Microbiology

Projects

Projects per year 2000 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2021 2022 2023

• 67 Active
• 147 Finished

Projects per year

Search results

• Finished

  Assessing, Regulating, and Adapting Cas nucleases

  Swartjes, T., van der Oost, J. & Staals, R.

  1/10/18 → 3/05/23

  Project: PhD

• Effect of non-digestible carbohydrates on microbiota composition and activity: towards microbiota stratification

  Liu, Z., Smidt, H. & Zoetendal, E.

  1/10/18 → 14/09/23

  Project: PhD

• Gut microbiota development and its relations to child mental development and health

  Ou, Y., Smidt, H. & Belzer, C.

  1/10/18 → 14/04/23

  Project: PhD

  • Mental Development 100%
  • Mental Health 65%
  • Puberty 61%
  • Breast Feeding 54%
  • Behavior Problems 52%

• Exploiting the anti-CRISPR potential to enhance the CRISPR genome engineering toolbox.

  Trasanidou, D. & van der Oost, J.

  3/09/18 → 16/05/23

  Project: PhD

• Anaerobic microbiology of Black Sea

  Fischer, P., Machado de Sousa, D. & Stams, F.

  1/08/18 → 12/05/23

  Project: PhD

  • Black Sea 100%
  • sulfate 68%
  • microbiology 55%
  • methanogenesis 55%
  • amine 50%

• Novel approaches for microbial syngas conversion to chemical building blocks

  Dykstra, J., Machado de Sousa, D., van der Oost, J. & Kengen, S.

  1/06/18 → 3/07/23

  Project: PhD

• Building a Synthetic Cell (BaSyC).

  Finger Bou, M., van der Oost, J., Claassens, N. J. H. P. & Staals, R.

  1/05/18 → 8/09/23

  Project: PhD

• Danone Early Life.

  Schimmel, P., Knol, J. & Belzer, C.

  3/04/18 → 6/12/22

  Project: PhD

  • Nitrogen 100%
  • Metabolism 75%

• From healthy defecation to functional constipation in children and adults a clinical and microbiological perspective

  Wegh, C., Smidt, H. & Belzer, C.

  1/02/18 → 11/11/22

  Project: PhD

  • Constipation 100%
  • Defecation 57%
  • Child 36%
  • Microbiota 35%
  • Fecal Incontinence 29%

• Development of a novel, interdisciplinary model to study interactions between foodborne xenobiotics, the intestinal microbiome and the intestinal epithelium.

  van Dongen, K., Rietjens, I., Beekmann, K. & Belzer, C.

  1/12/17 → 10/06/22

  Project: PhD

  • glycation 100%
  • intestinal microorganisms 73%
  • dietary exposure 66%
  • infant formulas 44%
  • breasts 33%

• Microbes, models and mucins: Modelling host-microbe interactions at the intestinal mucus layer in vitro

  Elzinga, J., Smidt, H. & Belzer, C.

  15/11/17 → 31/05/23

  Project: PhD

  • Host Microbial Interactions 100%
  • Mucins 86%
  • In Vitro Techniques 69%
  • Mucus 42%
  • Polysaccharides 37%

• The effect of a synbiotic nutritional supplement on white matter injury in preterm infants.

  Henderickx, J., Knol, J. & Belzer, C.

  16/10/17 → 25/03/22

  Project: PhD

  • Premature Infants 100%
  • Gastrointestinal Tract 90%
  • Microbiota 37%
  • Infant Care 29%
  • Fungi 24%

• Biobased Production of Valuable Ester Compounds by a Novel Type Alcohol Acetyl Transferase.

  Patinios, C., Weusthuis, R., van der Oost, J. & Kengen, S.

  9/10/17 → 22/04/22

  Project: PhD

  • microbiology 100%
  • engineering 80%
  • esters 69%
  • genome 49%
  • alcoholysis 40%

• ShaPR (Shaping CRISPR scissors and synthetic tools for multiplexed, high-throughput genome editing in yeast).

  Adiego Pérez, B., van der Oost, J. & D'Adamo, S.

  1/10/17 → 13/09/22

  Project: PhD

• Akkermansia muciniphila as a model organism representing Verrucomicrobia in the gut.

  Geerlings, S., de Vos, W. & Belzer, C.

  1/09/17 → 18/01/23

  Project: PhD

• Unravelling ecological concepts that drive general composition patterns, stability, perturbations, and major metabolite production in the intestine.

  Wang, T., Smidt, H. & Zoetendal, E.

  1/09/17 → 21/06/22

  Project: PhD

  • microbiome 100%
  • digestive system 83%
  • irritable bowel syndrome 82%
  • Methanobrevibacter smithii 59%
  • intestinal microorganisms 55%

• Diet as treatment of irritable bowel syndrome.

  Rijnaarts-Modder, I., Witteman, B., Zoetendal, E., de Roos, N. & de Wit, N.

  1/09/17 → 24/06/22

  Project: PhD

  • Irritable Bowel Syndrome 100%
  • Gastrointestinal Microbiome 86%
  • Emotions 69%
  • Diet 60%
  • Dietary Fiber 50%

• Tailored microalgae as a sustainable oil crop production platform.

  Naduthodi, M., Barbosa, M., van der Oost, J. & D'Adamo, S.

  1/09/17 → 13/12/21

  Project: PhD

  • Nannochloropsis 100%
  • gene editing 96%
  • microalgae 73%
  • eicosapentaenoic acid 60%
  • engineering 48%

• Towards a synthetic cell: designing, testing and optimizing functional genomic modules in E. coli

  Houkes, J., van der Oost, J. & Claassens, N. J. H. P.

  1/09/17 → 11/01/23

  Project: PhD

  • Escherichia coli 100%
  • Genomics 82%
  • Cells 76%
  • Testing 40%

• Acidothermophilic Sulphur Bioreduction

  van der Graaf, L., Stams, F. & Sanchez Andrea, I.

  1/07/17 → 5/07/22

  Project: PhD

  • pyrite 100%
  • wastewater 75%
  • acid mine drainage 65%
  • sulfate-reducing bacterium 45%
  • lake 42%

• Zooming into the sponge microbiome in the omics era

  Gavriilidou, A., Sipkema, D. & Smidt, H.

  18/04/17 → 25/05/22

  Project: PhD

  • Porifera 100%
  • microbiome 49%
  • multigene family 15%
  • genome mining 11%
  • microorganisms 10%

• Bioprocess engineering for ethyl acetate production

  Bohnenkamp, A., Weusthuis, R., Wijffels, R. & Kengen, S.

  1/04/17 → 12/11/21

  Project: PhD

  • metabolic engineering 100%
  • ethyl acetate 85%
  • Escherichia coli 56%
  • electrons 21%
  • carbon 19%

• Improving heterologous protein production by tweaking transcript elements.

  Nieuwkoop, T., van der Oost, J. & Claassens, N. J. H. P.

  16/01/17 → 8/12/21

  Project: PhD

  • Codon Usage 100%
  • Proteins 93%
  • Therapeutic Human Experimentation 49%
  • Biotechnology 42%
  • Codon 35%

• The role of the gut microbiota in toxicity and risk assessment of masked Fusarium mycotoxins.

  Jin, J. & Rietjens, I.

  31/12/16 → 9/11/22

  Project: PhD

  • risk assessment 100%
  • toxicity 95%
  • toxin 67%
  • food chain 66%
  • project 33%

• Host-metabolite interactions in the piglet intestine and its relation to diarrhea

  van der Hee, B., Wells, J. & Smidt, H.

  1/11/16 → 28/06/23

  Project: PhD

  • diarrhea 100%
  • piglets 95%
  • comorbidity 83%
  • metabolites 68%
  • intestinal mucosa 57%

• Resilience and stress response pathways of microorganisms used for bioremediation

  Zhang, C., Smidt, H., Atashgahi, S. & Bosma, T.

  1/11/16 → 5/07/23

  Project: PhD

• Colonic and ileal carbohydrate degradation in healthy adults and elderly

  An, R., Smidt, H. & Zoetendal, E.

  15/06/16 → 10/12/20

  Project: PhD

  • microbiome 100%
  • dietary supplements 90%
  • intestinal microorganisms 47%
  • Bifidobacterium 27%
  • small intestine 21%

• Glycans in early life effect the microbiome and determine health

  Kostopoulos, I., Knol, J. & Belzer, C.

  4/04/16 → 8/01/21

  Project: PhD

  • mucins 100%
  • breast milk 92%
  • oligosaccharides 82%
  • digestive system 70%
  • polysaccharides 44%

• Create a toolbox using Cpf1 for bacterial genome engineering

  Wu, W., van der Oost, J. & Staals, R.

  1/03/16 → 12/02/21

  Project: PhD

  • CRISPR-Cas Systems 100%
  • Clustered Regularly Interspaced Short Palindromic Repeats 72%
  • Gene Editing 38%
  • Escherichia coli 17%
  • Ointments 13%

• The host-microbiota interactome in early life and its role in gut immune development

  de Vries, H., Smidt, H. & Wells, J.

  1/02/16 → 14/12/22

  Project: PhD

  • weaning 100%
  • digestive system 92%
  • microbiome 55%
  • antibiotics 42%
  • oral vaccination 40%

• Fermentation and cooperation by marine anaerobes

  van Vliet, D., Stams, F. & Sanchez Andrea, I.

  2/11/15 → 8/09/21

  Project: PhD

  • Black Sea 100%
  • microorganism 74%
  • sulfur 73%
  • seawater 69%
  • sediment 46%

• Sporulation and its significance to butanol production in C. acetobutylicum

  Diallo, M., van der Oost, J., Kengen, S. & Lopez Contreras, A.

  19/10/15 → 7/04/21

  Project: PhD

  • Clostridium beijerinckii 100%
  • sporulation 66%
  • genomics 41%
  • Clostridia 36%
  • mutants 21%

• Metabolic engineering of thermophilic clostridia for production of dicarboxylic acids

  Koendjbiharie, J. & van Kranenburg, R.

  1/10/15 → 4/03/20

  Project: PhD

  • NAD (coenzyme) 100%
  • succinic acid 92%
  • transaldolase 84%
  • succinate dehydrogenase (quinone) 74%
  • phosphofructokinases 65%

• Genetic tool development and sporulation mechanisms in thermophilic clostridia

  Ganguly, J. & van Kranenburg, R.

  1/10/15 → 20/05/20

  Project: PhD

  • Clostridia 100%
  • xylose 75%
  • plasmids 40%
  • fermentation 36%
  • crossover interference 36%

• Molecular characterization of the novel Cpf1-type CRISPR-Cas system

  Mohanraju, P., van der Oost, J. & Swarts, D.

  2/03/15 → 25/10/19

  Project: PhD

  • Clustered Regularly Interspaced Short Palindromic Repeats 100%
  • Gene Editing 94%
  • Temperature 48%
  • DNA 37%
  • Geobacillus 33%

• Functional metagenomics of microalgae-bacteria consortia to imrpove large-scale outdoor algae cultivation

  Lian, J., Smidt, H., Wijffels, R. & Sipkema, D.

  20/10/14 → 2/07/20

  Project: PhD

  • photobioreactors 100%
  • bacterial communities 71%
  • algae 65%
  • Nannochloropsis 55%
  • bacteria 44%

• Microbial networks as biocatalysts for anaerobic syngas conversion

  Diender, M., Stams, F. & Machado de Sousa, D.

  1/10/14 → 8/02/19

  Project: PhD

  • fermentation 100%
  • gas 64%
  • chemical 62%
  • metabolism 46%
  • carbon monoxide 35%

• The Journey of the Agronautes

  Hegge, J., van der Oost, J. & Staals, R.

  1/10/14 → 10/05/19

  Project: PhD

  • Pyrococcus furiosus 100%
  • Clostridium butyricum 99%
  • Thermus thermophilus 92%
  • gene editing 84%
  • single-stranded DNA 78%

• High-throughput alternatives for generration and screening of variant bacterial production strains

  Mougiakos, I., van Kranenburg, R. & van der Oost, J.

  1/10/14 → 15/03/19

  Project: PhD

  • Fuel 100%
  • Metabolic 99%
  • Green 83%
  • Biofuel 66%
  • Dicarboxylic Acid 64%

• Isolation, identification and characterization of sponge-associated microbes producing novel antibiotics

  Indraningrat, A., Smidt, H., Becking, L. & Sipkema, D.

  22/09/14 → 29/05/19

  Project: PhD

  • sponge 100%
  • community composition 40%
  • antimicrobial activity 36%
  • deep sea 25%
  • metabolite 19%

• Anaerobic microorganisms in the human intestine

  Shetty, S., Smidt, H. & de Vos, W.

  1/08/14 → 20/03/19

  Project: PhD

  • intestinal microorganisms 100%
  • microbiome 96%
  • ecosystems 20%
  • Eubacterium hallii 17%
  • intestines 15%

• Design and properties of the complex microbial communities derived from wildlife, domestic animals and human

  Umanetc, A. & Smidt, H.

  14/07/14 → 17/10/19

  Project: PhD

  • wild animals 100%
  • domestic animals 96%
  • intestinal microorganisms 92%
  • microbiome 89%
  • environmental factors 58%

• Microbial Host-virus interaction in human GI tract

  Zhu, Y., de Vos, W., van der Oost, J. & Staals, R.

  1/04/14 → 3/05/19

  Project: PhD

  • Cleavage 100%
  • Application 45%

• Novel Anaerobes

  Strepis, N., Stams, F., Machado de Sousa, D. & Schaap, P.

  17/03/14 → 16/01/19

  Project: PhD

  • Trichococcus 100%
  • inulin 58%
  • propanediols 50%
  • Thiocystis minor 26%
  • screening 18%

• Unravelling details of microbial transformation of polychlorinated dibenzo-p-dioxins and dibenzofurans

  Peng, P., Smidt, H. & Atashgahi, S.

  24/02/14 → 6/09/19

  Project: PhD

  • organohalogen 100%
  • halogen 74%
  • chloroform 53%
  • gene 35%
  • bacterium 35%

• How invaders suppress CRISPR-mediated immunity

  Vlot, M., van der Oost, J. & Brouns, S.

  1/02/14 → 29/08/18

  Project: PhD

  • Bacteriophages 100%
  • CRISPR-Cas Systems 20%
  • Clustered Regularly Interspaced Short Palindromic Repeats 14%
  • DNA 14%
  • Nucleic Acids 12%

• Co-Cultivation of Sponge Cells and Microorganisms

  Gutleben, J., Smidt, H., Wijffels, R. & Sipkema, D.

  1/02/14 → 21/11/19

  Project: PhD

  • Porifera 100%
  • microorganisms 56%
  • multiomics 25%
  • microbial communities 9%
  • Otus 8%

• The effect of the nutrient matrix on biofilm formation in membrane filtration units

  de Vries, R., Stams, F. & Plugge, C.

  15/01/14 → 11/03/22

  Project: PhD

  • fouling 100%
  • membrane 70%
  • bacterium 66%
  • biofilm 21%
  • nutrient limitation 16%

• Mucosal syntrophy and early life imprinting.

  Chia, L. W., Knol, J. & Belzer, C.

  9/12/13 → 20/06/18

  Project: PhD

  • mucins 100%
  • breast milk 92%
  • symbionts 85%
  • oligosaccharides 82%
  • butyrates 77%

• The development of intestinal microbiota in early infancy and its role in allergy

  Wopereis, H. J., Knol, J., de Vos, W. & Belzer, C.

  1/11/13 → 22/05/19

  Project: PhD

  • intestinal microorganisms 100%
  • microbiome 96%
  • early development 91%
  • prebiotics 56%
  • eczema 52%