Bas Teusink

Bas Teusink
Vrije Universiteit Amsterdam | VU · Amsterdam Institute of Molecular and Life Sciences (AIMMS)

PhD

About

296
Publications
41,781
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
10,149
Citations
Introduction
Bas Teusink currently works at the Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam. Bas does research in Bioinformatics, Microbiology and Systems Biology.
Additional affiliations
August 2008 - present
Vrije Universiteit Amsterdam
November 2002 - July 2008
TI Food and Nutrition / NIZO food research
Position
  • Research: TI Food and Nutrition / NIZO food research
November 2002 - July 2008
Radboud University
Description
  • guest researcher

Publications

Publications (296)
Preprint
In Nature, microbes live in very nutrient-dynamic environments. Rapid scavenging and consumption of newly introduced nutrients therefore offer a way to outcompete competitors. This may explain the observation that many microorganisms, including the budding yeast Saccharomyces cerevisiae , appear to keep “excess” glycolytic proteins at low growth ra...
Preprint
The fission yeast Schizosaccharomyces pombe is a popular eukaryal model organism for cell division and cell cycle studies. With this extensive knowledge of its cell and molecular biology, S. pombe also holds promise for use in metabolism research and industrial applications. However, unlike the baker's yeast Saccharomyces cerevisiae, a major workho...
Article
Full-text available
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the r...
Article
Full-text available
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on gly...
Article
Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here, we experimentally evolved bacteria without nutrient competitio...
Article
Microbes are key to creating safe, edible and enriched fermented food products. This is largely achieved by their metabolism. Thus, the ability to understand the wiring of the complete cellular metabolism is critical to control the fermentation processes. Metabolic modelling is a useful tool for integration of large datasets to link genotype to phe...
Article
Full-text available
Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts' metab...
Preprint
Full-text available
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the r...
Chapter
Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the metabolic and physiological phenomena taking place during this process can be now attained at a genome scale with the help of metabolic models. In this chapter, we present a detailed protocol for modelling w...
Preprint
Full-text available
Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here we experimentally evolved bacteria without nutrient competition...
Article
Full-text available
As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these...
Article
The cAMP-PKA signalling cascade in budding yeast regulates adaptation to changing environments. We developed yEPAC, a FRET-based biosensor for cAMP measurements in yeast. We used this sensor with flow cytometry for high-throughput single cell-level quantification during dynamic changes in response to sudden nutrient transitions. We found that the c...
Article
Full-text available
Genome-scale stoichiometric modeling methods, in particular Flux Balance Analysis (FBA) and variations thereof, are widely used to investigate cell metabolism and to optimize biotechnological processes. Given (1) a metabolic network, which can be reconstructed from an organism’s genome sequence, and (2) constraints on reaction rates, which may be b...
Article
Full-text available
Cells adapt to different conditions via gene expression that tunes metabolism for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs. Resource allocation under proteome constraints has explained regulatory strategies in bacteria. It is unclear, however, to what extent these constraints ca...
Article
Full-text available
The turbidity of milk prohibits the use of optical density measurements for strain characterizations. This often limits research to laboratory media. Here, we cleared milk through centrifugation to remove insoluble milk solids. This resulted in a clear liquid phase, termed milk serum, in which optical density measurements can be used to track micro...
Preprint
Full-text available
Yeasts constitute over 1500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabol...
Preprint
Full-text available
Yeasts constitute over 1500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts' metabol...
Article
Full-text available
Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural m...
Article
Full-text available
In S. cerevisiae and many other micro-organisms an increase in metabolic efficiency (i.e. ATP yield on carbon) is accompanied by a decrease in growth rate. From a fundamental point of view, studying these yield-rate trade-offs provides insight in for example microbial evolution and cellular regulation. From a biotechnological point of view, increas...
Article
Full-text available
In-depth understanding of microbial growth is crucial for the development of new advances in biotechnology and for combating microbial pathogens. Condition-specific proteome expression is central to microbial physiology and growth. A multitude of processes are dependent on the protein expression, thus, whole-cell analysis of microbial metabolism us...
Article
Full-text available
The metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterization is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be...
Article
Full-text available
Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selectiv...
Preprint
Full-text available
Cells adapt to different conditions via gene expression that tunes metabolism and stress resistance for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs; Resource allocation under proteome constraints has emerged as a powerful paradigm to explain regulatory strategies in bacteria. It is...
Article
Full-text available
Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional syste...
Article
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights in the species L. lactis, including the resolution of...
Article
Full-text available
In this study, we have investigated the cheese starter culture as a microbial community through a question: can the metabolic behaviour of a co-culture be explained by the characterized individual organism that constituted the co-culture? To address this question, the dairy-origin lactic acid bacteria Lactococcus lactis subsp. cremoris, Lactococcus...
Preprint
Full-text available
The metabolic capabilities of cells determine their biotechnological potential, role in ecosystems, or threat level as a pathogen. Their comprehensive experimental characterisation is generally not feasible, in particular for unculturable or extremophile microorganisms. In principle, all metabolic capabilities can be computed from an organism's ann...
Article
Full-text available
Amino acids are attractive metabolites for the pharmaceutical and food industry field. On one hand, the construction of microbial cell factories for large-scale production aims to satisfy the demand for amino acids as bulk biochemical. On the other hand, amino acids enhance flavor formation in fermented foods. Concerning the latter, flavor formatio...
Article
Full-text available
Many cancer cells consume glutamine at high rates; counterintuitively, they simultaneously excrete glutamate, the first intermediate in glutamine metabolism. Glutamine consumption has been linked to replenishment of tricarboxylic acid cycle (TCA) intermediates and synthesis of adenosine triphosphate (ATP), but the reason for glutamate excretion is...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Systems biologists have been working out the contours of a general theory of microbial physiology for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, cellular metabolism, cellular composition, and steady-state cell growth. The theory makes predictions about f...
Article
Full-text available
Adenosine 5-triphosphate (ATP) is the main free energy carrier in metabolism. In budding yeast, shifts to glucose-rich conditions cause dynamic changes in ATP levels, but it is unclear how heterogeneous these dynamics are at the single-cell level. Furthermore, pH also changes and affects readout of fluorescence-based biosensors for single-cell meas...
Article
Full-text available
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent suc...
Article
Full-text available
Living cells can express different metabolic pathways that support growth. The criteria that determine which pathways are selected in which environment remain unclear. One recurrent selection is overflow metabolism: the simultaneous usage of an ATP-efficient and -inefficient pathway, shown for example in Escherichia coli, Saccharomyces cerevisiae a...
Article
Full-text available
In this paper we try to describe all possible molecular states (phenotypes) for a cell that fabricates itself at a constant rate, given its enzyme kinetics and the stoichiometry of all reactions. For this, we must understand the process of cellular growth: steady-state self-fabrication requires a cell to synthesize all of its components, including...
Preprint
Full-text available
Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional syste...
Chapter
Fungi have received special interest from the biotechnological sector focused on the production of active biomolecules and strain engineering. Genome-scale metabolic models (GEMs) are used to understand and improve their metabolism. GEMs can be obtained using computational methods, but they are susceptible to errors. Here, we describe the process t...
Article
Full-text available
The metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterisation is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be...
Preprint
Full-text available
Adenosine 5-triphosphate (ATP) is the main free energy carrier in metabolism. In budding yeast, shifts to glucose-rich conditions cause dynamic changes in ATP levels, but it is unclear how heterogeneous these dynamics are at the single-cell level. Furthermore, pH also changes and affects readout of fluorescence-based biosensors for single-cell meas...
Article
Full-text available
Acetobacter pasteurianus 386B is a candidate functional starter culture for the cocoa bean fermentation process. To allow in silico simulations of its related metabolism in response to different environmental conditions, a genome-scale metabolic model for A. pasteurianus 386B was reconstructed. This is the first genome-scale metabolic model reconst...
Article
Full-text available
Background A central theme in (micro)biology is understanding the molecular basis of fitness i.e. which strategies are successful under which conditions; how do organisms implement such strategies at the molecular level; and which constraints shape the trade-offs between alternative strategies. Highly standardized microbial laboratory evolution exp...
Article
Microorganisms produce extracellular compounds that affect the final product quality in fermentation processes. Selection of overproducing mutants requires coupling of the extracellular product to the producer genotype, which can be achieved by single-cell compartmentalization. Emulsions contain up to billions of microdroplets/mL which significantl...
Preprint
Full-text available
The cAMP-PKA signalling cascade in budding yeast regulates adaptation to changing environments. Many questions remain about the function of cAMP dynamics, largely because no robust method for in vivo cAMP measurements exists for yeast. Here we developed yEPAC, a FRET-based biosensor for cAMP measurements in yeast. We show that this biosensor can be...
Article
Full-text available
Background Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not...
Article
Full-text available
Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own propert...
Preprint
Full-text available
In each environment, living cells can express different metabolic pathways that support growth. The criteria that determine which pathways are selected remain unclear. One recurrent selection is overflow metabolism: the seemingly wasteful, simultaneous usage of an efficient and an inefficient pathway, shown for example in E. coli, S. cerevisiae and...
Preprint
Full-text available
A major aim of biology is to predict phenotype from genotype. Here we ask if we can describe all possible molecular states (phenotypes) for a cell that fabricates itself at a constant rate, given its enzyme kinetics and the stoichiometry of all reactions (the genotype). For this, we must understand the autocatalytic process of cellular growth which...
Article
Full-text available
Leuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique feature of the obligate heterolactic fermentation, which leads to the production of lactate, ethanol, and/or acetate, and the final product prof...
Article
Full-text available
Growth rate is a near-universal selective pressure across microbial species. High growth rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be precisely tuned within the bounds set by physicochemical constraints. Yet, the metabolic behaviour of many species is characterized by simple relations between growth rat...
Data
Kinetic model of overflow metabolism. The Matlab-code used for modeling overflow metabolism is attached in a compressed folder as a supplement. In the compressed folder, we have also added a text-file with instructions. (ZIP)
Data
Supplementary text containing general derivations and modelled examples. In this text we present our results in full mathematical detail. The harder mathematical steps are illustrated with figures. (PDF)
Data
Core model of L. lactis switch. In this short text we analyse a core model of overflow metabolism in L. lactis using the extremum principle. Code for running the model is also provided. (PDF)
Data
Data analysis coconsumption experiment. All raw data and the Matlab-code used for data analysis can be found in the compressed folder attached to the supplements. (ZIP)
Data
Kinetic model of L. lactis. The Matlab-code used for the kinetic model of L. lactis is attached in a compressed folder as a supplement. In the compressed folder, we have also added a text-file with instructions. (ZIP)
Data
Core model of overflow metabolism. In this short text we analyse a core model of overflow metabolism using the extremum principle. Code for running the model is also provided. (PDF)
Data
Co-consumption of substrates. In this short text we first explain how we found EFMs that simultaneously take up several carbon sources in a genome-scale model. We then present the method and results of our own experiments on co-consumption. (PDF)
Data
Finding coconsumption EFMs. The Python and Matlab-code used for finding co-consuming EFMs are attached in a compressed folder as a supplement. In the compressed folder, we have also added a text-file with instructions. (ZIP)
Data
Estimated uptake rates co-consumption experiments. Shown are the estimated uptake rates (mean and standard deviation) of different carbon sources (normalized for initial concentration) on the different growth media. The letters that indicate the conditions denote the available carbon sources in the medium: S = Succinate, L = maLtose, M = Mannose, X...
Data
Growth rates co-consumption experiments. Estimated growth rates from separate biological replicates. (TXT)
Data
Substrate concentrations co-consumption experiments. For all different growth media, we include an excell-sheet. Shown are the measured concentrations of carbon sources (normalized for initial concentration), with the corresponding Optical Density (OD). The letters that indicate the conditions denote the available carbon sources in the medium: S =...