Research Output 1936 2020

2020

A systematic comparison of ectoine production from upgraded biogas using Methylomicrobium alcaliphilum and a mixed haloalkaliphilic consortium

Cantera, S., Phandanouvong-Lozano, V., Pascual, C., García-Encina, P. A., Lebrero, R., Hay, A. & Muñoz, R., 1 Feb 2020, In : Waste Management. 102, p. 773-781 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

biogas
bioreactor
tax incentive
biomass
competitiveness
1 Citation (Scopus)

Bacterial folate biosynthesis and colorectal cancer risk: more than just a gut feeling

Kok, D. E. G., Steegenga, W. T., Smid, E. J., Zoetendal, E. G., Ulrich, C. M. & Kampman, E., Jan 2020, In : Critical Reviews in Food Science and Nutrition. 60, 2, p. 244-256 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biosynthesis
colorectal neoplasms
Folic Acid
folic acid
Colorectal Neoplasms
Open Access
Fatty acids
methanol
Elongation
ethanol
Methanol

Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism

Vink, J. N. A., Martens, K. J. A., Vlot, M., McKenzie, R. E., Almendros, C., Estrada Bonilla, B., Brocken, D. J. W., Hohlbein, J. & Brouns, S. J. J., 2 Jan 2020, In : Molecular Cell. 77, 1, p. 39-50.e10

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Interspersed Repetitive Sequences
Bacteria
DNA
RNA

Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides

Orsi, E., Beekwilder, J., Peek, S., Eggink, G., Kengen, S. W. M. & Weusthuis, R. A., 1 Jan 2020, In : Metabolic Engineering. 57, p. 228-238 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolic Flux Analysis
Rhodobacter sphaeroides
Biosynthesis
Terpenes
Labeling
2019

0046 - Organoids as models to study probiotics

van der Hee, B., Loonen, L. M. P., Taverne, N., Taverne-Thiele, J. J., Smidt, H. & Wells, J. M., 19 Jun 2019, p. 57. 1 p.

Research output: Contribution to conferenceAbstractAcademic

Organoids
Probiotics
Cell Line
Stem Cells
Host-Pathogen Interactions
1 Citation (Scopus)

ABA-mediated regulation of leaf and root hydraulic conductance in tomato grown at elevated CO2 is associated with altered gene expression of aquaporins

Fang, L., Abdelhakim, L. O. A., Hegelund, J. N., Li, S., Liu, J., Peng, X., Li, X., Wei, Z. & Liu, F., 1 Sep 2019, In : Horticulture Research. 6, 1, 104.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
root hydraulic conductivity
Abscisic Acid
Aquaporins
aquaporins
Lycopersicon esculentum
5 Citations (Scopus)

A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation

O'Connell Motherway, M., Houston, A., O'Callaghan, G., Reunanen, J., O'Brien, F., O'Driscoll, T., Casey, P. G., de Vos, W. M., van Sinderen, D. & Shanahan, F., Jan 2019, In : Molecular Microbiology. 111, 1, p. 287-301

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Cell Proliferation
Fimbriae Proteins
Aptitude
Bifidobacterium
Human Development
1 Citation (Scopus)

Adaptation and application of a two-plasmid inducible CRISPR-Cas9 system in Clostridium beijerinckii

Diallo, M., Hocq, R., Collas, F., Chartier, G., Wasels, F., Wijaya, H. S., Werten, M. W. T., Wolbert, E. J. H., Kengen, S. W. M., van der Oost, J., Ferreira, N. L. & López-Contreras, A. M., 27 Jul 2019, In : Methods. 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium
Butanols
Plasmids

Addiction systems antagonize bacterial adaptive immunity

van Sluijs, L., van Houte, S., van der Oost, J., Brouns, S. J. J., Buckling, A. & Westra, E. R., 1 Mar 2019, In : FEMS Microbiology Letters. 366, 5, fnz047.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Adaptive Immunity
Plasmids
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Microbial Drug Resistance
7 Citations (Scopus)

Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity

Sovran, B., Hugenholtz, F., Elderman, M., Van Beek, A. A., Graversen, K., Huijskes, M., Boekschoten, M. V., Savelkoul, H. F. J., De Vos, P., Dekker, J. & Wells, J. M., 5 Feb 2019, In : Scientific Reports. 9, 1, 1437.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Mucus
Immunity
Paneth Cells
T-Lymphocytes
3 Citations (Scopus)

Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1 -/Δ7 mice

van der Lugt, B., van Beek, A. A., Aalvink, S., Meijer, B., Sovran, B., Vermeij, W. P., Brandt, R. M. C., de Vos, W. M., Savelkoul, H. F. J., Steegenga, W. T. & Belzer, C., 8 Mar 2019, In : Immunity and Ageing. 16, 1, 6.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Mucus
B-Lymphocytes
B-Lymphoid Precursor Cells
Transcriptome
Anti-Inflammatory Agents

Akkermansia muciniphila Exerts Lipid-Lowering and Immunomodulatory Effects without Affecting Neointima Formation in Hyperlipidemic APOE*3-Leiden.CETP Mice

Katiraei, S., de Vries, M. R., Costain, A. H., Thiem, K., Hoving, L. R., van Diepen, J. A., Smits, H. H., Bouter, K. E., Rensen, P. C. N., Quax, P. H. A., Nieuwdorp, M., Netea, M. G., de Vos, W. M., Cani, P. D., Belzer, C., van Dijk, K. W., Berbée, J. F. P. & van Harmelen, V., 6 Aug 2019, In : Molecular Nutrition and Food Research. 1900732.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Neointima
Lipids
lipid metabolism
B-lymphocytes
mice

Akkermansia muciniphila reduces Porphyromonas gingivalis-induced inflammation and periodontal bone destruction

Huck, O., Mulhall, H., Rubin, G., Kizelnik, Z., Iyer, R., Perpich, J. D., Haque, N., Cani, P. D., de Vos, W. M. & Amar, S., 1 Nov 2019, In : Journal of Clinical Periodontology.

Research output: Contribution to journalArticleAcademicpeer-review

Osteitis
Porphyromonas gingivalis
Periodontitis
Cadherins
Anti-Inflammatory Agents

Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome

Holster, S., Hooiveld, G. J., Repsilber, D., de Vos, W. M., Brummer, R. J. & König, J., 8 Oct 2019, In : Biomolecules. 9, 10, 586.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Irritable Bowel Syndrome
Microbiota
Colon
Mucous Membrane
Genes

Anaerobic Degradation of Non-Methane Alkanes by "Candidatus Methanoliparia" in Hydrocarbon Seeps of the Gulf of Mexico

Laso-Pérez, R., Hahn, C., van Vliet, D. M., Tegetmeyer, H. E., Schubotz, F., Smit, N. T., Pape, T., Sahling, H., Bohrmann, G., Boetius, A., Knittel, K. & Wegener, G., 20 Aug 2019, In : mBio. 10, 4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gulf of Mexico
Alkanes
Hydrocarbons
Archaea
Oils
3 Citations (Scopus)

Anaerobic Degradation of N-ϵ-Carboxymethyllysine, a Major Glycation End-Product, by Human Intestinal Bacteria

Bui, T. P. N., Troise, A. D., Fogliano, V. & De Vos, W. M., 12 Jun 2019, In : Journal of Agricultural and Food Chemistry. 67, 23, p. 6594-6602 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
glycation
intestinal microorganisms
anaerobic conditions
Bacteria
Degradation
2 Citations (Scopus)

Anaerobic degradation of sulfated polysaccharides by two novel Kiritimatiellales strains isolated from black sea sediment

van Vliet, D. M., Ayudthaya, S. P. N., Diop, S., Villanueva, L., Stams, A. J. M. & Sánchez-Andrea, I., 18 Feb 2019, In : Frontiers in Microbiology. 10, 253.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Black Sea
Sulfatases
Polysaccharides
Carrageenan
Verrucomicrobia
1 Citation (Scopus)

Anaerobic fungal communities differ along the horse digestive tract

Mura, E., Edwards, J., Kittelmann, S., Kaerger, K., Voigt, K., Mrázek, J., Moniello, G. & Fliegerova, K., Mar 2019, In : Fungal Biology. 123, 3, p. 240-246

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
fungal communities
horse
digestive tract
Horses
colon
7 Citations (Scopus)

Antibiotics-induced monodominance of a novel gut bacterial order

Hildebrand, F., Moitinho-Silva, L., Blasche, S., Jahn, M. T. T., Gossmann, T. I., Heuerta Cepas, J., Hercog, R., Luetge, M., Bahram, M., Pryszlak, A., Alves, R. J., Waszak, S. M., Zhu, A., Ye, L., Costea, P. I., Aalvink, S., Belzer, C., Forslund, S. K., Sunagawa, S., Hentschel, U. & 4 others, Merten, C., Patil, K. R., Benes, V. & Bork, P., 2019, In : Gut. 68, 10

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Anti-Bacterial Agents
Metagenomics
Ceftriaxone
Firearms
Probiotics

Argonaute bypasses cellular obstacles without hindrance during target search

Cui, T. J., Klein, M., Hegge, J. W., Chandradoss, S. D., van der Oost, J., Depken, M. & Joo, C., 26 Sep 2019, In : Nature Communications. 10, 4390.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
bypasses
nucleic acids
Nucleic Acids
proteins
Kinetics

Artificial viral capsid proteins: mimicking nature to deliver medicines

Willems, L., 2019, Wageningen: Wageningen University. 139 p.

Research output: Thesisinternal PhD, WU

Open Access
7 Citations (Scopus)

Asgard archaea capable of anaerobic hydrocarbon cycling

Seitz, K. W., Dombrowski, N., Eme, L., Spang, A., Lombard, J., Sieber, J. R., Teske, A. P., Ettema, T. J. G. & Baker, B. J., 23 Apr 2019, In : Nature Communications. 10, 1822.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Archaea
Hydrocarbons
hydrocarbons
cycles
genome
3 Citations (Scopus)

A specific synbiotic-containing amino acid-based formula in dietary management of cow's milk allergy: A randomized controlled trial

Fox, A. T., Wopereis, H., van Ampting, M. T. J., Oude Nijhuis, M. M., Butt, A. M., Peroni, D. G., Vandenplas, Y., Candy, D. C. A., Shah, N., West, C. E., Garssen, J., Harthoorn, L. F., Knol, J. & Michaelis, L. J., 15 Jan 2019, In : Clinical and Translational Allergy. 9, 1, 5.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Synbiotics
Milk Hypersensitivity
Randomized Controlled Trials
Eubacterium
Amino Acids

A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow's milk allergic infants: A randomized controlled trial

Wopereis, H., Van Ampting, M. T. J., Cetinyurek-Yavuz, A., Slump, R., Candy, D. C. A., Butt, A. M., Peroni, D. G., Vandenplas, Y., Fox, A. T., Shah, N., Roeselers, G., Harthoorn, L. F., Michaelis, L. J., Knol, J. & West, C. E., 31 May 2019, In : Clinical and Translational Allergy. 9, 1, 27.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Synbiotics
Milk Hypersensitivity
Milk
Randomized Controlled Trials
Amino Acids
1 Citation (Scopus)

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Odoni, D. I., Vazquez-Vilar, M., van Gaal, M. P., Schonewille, T., Martins Dos Santos, V. A. P., Tamayo-Ramos, J. A., Suarez-Diez, M. & Schaap, P. J., 1 Apr 2019, In : FEMS Microbiology Letters. 366, 7, fnz071.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Aspergillus niger
Citric Acid
Computational Biology
Saccharomyces cerevisiae
Arginine

Assessing cofactor usage in Pseudoclostridium thermosuccinogenes via heterologous expression of central metabolic enzymes

Koendjbiharie, J. G., Wevers, K. & van Kranenburg, R., 24 May 2019, In : Frontiers in Microbiology. 10, May, 1162.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Phosphofructokinase-1
Guanosine Triphosphate
Enzymes
water dikinase pyruvate
pyrophosphate-fructose 6-phosphate 1-phosphotransferase

Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis

Edwards, J. E., Hermes, G. D. A., Kittelmann, S., Nijsse, B. & Smidt, H., 18 Oct 2019, In : Frontiers in Microbiology. 10, 2370.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Neocallimastigomycota
Fungi
Clone Cells
Herbivory
Biomass

Associated bacteria of Botryococcus braunii (Chlorophyta)

Gouveia, J. D., Lian, J., Steinert, G., Smidt, H., Sipkema, D., Wijffels, R. H. & Barbosa, M. J., 27 Mar 2019, In : PeerJ. 2019, 3, e6610.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chlorophyta
Hydrocarbons
Bacteria
Bradyrhizobiaceae
Biomass
2 Citations (Scopus)

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women

Hechler, C., Borewicz, K., Beijers, R., Saccenti, E., Riksen-Walraven, M., Smidt, H. & de Weerth, C., 14 Mar 2019, In : Scientific Reports. 9, 1, 4463.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Pregnant Women
Mothers
Pregnancy
Anxiety

Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli

Claassens, N. J., Finger-Bou, M., Scholten, B., Muis, F., De Groot, J. J., De Gier, J. W., De Vos, W. M. & Van Der Oost, J., 17 Jun 2019, In : ACS synthetic biology. 8, 7, p. 1685-1690 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Escherichia coli
Membrane Proteins
Proteins
Membranes
Cell Engineering
2 Citations (Scopus)

Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems

Nicholson, T. J., Jackson, S. A., Croft, B. I., Staals, R. H. J., Fineran, P. C. & Brown, C. M., 7 May 2019, In : RNA Biology. 16, 4, p. 566-576

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Computational Biology
Archaeal Viruses
Bacteriophages

Bioprospecting of Trichococcus species

Strepis, N., 2019, Wageningen: Wageningen University. 228 p.

Research output: Thesisinternal PhD, WU

Open Access
5 Citations (Scopus)

Biotechnology of health-promoting bacteria

Douillard, F. P. & de Vos, W. M., 1 Nov 2019, In : Biotechnology Advances. 37, 6, 107369.

Research output: Contribution to journalArticleAcademicpeer-review

Biotechnology
Bacteria
Health
Probiotics
Functional Food
9 Citations (Scopus)

Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?

Tytgat, H. L. P., Nobrega, F. L., van der Oost, J. & de Vos, W. M., Jan 2019, In : Trends in Microbiology. 27, 1, p. 17-25

Research output: Contribution to journalArticleAcademicpeer-review

Biofilms
Mucous Membrane
Intestinal Diseases
Health
Colonic Neoplasms

Breakthrough in Marine Invertebrate Cell Culture: Sponge Cells Divide Rapidly in Improved Nutrient Medium

Conkling, M., Hesp, K., Munroe, S., Sandoval, K., Martens, D. E., Sipkema, D., Wijffels, R. H. & Pomponi, S. A., 21 Nov 2019, In : Scientific Reports. 9, 17321.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Porifera
Invertebrates
Cell Culture Techniques
Food
Cell Line

Can bacteria in your gut prevent diseases? The health implications of microbiota | WURcast

Belzer, C., 21 Mar 2019

Research output: Non-textual formDigital or Visual ProductsOther research output

Open Access
3 Citations (Scopus)

Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation

Almendros, C., Nobrega, F. L., McKenzie, R. E. & Brouns, S. J. J., 4 Jun 2019, In : Nucleic acids research. 47, 10, p. 5223-5230 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Gene Fusion
CRISPR-Cas Systems
Geobacter
Immunologic Memory

Causality in microbiome research | WURcast

Belzer, C., 12 Mar 2019

Research output: Non-textual formDigital or Visual ProductsOther research output

Open Access

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep

Thomas, N. A., Olvera-Ramírez, A. M., Abecia, L., Adam, C. L., Edwards, J. E., Cox, G. F., Findlay, P. A., Destables, E., Wood, T. A. & McEwan, N. R., 1 Sep 2019, In : Archives of Microbiology. 201, 7, p. 889-896 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Protozoa
Rumen
Fungi
Sheep
Chemical analysis

Characterization of bacterial community in the gut of Penaeus monodon and its culture water in shrimp ponds

Le, D. H., Nguyen, N. T., Dang, O. H. T., Steinert, G., Tran, T. T., Vu, T. H., Sipkema, D. & Chu, H. H., 1 Jan 2019, In : Turkish Journal of Fisheries and Aquatic Sciences. 19, 11, p. 977-986

Research output: Contribution to journalArticleAcademicpeer-review

Penaeus monodon
bacterial communities
rearing
shrimp
digestive system
3 Citations (Scopus)

Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium

Orsi, E., Folch, P. L., Monje-López, V. T., Fernhout, B. M., Turcato, A., Kengen, S. W. M., Eggink, G. & Weusthuis, R. A., Aug 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 8, p. 1179-1190

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Heterotrophic Processes
Terpenes
Rhodobacter sphaeroides
Sesquiterpenes
Biosynthesis

Clonal expansion of a virulent Streptococcus suis serotype 9 lineage distinguishable from carriage subpopulations

Willemse, N., van der Ark, K. C. H., Stockhofe-Zurwieden, N., Smith, H., Picavet, D. I., van Solt-Smits, C., Wisselink, H. J., Schultsz, C. & de Greeff, A., 28 Oct 2019, In : Scientific Reports. 9, 1, 15429.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Streptococcus suis
Virulence
Swine
Capsules
Infection
1 Citation (Scopus)

Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort

Korpela, K., Dikareva, E., Hanski, E., Kolho, K. L., De Vos, W. M. & Salonen, A., 1 Jun 2019, In : BMJ Open. 9, 6, e028500.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Parturition
Health
Life Style
Parents
Open Access
oral vaccination
Lactobacillus acidophilus
inulin
Salmonella Typhimurium
dietary supplements

Comparison of different invasive and non-invasive methods to characterize intestinal microbiota throughout a production cycle of broiler chickens

Kers, J. G., Fischer, E. A. J., Stegeman, J. A., Smidt, H. & Velkers, F. C., 1 Oct 2019, In : Microorganisms. 7, 10, 431.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chickens
Microbiota
Birds
16S Ribosomal RNA
Biological Factors
2 Citations (Scopus)

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon

Martijn, J., Lind, A. E., Schön, M. E., Spiertz, I., Juzokaite, L., Bunikis, I., Pettersson, O. V. & Ettema, T. J. G., Jul 2019, In : Environmental Microbiology. 21, 7, p. 2485-2498

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
rRNA Operon
prokaryote
operon
prokaryotic cells
rRNA Genes
1 Citation (Scopus)

Conserved motifs in the CRISPR leader sequence control spacer acquisition levels in Type I-D CRISPR-Cas systems

Kieper, S. N., Almendros, C. & Brouns, S. J. J., 1 Jun 2019, In : FEMS Microbiology Letters. 366, 11, fnz129.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Synechocystis
Integrases
Conserved Sequence
1 Citation (Scopus)

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation

Koistinen, V. M., Kärkkäinen, O., Borewicz, K., Zarei, I., Jokkala, J., Micard, V., Rosa-Sibakov, N., Auriola, S., Aura, A. M., Smidt, H. & Hanhineva, K., 10 Jul 2019, In : Microbiome. 7, 1, 103.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Betaine
Fermentation
Diet
Microbiota
Ruminococcus
3 Citations (Scopus)

Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants

Borewicz, K., Gu, F., Saccenti, E., Arts, I. C. W., Penders, J., Thijs, C., van Leeuwen, S. S., Lindner, C., Nauta, A., van Leusen, E., Schols, H. A. & Smidt, H., 24 Apr 2019, In : Molecular Nutrition and Food Research. 1801214.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Human Milk
breast milk
Oligosaccharides
oligosaccharides