Research Output 1983 2020

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2020

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 1 Mar 2020, In : Chemosphere. 242, 125102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chemostats
chemostat
Sewage
Biodegradation
community composition
2019

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
strength (mechanics)
glucose
mutation
chemostat
fitness

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

Özcan, E., Selvi, S. S., Nikerel, E., Teusink, B., Toksoy Öner, E. & Çakır, T., 1 Jan 2019, In : Applied Microbiology and Biotechnology.

Research output: Contribution to JournalArticleAcademicpeer-review

Metabolic Networks and Pathways
Citric Acid
Genome
Bacteria
phosphoketolase

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P. & Bachmann, H., 1 Dec 2019, In : Scientific Reports. 9, 1, 9867.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
ampicillin
antibiotics
viability
cells

A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, S. N., Olivier, B. G., Molenaar, D. & Teusink, B., 7 Aug 2019, In : Genome Biology. 20, 1, 158.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Software
genome
Genome
software
Benchmarking

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 30 Oct 2019, In : Ecotoxicology and Environmental Safety. 182, p. 1-10 10 p., 109414.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chemostats
Metformin
Biodegradability
Biodegradation
Sewage

Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations

Patty, C. H. L., Ariese, F., Buma, W. J., ten Kate, I. L., van Spanning, R. J. M. & Snik, F., May 2019, In : Photosynthesis Research. 140, 2, p. 129-139

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Circular Spectropolarimetric Sensing of Vegetation in the Field: Possibilities for the Remote Detection of Extraterrestrial Life

Patty, C. H. L., Ten Kate, I. L., Buma, W. J., Van Spanning, R. J. M., Steinbach, G., Ariese, F. & Snik, F., 3 Oct 2019, In : Astrobiology. 19, 10, p. 1221-1229 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Exobiology
extraterrestrial life
circular polarization
vegetation
polarization

Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity

Wels, M., Siezen, R., Van Hijum, S., Kelly, W. J. & Bachmann, H., 31 Jan 2019, In : Frontiers in Microbiology. 10, January, p. 1-18 18 p., 4.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Genotype
Genome
Phenotype
Dairying

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

Van Der Veer, C., Hertzberger, R. Y., Bruisten, S. M., Tytgat, H. L. P., Swanenburg, J., De Kat Angelino-Bart, A., Schuren, F., Molenaar, D., Reid, G., De Vries, H. & Kort, R., 29 Mar 2019, In : Microbiome. 7, 1, p. 1-14 14 p., 49.

Research output: Contribution to JournalArticleAcademicpeer-review

File
Microbiota
Genomics
Glycogen
Glycosylation
Lactobacillus

Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans

Kremer, K., van Teeseling, M. C. F., Schada von Borzyskowski, L., Bernhardsgrütter, I., van Spanning, R. J. M., Gates, A. J., Remus-Emsermann, M. N. P., Thanbichler, M. & Erb, T. J., 9 Jul 2019, In : mBio. 10, 4, p. 1-15 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Paracoccus denitrificans
Acetyl Coenzyme A
Carbon
Growth
Biomass

Finding functional differences between species in a microbial community: Case studies in wine fermentation and Kefir culture

Melkonian, C., Gottstein, W., Blasche, S., Kim, Y., Abel-Kistrup, M., Swiegers, H., Saerens, S., Edwards, N., Patil, K. R., Teusink, B. & Molenaar, D., 25 Jun 2019, In : Frontiers in Microbiology. 10, JUNE, p. 1-14 14 p., 01347.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Wine
Fermentation
Metagenomics
Gluconobacter
Pantoea

Harmonizing semantic annotations for computational models in biology

Neal, M. L., König, M., Nickerson, D., Misirli, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., Crook, S., De Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., Myers, C. & 8 othersOlivier, B. G., Sauro, H. M., Scharm, M., Snoep, J. L., Touré, V., Wipat, A., Wolkenhauer, O. & Waltemath, D., 22 Mar 2019, In : Briefings in bioinformatics. 20, 2, p. 540-550 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Semantics
Research Personnel
Biota
Biological Science Disciplines
Theoretical Models

In vivo characterisation of fluorescent proteins in budding yeast

Botman, D., de Groot, D. H., Schmidt, P., Goedhart, J. & Teusink, B., 19 Feb 2019, In : Scientific Reports. 9, p. 1-14 14 p., 2234.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Saccharomycetales
Proteins
Codon
Yeasts
Saccharomyces cerevisiae

Microbial Communities in Sediments From Four Mildly Acidic Ephemeral Salt Lakes in the Yilgarn Craton (Australia) - Terrestrial Analogs to Ancient Mars

Aerts, J. W., van Spanning, R. J. M., Flahaut, J., Molenaar, D., Bland, P. A., Genge, M. J., Ehrenfreund, P. & Martins, Z., 6 May 2019, In : Frontiers in Microbiology. 10

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms

Rijavec, T., Zrimec, J., van Spanning, R. & Lapanje, A., 1 Jan 2019, In : Advanced Science. 1901408.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
biofilms
Biofilms
Corrosion
Biofouling
corrosion

Stereoselective Chemoenzymatic Cascade Synthesis of the bis-THF Core of Acetogenins

van Lint, M. J., Hall, M., Faber, K., van Spanning, R. J. M., Ruijter, E. & Orru, R. V. A., 7 Feb 2019, In : European Journal of Organic Chemistry. 2019, 5, p. 1092-1101 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acetogenins
epoxy compounds
Epoxy Compounds
Biological Products
cascades

Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must

Sirén, K., Mak, S. S. T., Melkonian, C., Carøe, C., Swiegers, J. H., Molenaar, D., Fischer, U. & Thomas P Gilbert, M., 1 Jan 2019, In : Frontiers in Microbiology. 10, APR, 697.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fermentation
Metagenomics
Saccharomyces
Metschnikowia
Biodiversity

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

de Groot, D. H., van Boxtel, C., Planque, R., Bruggeman, F. J. & Teusink, B., 11 Mar 2019, In : PLoS Computational Biology. 15, 3, p. 1-24 24 p., e1006858.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
biochemical pathways
Pathway
enzyme
Fluxes
2018

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Atashgahi, S., Hornung, B., Van Der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., Van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 14 Mar 2018, In : Scientific Reports. 8, 1, p. 1-12 12 p., 4490.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbial Consortia
Benzene
Nitrates
Oxygen
Genes

Alignment of microbial fitness with engineered product formation: Obligatory coupling between acetate production and photoautotrophic growth

Du, W., Jongbloets, J. A., van Boxtel, C., Hernández, H. P., Lips, D., Olivier, B. G., Hellingwerf, K. J. & dos Santos, F. B., 13 Feb 2018, In : Biotechnology for Biofuels. 11, 38, p. 1-13 13 p., 38.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
acetate
Acetates
fitness
Cyanobacteria
production system

Altering textural properties of fermented milk by using surface-engineered Lactococcus lactis

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., 9 May 2018, In : Microbial Biotechnology.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fermented milk
Lactococcus lactis
Milk
Dairy products
Hydrophobicity

Dynamic elementary mode modelling of non-steady state flux data

Folch-Fortuny, A., Teusink, B., Hoefsloot, H. C. J., Smilde, A. K. & Ferrer, A., 18 Jun 2018, In : BMC Systems Biology. 12, p. 1-15 15 p., 71.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Flux Analysis
Fluxes
Discriminant Analysis
Metabolic Networks and Pathways
Modeling

Further elucidation of galactose utilization in Lactococcus lactis MG1363

Solopova, A., Bachmann, H., Teusink, B., Kok, J. & Kuipers, O. P., 3 Aug 2018, In : Frontiers in Microbiology. 9, AUGUST, p. 1-9 9 p., 1803.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Galactose
Lactose
Lactococcus
Membrane Transport Proteins

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry

Patty, C. H. L., Luo, D. A., Snik, F., Ariese, F., Buma, W. J., ten Kate, I. L., van Spanning, R. J. M., Sparks, W. B., Germer, T. A., Garab, G. & Kudenov, M. W., Jun 2018, In : Biochimica et Biophysica Acta - General Subjects. 1862, 6, p. 1350-1363 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Circular polarization
Polarimeters
Veins
Acer
Imaging techniques

Influence of lactococcal surface properties on cell retention and distribution in cheese curd

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., Oct 2018, In : International Dairy Journal. 85, p. 73-78 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Surface Properties
milk curds
Cheese
cheeses
cells

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

Bosdriesz, E., Wortel, M. T., Haanstra, J. R., Wagner, M. J., De La Torre Cortés, P. & Teusink, B., 3 Apr 2018, In : Scientific Reports. 8, 1, p. 1-9 9 p., 5576.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Facilitated Diffusion
Facilitative Glucose Transport Proteins
Glycolysis
Saccharomyces cerevisiae
Carrier Proteins

Maintaining maximal metabolic flux by gene expression control

Planqué, R., Hulshof, J., Teusink, B., Hendriks, J. C. & Bruggeman, F. J., 20 Sep 2018, In : PLoS Computational Biology. 14, 9, p. 1-20 20 p., e1006412.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolites
Metabolic Networks and Pathways
Gene expression
Gene Expression
gene expression

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Wortel, M. T., Noor, E., Ferris, M., Bruggeman, F. J. & Liebermeister, W., 16 Feb 2018, In : PLoS Computational Biology. 14, 2, e1006010.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
variable costs
microbial growth
Enzymes
Trade-offs
enzyme

Naturally fermented milk from northern Senegal: Bacterial community composition and probiotic enrichment with Lactobacillus rhamnosus

Parker, M., Zobrist, S., Donahue, C., Edick, C., Mansen, K., Nadjari, M. H. Z., Heerikhuisen, M., Sybesma, W., Molenaar, D., Diallo, A. M., Milani, P. & Kort, R., 21 Sep 2018, In : Frontiers in Microbiology. 9, September, p. 1-12 12 p., 2218.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

SBML Level 3 Package: Flux Balance Constraints version 2

Olivier, B. G. & Bergmann, F. T., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-39 39 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Social Planning
Genome
Proteins

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L. & Waltemath, D., 19 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-98 98 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Language
Reproduction
Software
Research

Sulfur cave (Romania), an extreme environment with microbial mats in a Co2-H2S/O2 gas chemocline dominated by mycobacteria

Sarbu, S. M., Aerts, J. W., Flot, J. F., van Spanning, R. J. M., Baciu, C., Ionescu, A., Kis, B. M., Incze, R., Siko-Barabasi, S., Para, Z., Hegyeli, B., Atudorei, N. V., Barr, C., Nealson, K. H., Forray, F. L., Lascu, C., Fleming, E. J., Bitter, W. & Popa, R., 1 Jan 2018, In : International Journal of Speleology. 47, 2, p. 173-187 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
microbial mat
cave
sulfur
gas
biofilm

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-182 182 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Systems Biology
Language
Software
Biological Phenomena
Metabolic Networks and Pathways

Training for translation between disciplines: A philosophy for life and data sciences curricula

Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J. & Heringa, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i4-i12 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Understanding start-up problems in yeast glycolysis

Overal, G. B., Teusink, B., Bruggeman, F. J., Hulshof, J. & Planqué, R., May 2018, In : Mathematical Biosciences. 299, May, p. 117-126 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Start-up
glycolysis
Yeast
Yeasts
2017

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates

Tarazanova, M., Huppertz, T., Beerthuyzen, M., van Schalkwijk, S., Janssen, P. W. M., Wels, M., Kok, J. & Bachmann, H., 7 Sep 2017, In : Frontiers in Microbiology. 8, SEP

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Surface Properties
Milk Proteins
Protein Binding
Hydrophobic and Hydrophilic Interactions

Circular spectropolarimetric sensing of chiral photosystems in decaying leaves

Patty, C. H. L., Visser, L. J. J., Ariese, F., Buma, W. J., Sparks, W. B., van Spanning, R. J. M., Röling, W. F. M. & Snik, F., 1 Mar 2017, In : Journal of Quantitative Spectroscopy and Radiative Transfer. 189, p. 303-311 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Circular polarization
circular polarization
leaves
chlorophylls
plant stress

Comparison of landfarming amendments to improve bioremediation of petroleum hydrocarbons in Niger Delta soils

Brown, D. M., Okoro, S., van Gils, J., van Spanning, R., Bonte, M., Hutchings, T., Linden, O., Egbuche, U., Bruun, K. B. & Smith, J. W. N., 15 Oct 2017, In : Science of the Total Environment. 596-597, p. 284-292 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bioremediation
Petroleum
petroleum hydrocarbon
Hydrocarbons
bioremediation

Draft genome Sequences of 11 Lactococcus lactis subsp. cremoris strains

Wels, M., Backus, L., Boekhorst, J., Dijkstra, A., Beerthuyzen, M., Siezen, R. J., Bachmann, H. & van Hijum, S. A. F. T., 2017, In : Genome Announcements. p. e01739-16

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Genome
Dairy Products
Fermentation
Lactic Acid

Draft genome sequences of 24 Lactococcus lactis strains

Backus, L., Wels, M., Boekhorst, J., Dijkstra, A. R., Beerthuyzen, M., Kelly, W. J., Siezen, R. J., van Hijum, S. A. F. T. & Bachmann, H., 2017, In : Genome Announcements. p. e01737-16

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Genome
Cultured Milk Products
Geographic Locations
Lactic Acid

Effects of growth rate and promoter activity on single-cell protein expression

Nordholt, N., Van Heerden, J., Kort, R. & Bruggeman, F. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 6299.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Noise
Growth
Proteins
Biochemical Phenomena
Synthetic Genes

Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria

Bachmann, H., Molenaar, D., Branco dos Santos, F. & Teusink, B., 1 Aug 2017, In : FEMS Microbiology Reviews. 41, Supp_1, p. S201-S219

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactic Acid
Bacteria
Resource Allocation
Population Dynamics
Research Design

Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest

Bisschops, M. M. M., Luttik, M. A. H., Doerr, A., Verheijen, P. J. T., Bruggeman, F., Pronk, J. T. & Daran-Lapujade, P., 1 Jan 2017, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1864, 1, p. 231-242 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Yeasts
Growth
Batch Cell Culture Techniques
G1 Phase
Eukaryotic Cells

Low affinity membrane transporters can increase net substrate uptake rate by reducing efflux

Bosdriesz, E., Wortel, M. T., Haanstra, J. R., Wagner, M., de la Torre Cortés, P. & Teusink, B., 2 Nov 2017, In : bioRxiv.

Research output: Contribution to JournalArticleAcademic

Maintaining maximal metabolic rates by gene expression control

Planque, R., Hulshof, J., Teusink, B., Hendriks, J. C. & Bruggeman, F. J., 9 Mar 2017, In : bioRxiv.

Research output: Contribution to JournalArticleAcademicpeer-review

Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough

dos Santos, F. B., Olivier, B. G., Boele, J., Krumpochova, P., Klau, G. W., Giera, M. & Teusink, B., 1 Nov 2017, In : Applied and Environmental Microbiology. 83, 21

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bordetella pertussis
whooping cough
Whooping Cough
thiosulfate
physiology

Statistics and simulation of growth of single bacterial cells: Illustrations with B. subtilis and E. coli

Van Heerden, J. H., Kempe, H., Doerr, A., Maarleveld, T., Nordholt, N. & Bruggeman, F. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 16094.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
statistics
cells
simulation
proteins
Bacillus

Systems biology of lactic acid bacteria: For food and thought

Teusink, B. & Molenaar, D., 1 Dec 2017, In : Current Opinion in Systems Biology. 6, p. 7-13 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Systems Biology
Lactic acid
Bacteria
Lactic Acid
Food

Targeting pathogen metabolism without collateral damage to the host.

Haanstra, J. R., Gerding, A., Dolga, A. M., Sorgdrager, F. J., Buist-Homan, M., du Toit, F., Faber, K. N., Holzhutter, H. G., Szoor, B., Matthews, K. R., Snoep, J. L., Westerhoff, H. V. & Bakker, B. M., 2017, In : Scientific Reports. 7, 40406.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access