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2020

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., 1 Feb 2020, In : Methods. 172, p. 51-60 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

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., Feb 2020, In : Journal of Clinical Periodontology. 47, 2, p. 202-212

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone

Huang, Z., Petersen, J. M., Martijn, J., Ettema, T. J. G. & Shao, Z., 19 Apr 2020, In : Environmental Microbiology Reports.

Research output: Contribution to journalArticleAcademicpeer-review

Antibiotics in early life associate with specific gut microbiota signatures in a prospective longitudinal infant cohort

Korpela, K., Salonen, A., Saxen, H., Nikkonen, A., Peltola, V., Jaakkola, T., de Vos, W. & Kolho, K. L., 18 Jan 2020, In : Pediatric Research.

Research output: Contribution to journalArticleAcademicpeer-review

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

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
1 Citation (Scopus)

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

de Vries, H. J., Stams, A. J. M. & Plugge, C. M., 1 Apr 2020, In : Water Research. 172, 115511.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili

Ligthart, K., Belzer, C., de Vos, W. M. & Tytgat, H. L. P., May 2020, In : Trends in Microbiology. 28, 5, 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Butyrate conversion by sulfate-reducing and methanogenic communities from anoxic sediments of Aarhus Bay, Denmark

Ozuolmez, D., Moore, E. K., Hopmans, E. C., Damsté, J. S., Stams, A. J. M. & Plugge, C. M., Apr 2020, In : Microorganisms. 8, 4, 606.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Calcium effect on microbial activity and biomass aggregation during anaerobic digestion at high salinity

Gagliano, M. C., Sudmalis, D., Temmink, H. & Plugge, C. M., 25 May 2020, In : New Biotechnology. 56, p. 114-122 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets

Vaidya, J. D., van Gastelen, S., Smidt, H., Plugge, C. M. & Edwards, J. E., 2 Mar 2020, In : PLoS ONE. 15, 3, e0229887.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Characterization of sporulation dynamics of Pseudoclostridium thermosuccinogenes using flow cytometry

Ganguly, J., Tempelaars, M., Abee, T. & van Kranenburg, R., Jun 2020, In : Anaerobe. 63, 102208.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Co-cultivation of Thermoanaerobacter strains with a methanogenic partner enhances glycerol conversion

Magalhães, C. P., Ribeiro, J. A., Guedes, A. P., Arantes, A. L., Sousa, D. Z., Stams, A. J. M., Alves, M. M. & Cavaleiro, A. J., 10 Mar 2020, In : Microbial Biotechnology. 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Comparative assessment of two biotrickling filters for siloxanes removal: Effect of the addition of an organic phase

Pascual, C., Cantera, S., Muñoz, R. & Lebrero, R., 1 Jul 2020, In : Chemosphere. 251, 126359.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss

Lewis, W. H., Lind, A. E., Sendra, K. M., Onsbring, H., Williams, T. A., Esteban, G. F., Hirt, R. P., Ettema, T. J. G. & Embley, T. M., Feb 2020, In : Molecular Biology and Evolution. 37, 2, p. 524-539

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313

Ganguly, J., Martin-Pascual, M. & van Kranenburg, R., Mar 2020, In : Microbial Biotechnology. 13, 2, p. 339-349

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients

Gutleben, J., Loureiro, C., Ramírez Romero, L. A., Shetty, S., Wijffels, R. H., Smidt, H. & Sipkema, D., 19 Feb 2020, In : Frontiers in Microbiology. 11, 175.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Dietary Isomalto/Malto-Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice

Mistry, R. H., Borewicz, K., Gu, F., Verkade, H. J., Schols, H. A., Smidt, H. & Tietge, U. J. F., 25 Apr 2020, In : Molecular Nutrition and Food Research.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

3 Citations (Scopus)

Disinfection exhibits systematic impacts on the drinking water microbiome

Dai, Z., Sevillano-Rivera, M. C., Calus, S. T., Bautista-De Los Santos, Q. M., Eren, A. M., Van Der Wielen, P. W. J. J., Ijaz, U. Z. & Pinto, A. J., 20 Mar 2020, In : Microbiome. 8, 1, 42.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Distal colonic transit is linked to gut microbiota diversity and microbial fermentation in humans with slow colonic transit

Müller, M., Hermes, G. D. A., Canfora, E. E., Smidt, H., Masclee, A. A. M., Zoetendal, E. G. & Blaak, E. E., 1 Feb 2020, In : American Journal of Physiology. Gastrointestinal and Liver Physiology. 318, 2, p. G361-G369

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment

Zwittink, R. D., van Zoeren-Grobben, D., Renes, I. B., van Lingen, R. A., Norbruis, O. F., Martin, R., Groot Jebbink, L. J., Knol, J. & Belzer, C., 7 May 2020, In : BMC Pediatrics. 20, 1, 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access

Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review

Swanson, K. S., de Vos, W. M., Martens, E. C., Gilbert, J. A., Menon, R. S., Soto-Vaca, A., Hautvast, J., Meyer, P. D., Borewicz, K., Vaughan, E. E. & Slavin, J. L., 27 Mar 2020, In : Beneficial Microbes. 11, 2, p. 101-129 29 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Effect of nickel, cobalt, and iron on methanogenesis from methanol and cometabolic conversion of 1,2-dichloroethene by Methanosarcina barkeri

Paulo, L. M., Hidayat, M. R., Moretti, G., Stams, A. J. M. & Sousa, D. Z., 13 Apr 2020, In : Biotechnology and applied biochemistry.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Effect of wheat bran derived prebiotic supplementation on gastrointestinal transit, gut microbiota, and metabolic health: a randomized controlled trial in healthy adults with a slow gut transit

Müller, M., Hermes, G. D. A., Canfora, E. E., Holst, J. J., Zoetendal, E. G., Smidt, H., Troost, F., Schaap, F. G., Damink, S. O., Jocken, J. W. E., Lenaerts, K., Masclee, A. A. M. & Blaak, E. E., 25 Jan 2020, In : Gut Microbes.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Effects of cold recovery technology on the microbial drinking water quality in unchlorinated distribution systems

Ahmad, J. I., Liu, G., van der Wielen, P. W. J. J., Medema, G. & Peter van der Hoek, J., 1 Apr 2020, In : Environmental Research. 183, 109175.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Enrichment of Anaerobic Syngas-Converting Communities and Isolation of a Novel Carboxydotrophic Acetobacterium wieringae Strain JM

Arantes, A. L., Moreira, J. P. C., Diender, M., Parshina, S. N., Stams, A. J. M., Alves, M. M., Alves, J. I. & Sousa, D. Z., 31 Jan 2020, In : Frontiers in Microbiology. 11, 58.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Scott, D., Shah, S. A., Siksnys, V., Terns, M. P., Venclovas, Č., White, M. F., Yakunin, A. F., Yan, W. & 6 others, Zhang, F., Garrett, R. A., Backofen, R., van der Oost, J., Barrangou, R. & Koonin, E. V., Feb 2020, In : Nature Reviews Microbiology. 18, p. 67-83 16 p.

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health

López Nadal, A., Ikeda-Ohtsubo, W., Sipkema, D., Peggs, D., McGurk, C., Forlenza, M., Wiegertjes, G. F. & Brugman, S., 5 Feb 2020, In : Frontiers in Immunology. 11, 114.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Functional replacement of isoprenoid pathways in Rhodobacter sphaeroides

Orsi, E., Beekwilder, J., van Gelder, D., van Houwelingen, A., Eggink, G., Kengen, S. W. M. & Weusthuis, R. A., 24 Mar 2020, In : Microbial Biotechnology.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Strepis, N., Naranjo, H. D., Meier-Kolthoff, J., Göker, M., Shapiro, N., Kyrpides, N., Klenk, H. P., Schaap, P. J., Stams, A. J. M. & Sousa, D. Z., 8 Jan 2020, In : BMC Genomics. 21, 1, 24.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Geoquímica microbiana del lago ácido y salino de la corta de la mina Brunita (La Unión, SE España)

Translated title of the contribution: Microbial Geochemistry of the Acidic Saline Pit Lake of Brunita Mine (La Unión, SE Spain)Sánchez-España, J., Yusta, I., Ilin, A., van der Graaf, C. & Sánchez-Andrea, I., 25 Jan 2020, In : Mine Water and the Environment. 21 p.

Research output: Contribution to journalArticleAcademicpeer-review

Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a

Creutzburg, S. C. A., Wu, W., Mohanraju, P., Swartjes, T., Alkan, F., Gorodkin, J., Staals, R. H. J. & van der Oost, J., 6 Apr 2020, In : Nucleic acids research. 48, 6, p. 3228–3243 gkz1240.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice

Tengeler, A. C., Dam, S. A., Wiesmann, M., Naaijen, J., Van Bodegom, M., Belzer, C., Dederen, P. J., Verweij, V., Franke, B., Kozicz, T., Arias Vasquez, A. & Kiliaan, A. J., 1 Apr 2020, In : Microbiome. 8, 1, 44.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics

Song, J., Hegge, J. W., Mauk, M. G., Chen, J., Till, J. E., Bhagwat, N., Azink, L. T., Peng, J., Sen, M., Mays, J., Carpenter, E. L., van der Oost, J. & Bau, H. H., 28 Feb 2020, In : Nucleic acids research. 48, 4, p. e19

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT

Filius, M., Cui, T. J., Ananth, A. N., Docter, M. W., Hegge, J. W., van der Oost, J. & Joo, C., 8 Apr 2020, In : Nano Letters. 20, 4, p. 2264-2270 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males

Hermes, G. D. A., Reijnders, D., Kootte, R. S., Goossens, G. H., Smidt, H., Nieuwdorp, M., Blaak, E. E. & Zoetendal, E. G., 5 May 2020, In : Scientific Reports. 10, 1, 7523.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Intestinimonas-like bacteria are important butyrate producers that utilize Nε-fructosyllysine and lysine in formula-fed infants and adults

Bui, T. P. N., Troise, A. D., Nijsse, B., Roviello, G. N., Fogliano, V. & de Vos, W. M., Jul 2020, In : Journal of Functional Foods. 70, 103974.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Investigating the gut microbiota composition of individuals with attention-deficit/hyperactivity disorder and association with symptoms

Szopinska-Tokov, J., Dam, S., Naaijen, J., Konstanti, P., Rommelse, N., Belzer, C., Buitelaar, J., Franke, B., Aarts, E. & Vasquez, A. A., Mar 2020, In : Microorganisms. 8, 3, 406.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Limited presence of Waddlia chondrophila in drinking water systems in the Netherlands

van Dooremalen, W. T. M., Learbuch, K. L. G., Morré, S. A., van der Wielen, P. W. J. J. & Ammerdorffer, A., 1 Mar 2020, In : New Microbes and New Infections. 34, 100635.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

Dharamshi, J. E., Tamarit, D., Eme, L., Stairs, C. W., Martijn, J., Homa, F., Jørgensen, S. L., Spang, A. & Ettema, T. J. G., 23 Mar 2020, In : Current Biology. 30, 6, p. 1032-1048.e7

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: The NU-AGE 1-year dietary intervention across five European countries

Ghosh, T. S., Rampelli, S., Jeffery, I. B., Santoro, A., Neto, M., Capri, M., Giampieri, E., Jennings, A., Candela, M., Turroni, S., Zoetendal, E. G., Hermes, G. D. A., Elodie, C., Brugere, C. M., Pujos-Guillot, E., Berendsen, A. M., De Groot, L. C. P. G. M., Feskins, E. J. M., Kaluza, J., Pietruszka, B. & 10 others, Bielak, M. J., Comte, B., Maijo-Ferre, M., Nicoletti, C., de Vos, W. M., Fairweather-Tait, S., Cassidy, A., Brigidi, P., Franceschi, C. & O'Toole, P. W., Mar 2020, In : Gut. 319654.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Medium-throughput in vitro detection of DNA cleavage by CRISPR-Cas12a

Creutzburg, S. C. A., Swartjes, T. & van der Oost, J., 1 Feb 2020, In : Methods. 172, p. 27-31 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

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
1 Citation (Scopus)

Metagenomic-and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Peng, P., Lu, Y., Bosma, T. N. P., Nijenhuis, I., Nijsse, B., Shetty, S. A., Ruecker, A., Umanets, A., Ramiro-Garcia, J., Kappler, A., Sipkema, D., Smidt, H. & Atashgahi, S., May 2020, In : Microorganisms. 8, 5, 665.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Microbial Community Drivers in Anaerobic Granulation at High Salinity

Gagliano, M. C., Sudmalis, D., Pei, R., Temmink, H. & Plugge, C. M., 26 Feb 2020, In : Frontiers in Microbiology. 11, 235.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut

Hynönen, U., Zoetendal, E. G., Virtala, A. M. K., Shetty, S., Hasan, S., Jakava-Viljanen, M., de Vos, W. M. & Palva, A., Apr 2020, In : Anaerobe. 62, 102104.

Research output: Contribution to journalArticleAcademicpeer-review

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species

Edwards, J. E., Shetty, S. A., van den Berg, P., Burden, F., van Doorn, D. A., Pellikaan, W. F., Dijkstra, J. & Smidt, H., 12 Feb 2020, In : Animal Microbiome. 2, 6.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access