Research Output

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2019

Synthetic Methanol and Formate Assimilation Via Modular Engineering and Selection Strategies

Claassens, N. J., He, H. & Bar-Even, A., 2019, Methylotrophs and Methylotroph Communities. Chistoserdova, L. (ed.). Caister Academic Press, Vol. 33. p. 237-248

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
2017

Copy, cut and paste: From single genes to synthetic chromosomes

Claassens, N. J., Gibson, D., Hutchison III, C. A. & van der Oost, J., 2017, Mighty Microbes. p. 48-52

Research output: Chapter in Book/Report/Conference proceedingChapter

2016

Comparative genomics and transcriptomics of organohalide-respiring bacteria and regulation of rdh gene transcription

Hansen, T., Smidt, H. & Lechner, U., 2016, Organohalide-Respiring Bacteria. Adrian, L. & Löffler, F. E. (eds.). Springer Verlag, p. 345-376

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Citations (Scopus)

Correlating the Gut Microbiome to Health and Disease

Marques, T. M., Holster, S., Wall, R., König, J., Brummer, R. J. & de Vos, W., 2016, The Gut-Brain Axis Dietary, Probiotic, and Prebiotic Interventions on the Microbiota. Elsevier Inc. Academic Press, p. 261-291

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

How to manipulate the microbiota: Fecal microbiota transplantation

Fuentes Enriquez de Salamanca, S. & de Vos, W. M., 2016, Microbiota of the Human Body. Schwiertz, A. (ed.). Springer, Vol. 902. p. 143-153 (Advances in Experimental Medicine and Biology; vol. 902).

Research output: Chapter in Book/Report/Conference proceedingChapter

12 Citations (Scopus)

Overview of known organohalide-respiring bacteria-phylogenetic diversity and environmental distribution

Atashgahi, S., Lu, Y. & Smidt, H., 1 Jan 2016, Organohalide-Respiring Bacteria. Adrian, L. & Löffler, F. E. (eds.). Springer Verlag, p. 63-105

Research output: Chapter in Book/Report/Conference proceedingChapter

33 Citations (Scopus)

Studying the Mammalian Intestinal Microbiome Using Animal Models

Hugenholtz, F., Zhang, J., O'Toole, P. W. & Smidt, H., 2016, Manual of Environmental Microbiology. Yates, M. V., Nakatsu, C. H., Miller, R. V. & Pillai, S. D. (eds.). Fourth ed. Washington DC: ASM Press, p. 4.4.2-1-4.4.2-10

Research output: Chapter in Book/Report/Conference proceedingChapter

Tandem Mass Spectrometry in Resolving Complex Gut Microbiota Functions

Kolmeder, C., Lähteenmäki, K., Wacklin, P., Kotovuori, A., Ritamo, I., Mättö, J., Vos, W. M. & Valmu, L., 15 Sep 2016, MALDI-TOF and Tandem MS for Clinical Microbiology. Shah, H. N. & Gharbia, S. E. (eds.). Wiley, p. 505-528 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2015

Anaerobic Digestion of Lipid-Rich Waste

Cavaleiro, A. J., Picavet, M. A., Sousa, D. Z., Stams, A. J. M., Pereira, M. A. & Alves, M. M., 2015, Hydrocarbon and LIpid Microbiology Protocols, Springer Protocols Handbooks. McGenity, T. J. (ed.). Humana Press, p. 221-236

Research output: Chapter in Book/Report/Conference proceedingChapter

Carbohydrate [Presenting Self ]Assembled Monolayers: Preparation, Analysis, and Applications in Microbiology

Debrassi, A., de Vos, W. M., Zuilhof, H. & Wennekes, T., 2015, Carbohydrate Nanotechnology. Wiley, p. 1-52 488 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes

Künne, T. A., Westra, E. R. & Brouns, S. J. J., 2015, CRISPR : Methods and Protocols. Lundgren, M., Charpentier, E. & Fineran, P. C. (eds.). p. 171-184 371 p. (Methods Molecular Biology; no. 1311).

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Improving the Digestive Tract Robustness of Probiotic Lactobacilli

van Bokhorst-van de Veen, H., Bron, P. A. & Kleerebezem, M., 2015, Probiotics and Prebiotics: Current Research and Future Trends. Venema, K. & Paula do Carmo, A. (eds.). Norfolk, UK: Caister Academic Press, 560 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Lactic Acid Bacteria and the Human Intestinal Microbiome

Douillard, F. P. & de Vos, W. M., 2015, Biotechnology of Lactic Acid Bacteria: Novel Applications second edition. Mozzi, F., Vignolo, G. M. & Raya, R. R. (eds.). John Wiley and Sons, p. 120-133

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Primers That Target Functional Genes of Organohalide-Respiring Bacteria

Lu, Y., Atashgahi, S., Hug, L. A. & Smidt, H., 2015, Hydrocarbon and Lipid Microbiology Protocols. McGenity, T. J. (ed.). Berlin: Humana Press, p. 177-205 (Springer Protocols Handbooks).

Research output: Chapter in Book/Report/Conference proceedingChapter

2014

Darmmikrobiota: Kleine Organismen–große Wirkung

Kolmeder, C. A. & de Vos, W. M., 2014, Chancen und Risiken der modernen Biotechnologie. Schartl, M. & Erber-Schropp, J. M. (eds.). Wiesbaden: Springer, p. 53-68

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems biology and metabolic engineering of lactic acid bacteria for improved fermented foods

Flahaut, N. A. L. & de Vos, W. M., 2014, Advances in Fermented Foods and Beverages: Improving Quality, Technologies and Health Benefits. Holzapfel, W. (ed.). Elsevier, p. 177-196

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

The Family Victivallaceae

Plugge, C. M. & Zoetendal, E. G., 2014, The Prokaryotes : Other Major Lineages of Bacteria and The Archaea. Springer, p. 1019-1021

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)
2013

Anaerobic Degradation of Lindane and Other HCH Isomers

Mehboob, F., Langenhoff, A. A. M., Schraa, G. & Stams, A. J. M., 2013, Management of Microbial Resources in the Environment. Malik, A., Grohmann, E. & Alves, M. (eds.). p. 495-521 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Biomethanation potential of biological and other wastes

Costa, J. C., Sousa, D. Z., Pereira, M. A., Stams, A. J. M. & Alves, M. M., 2013, Biofuel Technologies. Berlin Heidelberg: Springer Verlag, p. 369-396

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Citations (Scopus)

crRNA biogenesis

Charpentier, E., van der Oost, J. & White, M., 2013, CRISPR-Cas Systems. Barrangou, R., O. J. V. D. (ed.). Berlin-Heidelberg: Springer Verlag, p. 115-144

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Citations (Scopus)

Distribution and mechanism of Type I-E CRISPR-Cas systems

Staals, R. H. J. & Brouns, S. J. J., 2013, CRISPR-Cas Systems. Barrangou, R., R. & van de Oost, J. (eds.). Berlin-Heidelberg: Springer Verlag, p. 145-169

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)

RNA-mediated Adaptive Immunity in Bacteria and Archaea

Barrangou, R. & van der Oost, J., 2013, CRISPR-Cas Systems. Berlin-Heidelberg: Springer Verlag, 299 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)
2012

Comparative genomic analysis of the central metabolism of the solventogenic species Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NCIMB 8052

Siemerink, M. A. J., Schwarz, K., Grimmler, C., Kuit, W., Ehrenreich, A. & Kengen, S. W. M., 2012, Systems Biology of Clostridia. Dürre, P. (ed.). p. 193-219 270 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Comparative genomic analysis of the general stress response in Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NCIMB 8052

Schwarz, K. M. & Kengen, S. W. M., 2012, Systems Biology of Clostridia. Dürre, P. (ed.). p. 75-89 270 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Lactic Acid Bacteria in the Gut

Stolaki, M., de Vos, W. M., Kleerebezem, M. & Zoetendal, E. G., 2012, Lactic Acid Bacteria. von Wright, A. (ed.). p. 385-401 779 p. (Microbial and Functional Aspects; no. 4).

Research output: Chapter in Book/Report/Conference proceedingChapter

Syntrophic degradation of fatty acids by methanogenic communities

Stams, A. J. M., Worm, P., Sousa, D. Z., Alves, M. M. & Plugge, C. M., 2012, Microbial technologies in advanced biofuels production. Hallenbeck, P. C. (ed.). Springer, p. 127-142

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)
2011

Afvalwaterzuivering: Bacteriën maken vuil water weer schoon

Stams, A. J. M. & Borger, A., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen, p. 204-206-57 (Natuur en Techniek).

Research output: Chapter in Book/Report/Conference proceedingChapter

Archaea: de ontdekking van een nieuwe vorm van leven

van der Oost, J., 2011, Microcanon. wat je beslist moet weten over microbiologie. Smit, H., Reijders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, p. Hfst. 3 246 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Engineering robust lactic acid bacteria

Bron, P. A., van Bokhorst-van de Veen, H., Wels, M. & Kleerebezem, M., 2011, Stress Responses of Lactic Acid Bacteria. Tsakalidou, E. & Papadimitriou, K. (eds.). New York, p. 369-394 (Food Microbiology and Food Safety).

Research output: Chapter in Book/Report/Conference proceedingChapter

Environmental biotechnology and microbiology of (per)chlorate reducing bacteria

Mehboob, F., Schraa, G. & Stams, A. J. M., 2011, Perchlorates: Production, uses and health effects. Matthews, L. E. (ed.). p. 211-235 (Chemical Engineering Methods and Technology).

Research output: Chapter in Book/Report/Conference proceedingChapter

Extremofiele micro-organismen: some like it hot

Kengen, S. W. M. & van der Oost, J., 2011, Microcanon. Smit, H., Reijners, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, p. 28-31 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access

Functional Intestinal Metagenomics (Chapter 18)

van den Bogert, B., Leimena, M. M., de Vos, W. M., Zoetendal, E. G. & Kleerebezem, M., 2011, Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. de Bruijn, F. J. (ed.). United Kingdom: Wiley-Blackwell, p. chap 18 640 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Methaan van archaea: broeikas effect of duurzame energie?

Kengen, S. W. M. & Plugge, C. M., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM

Research output: Chapter in Book/Report/Conference proceedingChapter

Microbiologische kweekmethoden: ook hier geldt de wet van Moore

Ingham, C. J. & de Vos, W. M., 2011, Microcanon. Smit, H., Reijners, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Micro-organismen in het menselijk lichaam: Een adembenemende reis door ons verteringsstelsel

Smidt, H. & Zoetendal, E. G., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Novel Strategies for Production of Medium and High Chain Length Alcohols

Lopez Contreras, A. M., Kuit, W., Springer, J. & Claassen, P. A. M., 2011, Microbial technologies in advanced biofuels production : Part 3 : Liquid biofuels. Hallenbeck, P. C. (ed.). Berlin: Springer, p. 183-211

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Opkomende infectieziekten, ongenode gasten uit verre streken

Moormann, R. J. M., Smit, H., van Doorn, J., van der Oost, J., Reijnders, W. & Willemsen, P. T. J., 2011, Microcanon. Smit, H. (ed.). Diemen, 3 p. (Wetenschappelijke bibliotheek; no. 109).

Research output: Chapter in Book/Report/Conference proceedingChapter

Overleven: De strijd om het bestaan

van der Oost, J., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Probiotica: Vriendelijke bacteriën die goed zijn voor je gezondheid?

Kleerebezem, M., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems biology of Host-Food-Microbe interactions in the mammalian gut

Martins Dos Santos, V. A. P., Müller, M. R., de Vos, W. M., Wells, J., te Pas, M. F. W., Hooiveld, G. J., van Baarlen, P., Smits, M. A. & Keijer, J., 2011, Systems Biology and Livestock Science. te Pas, M. (ed.). John Wiley and Sons, p. 109-135 332 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Variatie en adaptatie: Lifestyle van micro-organismen

van der Oost, J., 2011, Microcanon. Smit, H., Reijnders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2010

Microbial Energy Production from Biomass

Plugge, C. M., van Lier, J. B., Stams, A. J. M. & Jeison, D. A., 2010, Bioelectrochemical Systems: From Extracellular electron transfer to biotechnological application. Rabaey, K., Angenent, L., Schroder, U. & Keller, J. (eds.). London: IWA Publishing, p. 17-38 524 p. (Integrated Environmental Technology Series; no. 9).

Research output: Chapter in Book/Report/Conference proceedingChapter

Microbiology of methanogenesis

Stams, A. J. M. & Plugge, C. M., 2010, Methane and climate change. Reay, D. S., Smith, P. & van Amstel, A. (eds.). London, Washington: Earthscan, p. 2-2

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Citations (Scopus)

Production of longer-chain alcohols from biomass - butanol, isopropanol and 2,3-butanediol

Lopez Contreras, A. M., Kuit, W., Siemerink, M. A. J., Kengen, S. W. M., Springer, J. & Claassen, P. A. M., 2010, Bioalcohol production: Biochemical conversion of lignocellulosic biomass. Waldron, K. W. (ed.). Abington, Cambridge, p. 415-460 560 p. (Woodhead Energy Series; no. 3).

Research output: Chapter in Book/Report/Conference proceedingChapter

13 Citations (Scopus)

RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements

Jore, M. M., Brouns, S. J. J. & van der Oost, J., 2010, RNA Worlds: From Life’s Origins to Diversity in Gene Regulation. Atkins, J. F., Gesteland, R. F. & Cech, T. R. (eds.). New York, U.S.A.: Cold Spring Harbor Laboratory Press, p. 231-242 361 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Syntrophy in Methanogenic Degradation

Worm, P., Müller, N., Plugge, C. M., Stams, A. J. M. & Schink, B., 2010, (Endo)symbiotic Mathanogenic Archaea. Hackstein, J. H. P. (ed.). Berlin, Heidelberg, p. 32-9 240 p. (Microbiology Monographs; no. 19).

Research output: Chapter in Book/Report/Conference proceedingChapter

2009

Assimilation of Unusual Carbon Compounds

Middelhoven, W. J., 2009, Yeast Biotechnology: Diversity and applications. Pt. 1. Satyanarayana, T. & Kunze, G. (eds.). Dordrecht: Springer Netherlands, p. 135-150 744 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Degradation of long-chain fatty acids by sulfate-reducing and methanogenic communities

Sousa, D. Z., Balk, M., Alves, M. M., Schink, B., McInerney, M. J., Smidt, H., Plugge, C. M. & Stams, A. J. M., 2009, Handbook of hydrocarbon and lipid microbiology. Timmis, K., MeGenity, T., van der Meer, JR. & de Lorenzo, V. (eds.). New York, Berlin: Springer

Research output: Chapter in Book/Report/Conference proceedingChapter

Methanogenesis: Syntrophic metabolism

Sieber, J. R., McInerney, M. J., Plugge, C. M., Schink, B. & Gunsales, R. P., 2009, Handbook of Hydrocarbon Microbiology: microbial interactions with hydrocarbons, oils, fats and related hydrophobic substrates and products. Timmis, K., McGenity, T., van der Meer, JR. & de Lorenzo, V. (eds.). New York, Berlin: Springer

Research output: Chapter in Book/Report/Conference proceedingChapter

Microbial degradation of aliphatic and aromatic hydrocarbons with (per)chlorate as electron acceptor

Mehboob, F., Weelink, S. A. B., Talarico Saia, F., Junca, H., Stams, A. J. M. & Schraa, G., 2009, Handbook of hydrocarbon and lipid microbiology. Timmis, K., McGenity, T., van der Meer, JR. & de Lorenzo, V. (eds.). New York, Berlin: Springer

Research output: Chapter in Book/Report/Conference proceedingChapter