1988 …2019
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Research Output 1988 2019

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Article
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

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

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

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

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
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

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

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
2017

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

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
2016

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

Dols, J. A. M., Molenaar, D., van der Helm, J. J., Caspers, M. P., de Kat Angelino-Bart, A., Schuren, F. H., Speksnijder, A. G., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de Vries, H. J. & Kort, R., 2016, In : BMC Infectious Diseases. 16, 180.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Non-hierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp PCC6803.

Du, W., Angermayr, S. A., Jongbloets, J. A., Molenaar, D., Bachmann, H., Hellingwerf, K. J. & Santos, F., 2016, In : ACS synthetic biology. 2016/12/12

Research output: Contribution to JournalArticleAcademicpeer-review

Public goods and metabolic strategies

Bachmann, H., Bruggeman, F. J., Molenaar, D., Santos, F. & Teusink, B., Jun 2016, In : Current Opinion in Microbiology. 31, p. 109-115

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2015

Amino acid analysis using chromatography–mass spectrometry: An inter platform comparison study

Krumpochova, P., Bruyneel, B., Molenaar, D., Koukou, A., Wuhrer, M., Niessen, W. M. A. & Giera, M. A., 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 114, p. 398-407

Research output: Contribution to JournalArticleAcademicpeer-review

Spectrometry
Spectrum Analysis
Liquid chromatography
Liquid Chromatography
Amino Acids

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

Bosdriesz, E., Magnúsdóttir, S., Bruggeman, F. J., Teusink, B. & Molenaar, D., 2015, In : The FEBS Journal. 282, p. 2394-2407 12.

Research output: Contribution to JournalArticleAcademicpeer-review

Carrier Proteins
Substrates
Nutrients
Food
Active Biological Transport

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

Weerdenburg, E. M., Abdallah, A., Rangkuti, F., Abd El Ghany, M., Otto, T. D., Adroub, S. A., Molenaar, D., Ummels, R., Ter Veen, K., van Stempvoort, G., van der Sar, A. M., Ali, S., Langridge, G. C., Thomson, N. R., Pain, A. & Bitter, W., 2015, In : Infection and Immunity. 83, p. 1778-1788 5.

Research output: Contribution to JournalArticleAcademicpeer-review

Mycobacterium marinum
Mutagenesis
Virulence
Genome
Phagocytes

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization.

Bosdriesz, E., Molenaar, D., Teusink, B. & Bruggeman, F. J., 2015, In : The FEBS Journal. 282, p. 2029-2044 10.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ribosomes
Bacteria
Escherichia coli
Growth
Ribosomal Proteins

Molecular analysis of the vaginal microbiome: an alternative for the diagnosis of bacterial vaginosis?

Dols, J. A. M., Molenaar, D., Helm, J., Caspers, M. P. M., de Kat-Angelino, A., Speksnijder, A. G. C. L., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de vries, H. J. C. & Kort, R., 2015, In : BMC Infectious Diseases.

Research output: Contribution to JournalArticleAcademicpeer-review

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Santos, F., Giera, M. A., Fusetti, F., Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P. & Teusink, B., 2015, In : Molecular Microbiology. 97, p. 77-92 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Fermentation
Costs and Cost Analysis
Glucose
Growth
Proteins
2013

Availability of public goods shapes the evolution of competing metabolic strategies.

Bachmann, H., Fischlechner, M., Rabbers, I., Barfa, N., Branco dos Santos, F., Molenaar, D. & Teusink, B., 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, p. 14302-14307

Research output: Contribution to JournalArticleAcademicpeer-review

biomass
emulsions
organisms
privatization
Lactococcus lactis

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C., Teusink, B. & Heringa, J., Sep 2013, In : Briefings in bioinformatics. 14, 5, p. 589-98 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
Bioinformatics
Computational Biology
Students
Teaching

Genome instability in Lactobacillus rhamnosus GG

Sybesma, W., Molenaar, D., Ijcken, W., Venema, K. & Kort, R., 2013, In : Applied and Environmental Microbiology. 79, p. 2233-2239

Research output: Contribution to JournalArticleAcademicpeer-review

Lactobacillus rhamnosus
Genomic Instability
probiotics
genome
gene

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism

Berkhout, J., Bosdriesz, E., Nikerel, E., Molenaar, D., de Ridder, D., Teusink, B. & Bruggeman, F. J., 2013, In : Genetics. 194, 2, p. 505-512

Research output: Contribution to JournalArticleAcademicpeer-review

Vesicle trafficking via the Spitzenkoerper during hyphal tip growth in Rhizoctonia solani

Dijksterhuis, J. & Molenaar, D., 2013, In : Antonie van Leeuwenhoek. 103, p. 921-931

Research output: Contribution to JournalArticleAcademicpeer-review

Rhizoctonia
Secretory Vesicles
Cytoplasm
Growth
Cell Membrane
2012

A standardized assay medium to measure enzyme activities of lactococcus lactis while mimicking intracellular conditions.

Goel, A., Santos, F., Vos, W. M., Teusink, B. & Molenaar, D., 2012, In : Applied and Environmental Microbiology. 78, 8, p. 134-143

Research output: Contribution to JournalArticleAcademicpeer-review

Lactococcus lactis
enzyme activity
assay
assays
Enzymes

Metabolic shifts: a fitness perspective for microbial cell factories.

Goel, A., Wortel, M. T., Molenaar, D. & Teusink, B., 2012, In : Biotechnology Letters. 34, p. 2147-2160

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Industrial plants
Metabolism
Microorganisms
Nutrients
Systems Biology
Lactococcus lactis
Milk
Plasmids
Growth
Genome

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution.

Bachmann, H., Starrenburg, M. J., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2012, In : Genome Research. 22, p. 115-124

Research output: Contribution to JournalArticleAcademicpeer-review

Lactococcus lactis
Milk
Plasmids
Growth
Genome

"PhenoLink - a webtool for linking phenotype to -omics data for bacteria: application to gene-trait matching for lactobacillus plantarum strains.

Bayjanov, J. R., Molenaar, D., Tzeneva, V., Siezen, R. J. & Hijum, S. A., 2012, In : BMC Genomics. 13, p. 170

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Lactobacillus plantarum
Bacteria
Phenotype
Genes
Nitrogen Dioxide
2011

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4+/NH3

Boogerd, F. C., Ma, H., Bruggeman, F. J., van Heeswijk, W. C., Garcia-Contreras, R., Molenaar, D., Krab, K. & Westerhoff, H. V., 3 Jan 2011, In : FEBS Letters. 585, 1, p. 23-28

Research output: Contribution to JournalArticleAcademicpeer-review

Explorin metabolic pathway reconstruction and genome-wide expression profiling in lactobacillus reuteri to define functional probiotic features.

Saulnier, D. M. A., Santos, F., Roos, S., Mistretta, T-A., Spinler, J. K., Molenaar, D., Teusink, B. & Versalovic, J., 2011, In : PLoS ONE. 6, p. e18783

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Lactobacillus reuteri
Probiotics
Metabolic Networks and Pathways
probiotics
biochemical pathways

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis

Rud, I., Naterstad, K., Bongers, R. S., Molenaar, D., Kleerebezem, M. & Axelsson, L., 2011, In : Microbial Biotechnology. 4, p. 345-356

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Functional Identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis.

Santos, F., Spinler, J. K., Saulnier, D. M. A., Molenaar, D., Teusink, B., de Vos, D. L., Versalovic, J. & Hugenholtz, J., 2011, In : Microbial Cell Factories. 10, p. 55

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Lactobacillus reuteri
Vitamin B Complex
Transcription factors
Vitamins
Vitamin B 12

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

Siezen, R. J., Bayjanov, J. R., Felis, G. E., van der Sijde, M. R., Starrenburg, M., Molenaar, D., Wels, M., Hijum, S. A. & van Hylckama Vlieg, J. E. T., 2011, In : Microbial Biotechnology. 4, p. 383-402

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Comparative Genomic Hybridization
Genes
Genome
Multigene Family

High local substrate availability stabilizes a cooperative trait.

Bachmann, H., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2011, In : ISME Journal. 5, p. 929-932

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
peptide
milk
cooperatives
Peptide Hydrolases
proteinases

Identification of lactobacillus plantarum genes modulating, the cytokine response of human peripheral blood mononuclear cells.

van Hemert, S., Meijerink, M., Molenaar, D., Bron, P. A., de Vos, D. L., Kleerebezem, M., Wells, J. M. & Marco, M. L., 2011, In : BMC Microbiology. 10, p. 293

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Lactobacillus plantarum
Blood Cells
Cytokines
Interleukin-12
Genes

Systems Biology of lactic acid bacteria: a critical review.

Teusink, B., Bachmann, H. & Molenaar, D., 2011, In : Microbial Cell Factories. 10, A11, 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Systems Biology
Lactic acid
Systems Analysis
Lactic Acid
Bacteria

Volatile compound fingerprinting of mixed-culture fermentations.

de Bok, F. A. M., Janssen, P. W. M., Bayjanov, J. R., Sieuwerts, S., Lommen, A., van Hylckama Vlieg, J. E. T. & Molenaar, D., 2011, In : Applied and Environmental Microbiology. 77, p. 6233-6239

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
2010

Characterization of cellular composition of evolved strains of Lactococcus lactis

Price, C. J., Santos, F., Molenaar, D., Teusink, B., Poolman, B. & Kuipers, O. P., Jun 2010, In : The FEBS Journal. 277, p. 114-114

Research output: Contribution to JournalArticleAcademicpeer-review

Complete genome sequence of Lactococcus lactis subsp. Lactis KF147, a plant-associated lactic acid bacterium.

Siezen, R. J., Bayjanov, J., Renckens, B., Wels, M., van Hijum, S. A. F. T., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Journal of Bacteriology. 192, p. 2649-2650

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

Marco, M. L., de Vries, M. C., Wels, M., Molenaar, D., Mangell, P., Ahrne, S., de Vos, W. M., Vaughan, E. E. & Kleerebezem, M., 2010, In : ISME Journal. 4, p. 1481-1484

Research output: Contribution to JournalArticleAcademicpeer-review

Gene expression analysis reveals a gene set discriminatory to different metals in soil.

Nota, B., Verweij, R. A., Molenaar, D., Ylstra, B., van Straalen, N. M. & Roelofs, D., 2010, In : Toxicological Sciences. 115, 1, p. 34-40

Research output: Contribution to JournalArticleAcademicpeer-review

Gene expression
Soil
Genes
Metals
Soils

Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide-stress tolerance.

Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Applied and Environmental Microbiology. 76, p. 3748-3752

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
RNA Polymerase Sigma 54
sigma factors
Lactobacillus plantarum
gene deletion
Peroxides

Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in Streptococcus thermophilus and Lactobacillus bulgaricus

Sieuwerts, S., Molenaar, D., van Hijum, S. A. F. T., Beerthuyzen, M., Stevens, M. J. A., Janssen, P. W. M., Ingham, C. J., de Bok, F. A. M., de Vos, W. M. & Vlieg, J. E. T. V. H., Dec 2010, In : Applied and Environmental Microbiology. 76, 23, p. 7775-7784

Research output: Contribution to JournalArticleAcademicpeer-review

Phenotypic and genomic diversity of Lactobacillues plantarum strains isolated from various environmental niches.

Siezen, R. J., Tzeneva, V. A., Castioni, A., Wels, M., Phan, H. T. K., Rademaker, J. L. W., Starrenburg, M. J. C., Kleerebezem, M., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Environmental Microbiology. 12, 3, p. 758-773

Research output: Contribution to JournalArticleAcademicpeer-review

Physiological responses to folate overproduction in lactobacillys plantarum WCFS1.

Wegkamp, H. B. A., Mars, A. E., Faijes, M., Molenaar, D., de Vos, R. C. H., Klaus, S. M. J., Hanson, A. D., Vos, W. M. & Smid, E. J., 2010, In : Microbial Cell Factories. 9, p. 100 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Sigma 54 mediated control of the mannose PTS in Lactobacillus plantarum impacts on carbohydrate metabolism.

Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Microbiology. 156, p. 695-707

Research output: Contribution to JournalArticleAcademicpeer-review

Bacterial RNA
Sigma Factor
Lactobacillus plantarum
Carbohydrate Metabolism
DNA-Directed RNA Polymerases

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis.

van der Veen, S. ., van Schalkwijk, S., Molenaar, D., de Vos, W. M., Abee, T. & Wells-Bennik, M. H. J., 2010, In : Microbiology. 156, p. 374-384

Research output: Contribution to JournalArticleAcademicpeer-review

2009

A high-throughput cheese manufacturing model for effective cheese starter screening.

Bachmann, H., Kruijswijk, Z., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2009, In : Journal of Dairy Science. 92, p. 5868-5882

Research output: Contribution to JournalArticleAcademicpeer-review

cheese starters
cheesemaking
Cheese
cheeses
screening