Biotechnology

(2019) Adrie J.J. Straathof et al.   TRENDS IN BIOTECHNOLOGY

Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment

(2019) Nandita Pasari et al.   Scientific Reports

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

(2019) Henry H. Lee et al.   Nature Microbiology

Mixed-species biofilms for high-cell-density application of Synechocystis sp. PCC 6803 in capillary reactors for continuous cyclohexane oxidation to cyclohexanol

(2019) Anna Hoschek et al.   BIORESOURCE TECHNOLOGY

Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas

(2019) Maike Otto et al.   ACS Synthetic Biology

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

(2019) Chuankai Cheng et al.   PLoS Computational Biology

Pseudomonas putida KT 2440 is HV 1 certified, not GRAS

(2019) Linde F. C. Kampers et al.   Microbial Biotechnology

High-Yield Production of 4-Hydroxybenzoate From Glucose or Glycerol by an Engineered Pseudomonas taiwanensis VLB120

(2019) Christoph Lenzen et al.   Frontiers in Bioengineering and Biotechnology

Microbial production of 2,3-butanediol for industrial applications

(2019) Chan Woo Song et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Exploiting Hydrogenophaga pseudoflava for aerobic syngas-based production of chemicals

(2019) Sebastian Grenz et al.   METABOLIC ENGINEERING

Streamlined Pseudomonas taiwanensis VLB120 Chassis Strains with Improved Bioprocess Features

(2019) Benedikt Wynands et al.   ACS Synthetic Biology

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

(2019) Juan Nogales et al.   ENVIRONMENTAL MICROBIOLOGY

Rational Engineering of Phenylalanine Accumulation in Pseudomonas taiwanensis to Enable High-Yield Production of Trans-Cinnamate

(2019) Maike Otto et al.   Frontiers in Bioengineering and Biotechnology

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology

(2019) Peter D Karp et al.   BRIEFINGS IN BIOINFORMATICS

Towards sustainable feedstocks: A guide to electron donors for microbial carbon fixation

(2018) Nico Joannes Claassens et al.   CURRENT OPINION IN BIOTECHNOLOGY

Thermochemical wastewater valorization via enhanced microbial toxicity tolerance

(2018) Lahiru N. Jayakody et al.   Energy & Environmental Science

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans -metabolism

(2018) Pablo I. Nikel et al.   METABOLIC ENGINEERING

Metabolic engineering of Pseudomonas taiwanensis VLB120 with minimal genomic modifications for high-yield phenol production

(2018) Benedikt Wynands et al.   METABOLIC ENGINEERING

From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida

(2018) Michael Kohlstedt et al.   METABOLIC ENGINEERING

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Using gas mixtures of CO, CO2 and H2 as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale

(2018) Ralf Takors et al.   Microbial Biotechnology

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13 C metabolic flux analysis

(2017) Christopher P. Long et al.   METABOLIC ENGINEERING

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology

(2017) Ayca Cankorur-Cetinkaya et al.   MICROBIOLOGY-SGM

Production of High Levels of Chirally Pure d-2,3-Butanediol with a Newly Isolated Bacillus Strain

(2017) Peng-Fei Yan et al.   ACS Sustainable Chemistry & Engineering

Speeding up bioproduction of selenium nanoparticles by using Vibrio natriegens as microbial factory

(2017) Helga Fernández-Llamosas et al.   Scientific Reports

Mixed consortia in bioprocesses: role of microbial interactions

(2016) Shiladitya Ghosh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production

(2016) Brian Weselowski et al.   BMC MICROBIOLOGY

The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli , Corynebacterium glutamicum , Pseudomonas , Bacillus and yeast strains for access to alternative carbon sources

(2016) Volker F. Wendisch et al.   JOURNAL OF BIOTECHNOLOGY

Quantitative metabolomics of the thermophilic methylotroph Bacillus methanolicus

(2016) Marc Carnicer et al.   Microbial Cell Factories

Current knowledge and perspectives of Paenibacillus: a review

(2016) Elliot Nicholas Grady et al.   Microbial Cell Factories

Vibrio natriegens as a fast-growing host for molecular biology

(2016) Matthew T Weinstock et al.   NATURE METHODS

Harnessing the power of microbial autotrophy

(2016) Nico J. Claassens et al.   NATURE REVIEWS MICROBIOLOGY

Genome-Based Genetic Tool Development for Bacillus methanolicus: Theta- and Rolling Circle-Replicating Plasmids for Inducible Gene Expression and Application to Methanol-Based Cadaverine Production

(2016) Marta Irla et al.   Frontiers in Microbiology

Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008

(2015) Nidhi Adlakha et al.   Biotechnology for Biofuels

Guiding bioprocess design by microbial ecology

(2015) Jan Volmer et al.   CURRENT OPINION IN MICROBIOLOGY

Growth of Bacillus methanolicus in 2 M methanol at 50 °C: the effect of high methanol concentration on gene regulation of enzymes involved in formaldehyde detoxification by the ribulose monophosphate pathway

(2015) Ahmet Bozdag et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Engineering Escherichia coli for methanol conversion

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

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Enhanced annotations and features for comparing thousands ofPseudomonasgenomes in the Pseudomonas genome database

(2015) Geoffrey L. Winsor et al.   NUCLEIC ACIDS RESEARCH

Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol

(2014) Jonas E. N. Müller et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates

(2014) Haitao Yue et al.   Biotechnology for Biofuels

Cell factories for insulin production

(2014) Nabih A Baeshen et al.   Microbial Cell Factories

Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida

(2014) José Borrero-de Acuña et al.   Microbial Cell Factories

Lignin valorization through integrated biological funneling and chemical catalysis

(2014) J. G. Linger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

Genome Sequence of Thermotolerant Bacillus methanolicus: Features and Regulation Related to Methylotrophy and Production of l-Lysine and l-Glutamate from Methanol

(2012) Tonje M. B. Heggeset et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced fed-batch fermentation of 2,3-butanediol by Paenibacillus polymyxa DSM 365

(2012) Thomas Häßler et al.   BIORESOURCE TECHNOLOGY

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Biofilms as living catalysts in continuous chemical syntheses

(2012) Babu Halan et al.   TRENDS IN BIOTECHNOLOGY

Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals

(2012) Alan G Fast et al.   Current Opinion in Chemical Engineering

Experimental Evolution of a Facultative Thermophile from a Mesophilic Ancestor

(2011) Ian K. Blaby et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand

(2011) Birgitta E. Ebert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

In situ phenol removal from fed-batch fermentations of solvent tolerant Pseudomonas putida S12 by pertraction

(2010) Louise Heerema et al.   BIOCHEMICAL ENGINEERING JOURNAL

Metabolic flux analysis of a phenol producing mutant of Pseudomonas putida S12: Verification and complementation of hypotheses derived from transcriptomics

(2009) Nick Wierckx et al.   JOURNAL OF BIOTECHNOLOGY

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Bioproduction of p-Hydroxystyrene from Glucose by the Solvent-Tolerant Bacterium Pseudomonas putida S12 in a Two-Phase Water-Decanol Fermentation

(2008) S. Verhoef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase

(2008) Lars M. Blank et al.   FEBS Journal