Publications

Guo, L., Stoffels, K., Broos, J., & Kuipers, O. P. (2024). Altering Specificity and Enhancing Stability of the Antimicrobial Peptides Nisin and Rombocin through Dehydrated Amino Acid Residue Engineering. Peptides, 174, Article 171152. https://doi.org/10.1016/j.peptides.2024.171152

Lilge, L., & Kuipers, O. P. (2024). A two-step regulatory circuit involving Spo0A-AbrB activates mersacidin biosynthesis in Bacillus subtilis. International journal of antimicrobial agents, 63(5), Article 107155. https://doi.org/10.1016/j.ijantimicag.2024.107155

Liu, F., van Heel, A. J., & Kuipers, O. P. (2024). Engineering circular bacteriocins: structural and functional effects of α-helix exchanges and disulfide introductions in circularin A. Frontiers in Microbiology, 15, Article 1337647. https://doi.org/10.3389/fmicb.2024.1337647

Guo, L., Stoffels, K., Broos, J., & Kuipers, O. P. (2024). Engineering hybrid lantibiotics yields the highly stable and bacteriocidal peptide cerocin V. Microbiological Research, 282, Article 127640. https://doi.org/10.1016/j.micres.2024.127640

Fernandez-Cantos, M. V., Babu, A. F., Hanhineva, K., & Kuipers, O. P. (2024). Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC-MS/MS metabolite profiling. Microbiological Research, 283, Article 127700. https://doi.org/10.1016/j.micres.2024.127700

Garcia-Morena, D., Fernandez-Cantos, M. V., Escalera, S. L., Lok, J., Iannone, V., Cancellieri, P., Maathuis, W., Panagiotou, G., Aranzamendi, C., Aidy, S. E., Kolehmainen, M., El-Nezami, H., Wellejus, A., & Kuipers, O. P. (2024). In Vitro Influence of Specific Bacteroidales Strains on Gut and Liver Health Related to Metabolic Dysfunction-Associated Fatty Liver Disease. Probiotics and Antimicrobial Proteins. Advance online publication. https://doi.org/10.1007/s12602-024-10219-1

Guo, L., Wambui, J., Wang, C., Broos, J., Stephan, R., & Kuipers, O. P. (2024). Rombocin, a Short Stable Natural Nisin Variant, Displays Selective Antimicrobial Activity against Listeria monocytogenes and Employs a Dual Mode of Action to Kill Target Bacterial Strains. ACS Synthetic Biology, 13(1), 370–383. Article 3c00612. https://doi.org/10.1021/acssynbio.3c00612

Vargiu, M., Xu, Y., Kuipers, O., & Roelfes, G. (2024). Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. ChemBioChem, 25(7), Article e202400043. https://doi.org/10.1002/cbic.202400043

Van Eldijk, T. J. B., Sheridan, E. A., Martin, G., Weissing, F. J., Kuipers, O. P., & Van Doorn, G. S. (2024). Temperature dependence of the mutation rate towards antibiotic resistance. JAC-Antimicrobial Resistance, 6(3), Article dlae085. https://doi.org/10.1093/jacamr/dlae085

Arias-Orozco, P., Zhou, L., Yi, Y., Cebrián, R., & Kuipers, O. P. (2024). Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiology Spectrum, 12(1), 1-19. https://doi.org/10.1128/spectrum.03611-23

Cebrián, R., Martínez-García, M., Fernández, M., García, F., Martínez-Bueno, M., Valdivia, E., Kuipers, O. P., Montalbán-López, M., & Maqueda, M. (2023). Advances in the preclinical characterization of the antimicrobial peptide AS-48. Frontiers in Microbiology, 14, Article 1110360. https://doi.org/10.3389/fmicb.2023.1110360

Fernandez-Cantos, M. V., Garcia de la Morena, D., Yi, Y., Liang, L., Gomez Vazquez, E., & Kuipers, O. (2023). Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Frontiers in Microbiology, 14, Article 1219272. https://doi.org/10.3389/fmicb.2023.1219272

Morawska, L. P., & Kuipers, O. P. (2023). Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microbial Biotechnology, 16(4), 784-798. https://doi.org/10.1111/1751-7915.14195

Guo, L., Wambui, J., Wang, C., Muchaamba, F., Fernandez-Cantos, M. V., Broos, J., Tasara, T., Kuipers, O. P., & Stephan, R. (2023). Cesin, a short natural variant of nisin, displays potent antimicrobial activity against major pathogens despite lacking two C-terminal macrocycles. Microbiology Spectrum, 11(5), Article e0531922. https://doi.org/10.1128/spectrum.05319-22

Fu, Y., Zhou, L., & Kuipers, O. P. (2023). Discovery, biosynthesis, and characterization of a lanthipeptide from Bacillus subtilis EH11 with a unique lanthionine ring pattern. Cell Reports Physical Science, 4(8), Article 101524. https://doi.org/10.1016/j.xcrp.2023.101524

Zhao, X., Zhong, X., Yang, S., Deng, K., Liu, L., Song, X., Zou, Y., Li, L., Zhou, X., Jia, R., Lin, J., Tang, H., Ye, G., Yang, J., Zhao, S., Lang, Y., Wan, H., Yin, Z., & Kuipers, O. P. (2023). Elucidating the Mechanism of Action of the Gram-Negative-Pathogen-Selective Cyclic Antimicrobial Lipopeptide Brevicidine. Antimicrobial Agents and Chemotherapy, 67(5). https://doi.org/10.1128/aac.00010-23

Fu, Y., Xu, Y., Ruijne, F., & Kuipers, O. P. (2023). Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides. FEMS Microbiology Reviews, 47(3), Article fuad017. https://doi.org/10.1093/femsre/fuad017

Hammad, M., Ali, H., Hassan, N., Tawab, A., Salman, M., Jawad, I., de Jong, A., Moreno, C. M., Kuipers, O. P., Feroz, Y., & Rashid, M. H. (2023). Food safety and biological control; genomic insights and antimicrobial potential of Bacillus velezensis FB2 against agricultural fungal pathogens. PLoS ONE, 18(11), Article e0291975. https://doi.org/10.1371/journal.pone.0291975

Liu, F., van Heel, A. J., & Kuipers, O. P. (2023). Leader- and Terminal Residue Requirements for Circularin A Biosynthesis Probed by Systematic Mutational Analyses. ACS Synthetic Biology, 12(3), 852-862. https://doi.org/10.1021/acssynbio.2c00661

Guo, L., Wang, C., Broos, J., & Kuipers, O. P. (2023). Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity. The Journal of Biological Chemistry, 229(7), Article 104845. https://doi.org/10.1016/j.jbc.2023.104845

Li, L., Zhang, L., Zhang, T., Liu, Y., Lü, X., Kuipers, O. P., & Yi, Y. (2023). (Meta)genomics -assisted screening of novel antibacterial lactic acid bacteria strains from traditional fermented milk from Western China and their bioprotective effects on cheese. LWT, 175, Article 114507. https://doi.org/10.1016/j.lwt.2023.114507

Abraham Versloot, R. C., Arias-Orozco, P., Tadema, M. J., Rudolfus Lucas, F. L., Zhao, X., Marrink, S. J., Kuipers, O. P., & Maglia, G. (2023). Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. Journal of the American Chemical Society, 145(33), 18355-18365. Article 4076. https://doi.org/10.1021/jacs.3c04076

Cebrián, R., Lucas, R., Fernández-Cantos, M. V., Slot, K., Peñalver, P., Martínez-García, M., Párraga-Leo, A., de Paz, M. V., García, F., Kuipers, O. P., & Morales, J. C. (2023). Synthesis and antimicrobial activity of aminoalkyl resveratrol derivatives inspired by cationic peptides. Journal of enzyme inhibition and medicinal chemistry, 38(1), 267-281. https://doi.org/10.1080/14756366.2022.2146685

Cacace, E., Kim, V., Varik, V., Knopp, M., Tietgen, M., Brauer-Nikonow, A., Inecik, K., Mateus, A., Milanese, A., Mårli, M. T., Mitosch, K., Selkrig, J., Brochado, A. R., Kuipers, O. P., Kjos, M., Zeller, G., Savitski, M. M., Göttig, S., Huber, W., & Typas, A. (2023). Systematic analysis of drug combinations against Gram-positive bacteria. Nature Microbiology, 8(11), 2196-2212. https://doi.org/10.1038/s41564-023-01486-9

Arias-Orozco, P., Yi, Y., Ruijne, F., Cebrián, R., & Kuipers, OP. (2023). Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synthetic Biology, 12, 164–177. https://doi.org/10.1021/acssynbio.2c00455

Muñoz, C. Y., Zhou, L., Yi, Y., & Kuipers, O. P. (2022). Biocontrol properties from phyllospheric bacteria isolated from Solanum lycopersicum and Lactuca sativa and genome mining of antimicrobial gene clusters. BMC Genomics, 23(1), Article 152. https://doi.org/10.1186/s12864-022-08392-0

Cebrián, R., Li, Q., Peñalver, P., Belmonte-Reche, E., Andrés-Bilbao, M., Lucas, R., de Paz, M. V., Kuipers, O. P., & Morales, J. C. (2022). Chemically Tuning Resveratrol for the Effective Killing of Gram-Positive Pathogens. Journal of Natural Products, 85(6), 1459-1473. Article 1c01107. https://doi.org/10.1021/acs.jnatprod.1c01107

Farooq, S. A., de Jong, A., Khaliq, S., & Kuipers, O. P. (2022). Draft Genome Sequences of Bacillus velezensis Strains AF_3B and OS2, Bacillus amyloliquefaciens Strain BS9, Bacillus halotolerans Strain A1, and Bacillus sp. Strain BS3, Producing Biosurfactants with Antimicrobial Potential. Microbiology resource announcements, 11(10), Article e0048222. https://doi.org/10.1128/mra.00482-22

Mordhorst, S., Ruijne, F., Vagstad, A. L., Kuipers, O. P., & Piel, J. (2022). Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chemical Biology, 4, 7-36. https://doi.org/10.1039/d2cb00169a

de Jong, A., Kuipers, O. P., & Kok, J. (2022). FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. Nucleic Acids Research, 50(W1), 330-336. Article gkac441. https://doi.org/10.1093/nar/gkac441

Liu, F., van Heel, A. J., Chen, J., & Kuipers, O. P. (2022). Functional production of clostridial circularin A in Lactococcus lactis NZ9000 and mutational analysis of its aromatic and cationic residues. Frontiers in Microbiology, 13, Article 1026290. https://doi.org/10.3389/fmicb.2022.1026290

Pinto, J. P. C., Brouwer, R., Zeyniyev, A., Kuipers, O. P., & Kok, J. (2022). High-Resolution Chrono-Transcriptome of Lactococcus lactis Reveals That It Expresses Proteins with Adapted Size and pI upon Acidification and Nutrient Starvation. Applied and environmental microbiology, 88(9), Article e0247621. https://doi.org/10.1128/aem.02476-21

Viel, J. H., & Kuipers, O. P. (2022). Modular Use of the Uniquely Small Ring A of Mersacidin Generates the Smallest Ribosomally Produced Lanthipeptide. ACS Synthetic Biology, 11(9), 3078-3087. Article 2c00343. https://doi.org/10.1021/acssynbio.2c00343

Viel, J. H., & Kuipers, O. P. (2022). Mutational Studies of the Mersacidin Leader Reveal the Function of Its Unique Two-Step Leader Processing Mechanism. ACS Synthetic Biology, 11(5), 1949–1957 . https://doi.org/10.1021/acssynbio.2c00088

Schouten, G. K., Paulussen, F. M., Kuipers, O. P., Bitter, W., Grossmann, T. N., & van Ulsen, P. (2022). Stapling of Peptides Potentiates the Antibiotic Treatment of Acinetobacter baumannii In Vivo. Antibiotics , 11(2), Article 11020273. https://doi.org/10.3390/antibiotics11020273

Morawska, L. P., Detert Oude Weme, R. G. J., Frenzel, E., Dirkzwager, M., Hoffmann, T., Bremer, E., & Kuipers, O. P. (2022). Stress-induced activation of the proline biosynthetic pathway in Bacillus subtilis: A population-wide and single-cell study of the osmotically controlled proHJ promoter. Microbial Biotechnology, 15(9), 2411-2425. https://doi.org/10.1111/1751-7915.14073

Ekkers, D. M., Tusso, S., Moreno-Gamez, S., Rillo, M. C., Kuipers, O. P., & van Doorn, G. S. (2022). Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification. Molecular Biology and Evolution, 39(6), Article msac124. https://doi.org/10.1093/molbev/msac124

Morawska, L. P., & Kuipers, O. P. (2022). Transcriptome analysis and prediction of the metabolic state of stress-induced viable but non-culturable Bacillus subtilis cells. Scientific Reports, 12(1), Article 18015. https://doi.org/10.1038/s41598-022-21102-w

Yu, Y., van der Zwaag, M., Wedman, J. J., Permentier, H., Plomp, N., Jia, X., Kanon, B., Eggens-Meijer, E., Buist, G., Harmsen, H., Kok, J., Salles, J. F., Wertheim, B., Hayflick, S. J., Strauss, E., Grzeschik, N. A., Schepers, H., & Sibon, O. C. M. (2022). Coenzyme A precursors flow from mother to zygote and from microbiome to host. Molecular Cell, 82(14), 2650-2665.e12. https://doi.org/10.1016/j.molcel.2022.05.006

Kong, C., de Jong, A., de Haan, B. J., Kok, J., & de Vos, P. (2022). Human milk oligosaccharides and non-digestible carbohydrates reduce pathogen adhesion to intestinal epithelial cells by decoy effects or by attenuating bacterial virulence. Food Research International, 151, Article 110867. https://doi.org/10.1016/j.foodres.2021.110867

Chen, J., & Kuipers, O. P. (2022). Analysis of cross-functionality within LanBTC synthetase complexes from different bacterial sources with respect to production of fully modified lanthipeptides. Applied and environmental microbiology, 88(2), Article AEM0161821. https://doi.org/10.1128/AEM.01618-21

Morawska, L. P., Hernandez-Valdes, J. A., & Kuipers, O. P. (2022). Diversity of bet-hedging strategies in microbial communities-Recent cases and insights. Wires mechanisms of disease, 14(2), Article e1544. https://doi.org/10.1002/wsbm.1544

Cebrián, R., Belmonte-Reche, E., Pirota, V., de Jong, A., Morales, J. C., Freccero, M., Doria, F., & Kuipers, O. P. (2022). G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action. Journal of Medicinal Chemistry, 65(6), 4752-4766. https://doi.org/10.1021/acs.jmedchem.1c01905

van Tilburg, A. Y., Warmer, P., van Heel, A. J., Sauer, U., & Kuipers, O. P. (2022). Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10. Microbial Biotechnology, 15(5), 1633-1651. Article 13978. https://doi.org/10.1111/1751-7915.13978

Zhou, L., Song, C., Li, Z., & Kuipers, O. P. (2021). Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential. BMC Genomics, 22(1), Article 29. https://doi.org/10.1186/s12864-020-07346-8

Fu, Y., Jaarsma, A. H., & Kuipers, O. P. (2021). Antiviral activities and applications of ribosomally synthesized and post-translationally modified peptides (RiPPs). Cellular and molecular life sciences, 78, 3921–3940 . https://doi.org/10.1007/s00018-021-03759-0

Zhou, L., Song, C., Muñoz, C. Y., & Kuipers, O. P. (2021). Bacillus cabrialesii BH5 Protects Tomato Plants Against Botrytis cinerea by Production of Specific Antifungal Compounds. Frontiers in Microbiology, 12, Article 707609. https://doi.org/10.3389/fmicb.2021.707609

Zhao, X., Wang, X., Shukla, R., Kumar, R., Weingarth, M., Breukink, E., & Kuipers, O. P. (2021). Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an Exceptionally Low Hemolytic Activity. Frontiers in Microbiology, 12, Article 693725. https://doi.org/10.3389/fmicb.2021.693725

Zhao, X., Wang, X., Shukla, R., Kumar, R., Weingarth, M., Breukink, E., & Kuipers, O. P. (2021). Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes. Frontiers in Microbiology, 12, Article 694847. https://doi.org/10.3389/fmicb.2021.694847

Zhao, X., & Kuipers, O. P. (2021). BrevicidineB, a New Member of the Brevicidine Family, Displays an Extended Target Specificity. Frontiers in Microbiology, 12, Article 693117. https://doi.org/10.3389/fmicb.2021.693117

Viel, J. H., van Tilburg, A. Y., & Kuipers, O. P. (2021). Characterization of Leader Processing Shows That Partially Processed Mersacidin Is Activated by AprE After Export. Frontiers in Microbiology, 12, Article 765659. https://doi.org/10.3389/fmicb.2021.765659

Ruijne, F., & Kuipers, O. P. (2021). Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochemical Society Transactions, 49(1), 203-215. Article BST20200425. https://doi.org/10.1042/BST20200425

Muñoz, C. Y., de Jong, A., & Kuipers, O. P. (2021). Draft Genome Sequences of a Bacillus subtilis Strain, a Bacillus velezensis Strain, a Paenibacillus Strain, and an Acinetobacter baumannii Strain, All Isolated from the Phyllosphere of Lactuca sativa or Solanum lycopersicum. Microbiology resource announcements, 10(4), Article e01092-20. https://doi.org/10.1128/MRA.01092-20

Arias-Orozco, P., Yi, Y., & Kuipers, O. P. (2021). Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains. Microbiology resource announcements, 10(19), Article e00116-21. https://doi.org/10.1128/MRA.00116-21

Xia, Y., Cebrián, R., Xu, C., Jong, A. D., Wu, W., & Kuipers, O. P. (2021). Elucidating the mechanism by which synthetic helper peptides sensitize Pseudomonas aeruginosa to multiple antibiotics. PLoS Pathogens, 17(9), Article e1009909. https://doi.org/10.1371/journal.ppat.1009909

Arias-Orozco, P., Inklaar, M., Lanooij, J., Cebrián, R., & Kuipers, O. P. (2021). Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies. ACS Synthetic Biology, 10(10), 2579-2591. Article acssynbio.1c00224. https://doi.org/10.1021/acssynbio.1c00224

Gazioglu, O., Kareem, B. O., Afzal, M., Shafeeq, S., Kuipers, O. P., Ulijasz, A. T., Andrew, P. W., & Yesilkaya, H. (2021). Glutamate Dehydrogenase (GdhA) of Streptococcus pneumoniae Is Required for High Temperature Adaptation. Infection and Immunity, 89(12), Article IAI0040021. https://doi.org/10.1128/IAI.00400-21

Viel, J. H., Jaarsma, A. H., & Kuipers, O. P. (2021). Heterologous Expression of Mersacidin in Escherichia coli Elucidates the Mode of Leader Processing. ACS Synthetic Biology, 10(3), 600-608. Article acssynbio.0c00601. https://doi.org/10.1021/acssynbio.0c00601

Zhou, L., de Jong, A., Yi, Y., & Kuipers, O. P. (2021). Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From Pseudomonas mediterranea EDOX. Frontiers in Microbiology, 12, Article 732771. https://doi.org/10.3389/fmicb.2021.732771

Chen, J., & Kuipers, O. P. (2021). Isolation and Analysis of the Nisin Biosynthesis Complex NisBTC: Further Insights into Their Cooperative Action. mBio, 12(5), Article e02585-21. https://doi.org/10.1128/mBio.02585-21

Lauxen, A. I., Kobauri, P., Wegener, M., Hansen, M. J., Galenkamp, N. S., Maglia, G., Szymanski, W., Feringa, B. L., & Kuipers, O. P. (2021). Mechanism of Resistance Development in E. coli against TCAT, a Trimethoprim-Based Photoswitchable Antibiotic. Pharmaceuticals, 14(5), Article ph14050392. https://doi.org/10.3390/ph14050392

Zhao, X., & Kuipers, O. P. (2021). Nisin- and Ripcin-Derived Hybrid Lanthipeptides Display Selective Antimicrobial Activity against Staphylococcus aureus. ACS Synthetic Biology, 10(7), 1703–1714. https://doi.org/10.1021/acssynbio.1c00080

Li, Q., Cebrián, R., Montalbán-López, M., Ren, H., Wu, W., & Kuipers, O. P. (2021). Outer-membrane-acting peptides and lipid II-targeting antibiotics cooperatively kill Gram-negative pathogens. Communications biology, 4(1), Article 31. https://doi.org/10.1038/s42003-020-01511-1

Luo, Y., Korza, G., DeMarco, A. M., Kuipers, O. P., Li, Y.-Q., & Setlow, P. (2021). Properties of spores of Bacillus subtilis with or without a transposon that decreases spore germination and increases spore wet heat resistance. Journal of Applied Microbiology, 131(6), 2918-2928. https://doi.org/10.1111/jam.15163

Fernandez-Cantos, M. V., Garcia-Morena, D., Iannone, V., El-Nezami, H., Kolehmainen, M., & Kuipers, O. P. (2021). Role of microbiota and related metabolites in gastrointestinal tract barrier function in NAFLD. Tissue Barriers, 9(3), Article e1879719. https://doi.org/10.1080/21688370.2021.1879719

Zhao, X., Xu, Y., Viel, J. H., & Kuipers, O. P. (2021). Semisynthetic Macrocyclic Lipo-lanthipeptides Display Antimicrobial Activity Against Bacterial Pathogens. ACS Synthetic Biology, 10(8), 1980-1991. https://doi.org/10.1021/acssynbio.1c00161

Zhao, X., & Kuipers, O. P. (2021). Synthesis of silver-nisin nanoparticles with low cytotoxicity as antimicrobials against biofilm-forming pathogens. Colloids and Surfaces B: Biointerfaces, 206, Article 111965. https://doi.org/10.1016/j.colsurfb.2021.111965

Michalik, S., Reder, A., Richts, B., Faßhauer, P., Mäder, U., Pedreira, T., Poehlein, A., van Heel, A. J., van Tilburg, A. Y., Altenbuchner, J., Klewing, A., Reuß, D. R., Daniel, R., Commichau, F. M., Kuipers, O. P., Hamoen, L. W., Völker, U., & Stülke, J. (2021). The Bacillus subtilis Minimal Genome Compendium. ACS Synthetic Biology, 10(10), 2767-2771. Article acssynbio.1c00339. https://doi.org/10.1021/acssynbio.1c00339

Cebrián, R., Xu, C., Xia, Y., Wu, W., & Kuipers, O. P. (2021). The cathelicidin-derived close-to-nature peptide D-11 sensitizes Klebsiella pneumoniae to a range of antibiotics in vitro, ex vivo and in vivo. International journal of antimicrobial agents, 58(5), Article 106434. https://doi.org/10.1016/j.ijantimicag.2021.106434

Shlla, B., Gazioglu, O., Shafeeq, S., Manzoor, I., Kuipers, O. P., Ulijasz, A., Hiller, N. L., Andrew, P. W., & Yesilkaya, H. (2021). The Rgg1518 transcriptional regulator is a necessary facet of sugar metabolism and virulence in Streptococcus pneumoniae. Molecular Microbiology, 116(3), 996-1008. https://doi.org/10.1111/mmi.14788

van Tilburg, A. Y., Fülleborn, J. A., Reder, A., Völker, U., Stülke, J., van Heel, A. J., & Kuipers, O. P. (2021). Unchaining miniBacillus PG10: Relief of FlgM-mediated repression of autolysin genes. Applied and environmental microbiology, 87(18), Article e01123-21. https://doi.org/10.1128/AEM.01123-21

Chen, J., van Heel, A. J., & Kuipers, O. P. (2021). Visualization and Analysis of the Dynamic Assembly of a Heterologous Lantibiotic Biosynthesis Complex in Bacillus subtilis. mBio, 12(4), Article e01219-21. https://doi.org/10.1128/mBio.01219-21

Hernández-Ortega, E. P., van der Meulen, S., Kuijpers, L. J., & Kok, J. (2022). Riboswitch RSthiT as a molecular tool in Lactococcus lactis. Applied and environmental microbiology, 88(4), Article e01764-21. https://doi.org/10.1128/AEM.01764-21

Wakai, T., Kano, C., Karsens, H., Kok, J., & Yamamoto, N. (2021). Functional role of surface layer proteins of Lactobacillus acidophilus L-92 in stress tolerance and binding to host cell proteins. Bioscience of Microbiota, Food and Health, 40(1), 33-42. https://doi.org/10.12938/BMFH.2020-005

van Tatenhove-Pel, R. J., Rijavec, T., Lapanje, A., van Swam, I., Zwering, E., Hernandez-Valdes, J. A., Kuipers, O. P., Picioreanu, C., Teusink, B., & Bachmann, H. (2021). Microbial competition reduces metabolic interaction distances to the low µm-range. The ISME journal, 15, 688–701. https://doi.org/10.1038/s41396-020-00806-9

Montalbán-López, M., Scott, T. A., Ramesh, S., Rahman, I. R., van Heel, A. J., Viel, J. H., Bandarian, V., Dittmann, E., Genilloud, O., Goto, Y., Grande Burgos, M. J., Hill, C., Kim, S., Koehnke, J., Latham, J. A., Link, A. J., Martínez, B., Nair, S. K., Nicolet, Y., ... van der Donk, W. A. (2021). New developments in RiPP discovery, enzymology and engineering. Natural product reports, 38(1), 130-239. Article D0NP00027B. https://doi.org/10.1039/d0np00027b

de Vries, R. H., Viel, J. H., Kuipers, O. P., & Roelfes, G. (2021). Rapid and selective chemical editing of Ribosomally synthesized and Post-translationally modified Peptides (RiPPs) via Cu(II)-catalyzed β-borylation of dehydroamino acids. Angewandte Chemie (International ed. in English), 60(8), 3946-3950. https://doi.org/10.1002/anie.202011460

Teusink, B., Kuipers, O. P., & Moineau, S. (2021). Symposium on Lactic Acid Bacteria-reading while waiting for a meeting. FEMS Microbiology Reviews, 45(2), Article fuaa049. https://doi.org/10.1093/femsre/fuaa049

Xia, Y., Xu, C., Wang, D., Weng, Y., Jin, Y., Bai, F., Cheng, Z., Kuipers, O. P., & Wu, W. (2021). YbeY controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa. Applied and environmental microbiology, 87(5). https://doi.org/10.1128/AEM.02171-20

Boonstra, M., Schaffer, M., Sousa, J., Morawska, L., Holsappel, S., Hildebrandt, P., Sappa, P. K., Rath, H., de Jong, A., Lalk, M., Mäder, U., Völker, U., & Kuipers, O. P. (2020). Analyses of competent and non-competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence. Environmental Microbiology, 22(6), 2312-2328. https://doi.org/10.1111/1462-2920.15005

Zhao, X., Yin, Z., Breukink, E., Moll, G. N., & Kuipers, O. P. (2020). An Engineered Double Lipid II Binding Motifs-Containing Lantibiotic Displays Potent and Selective Antimicrobial Activity against Enterococcus faecium. Antimicrobial Agents and Chemotherapy, 64(6), Article e02050-19. https://doi.org/10.1128/AAC.02050-19

Hernandez-Valdes, J. A., Huang, C., Kok, J., & Kuipers, O. P. (2020). Another Breaker of the Wall: the Biological Function of the Usp45 Protein of Lactococcus lactis. Applied and environmental microbiology, 86(16), 1-14. Article e00903-20. https://doi.org/10.1128/AEM.00903-20

Hernandez-Valdes, J. A., van Gestel, J., & Kuipers, O. P. (2020). A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium. Nature Communications, 11(1), Article 1203. https://doi.org/10.1038/s41467-020-15017-1

Caro-Astorga, J., Frenzel, E., Perkins, J. R., Álvarez-Mena, A., de Vicente, A., Ranea, J. A. G., Kuipers, O. P., & Romero, D. (2020). Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus. NPJ biofilms and microbiomes, 6(1), Article 3. https://doi.org/10.1038/s41522-019-0112-7

Li, Z., Song, C., Yi, Y., & Kuipers, O. P. (2020). Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters. BMC Genomics, 21(1), Article 157. https://doi.org/10.1186/s12864-020-6563-7

Li, Z., Chakraborty, P., de Vries, R. H., Song, C., Zhao, X., Roelfes, G., Scheffers, D.-J., & Kuipers, O. P. (2020). Characterization of two relacidines belonging to a novel class of circular lipopeptides that act against Gram-negative bacterial pathogens. Environmental Microbiology, 22(12), 5125-5136. https://doi.org/10.1111/1462-2920.15145

Marcelli, B., de Jong, A., Janzen, T., Serrano, M., Kok, J., & Kuipers, O. P. (2020). Complete Genome Sequences of 28 Lactococcal Bacteriophages Isolated from Failed Dairy Fermentation Processes. Microbiology resource announcements, 9(12), Article e01535-19. https://doi.org/10.1128/MRA.01535-19

Deng, J., Viel, J. H., Kubyshkin, V., Budisa, N., & Kuipers, O. P. (2020). Conjugation of Synthetic Polyproline Moietes to Lipid II Binding Fragments of Nisin Yields Active and Stable Antimicrobials. Frontiers in Microbiology, 11, Article 575334. https://doi.org/10.3389/fmicb.2020.575334

Hernandez-Valdes, J. A., Solopova, A., & Kuipers, O. P. (2020). Development of Lactococcus lactis Biosensors for Detection of Diacetyl. Frontiers in Microbiology, 11, Article 1032. https://doi.org/10.3389/fmicb.2020.01032

Hernandez-Valdes, J. A., Dalglish, M. M., Hermans, J., & Kuipers, O. P. (2020). Development of Lactococcus lactis Biosensors for Detection of Sulfur-Containing Amino Acids. Frontiers in Microbiology, 11, Article 1654. https://doi.org/10.3389/fmicb.2020.01654

Hernandez-Valdes, J. A., de Jong, A., Kok, J., & Kuipers, O. P. (2020). Draft Genome Sequences of Three Amino Acid-Secreting Lactococcus lactis Strains. Microbiology resource announcements, 9(16), Article e00158. https://doi.org/10.1128/MRA.00158-20

Marcelli, B., Karsens, H., Nijland, M., Oudshoorn, R., Kuipers, O. P., & Kok, J. (2020). Employing lytic phage-mediated horizontal gene transfer in Lactococcus lactis. PLoS ONE, 15(9 ), Article e0238988. https://doi.org/10.1371/journal.pone.0238988

Xia, Y., Weng, Y., Xu, C., Wang, D., Pan, X., Tian, Z., Xia, B., Li, H., Chen, R., Liu, C., Jin, Y., Bai, F., Cheng, Z., Kuipers, O. P., & Wu, W. (2020). Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa. mBio, 11(3), Article e00659-20. https://doi.org/10.1128/mBio.00659-20

Hernandez-Valdes, J. A., Aan de Stegge, M., Hermans, J., Teunis, J., van Tatenhove-Pel, R. J., Teusink, B., Bachmann, H., & Kuipers, O. P. (2020). Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metabolic Engineering Communications, 11, Article e00133. https://doi.org/10.1016/j.mec.2020.e00133

Zhao, X., Cebrian, R., Fu, Y., Rink, R., Bosma, T., Moll, G. N., & Kuipers, O. P. (2020). High-throughput screening for substrate specificity-adapted mutants of the nisin dehydratase NisB. ACS Synthetic Biology, 9(6), 1468-1478. https://doi.org/10.1021/acssynbio.0c00130

Hernandez-Valdes, J. A., Zhou, L., de Vries, M. P., & Kuipers, O. P. (2020). Impact of spatial proximity on territoriality among human skin bacteria. NPJ biofilms and microbiomes, 6(1), Article 30. https://doi.org/10.1038/s41522-020-00140-0

Huang, C., Hernandez-Valdes, J. A., Kuipers, O. P., & Kok, J. (2020). Lysis of a Lactococcus lactis dipeptidase mutant and rescue by mutation in the pleiotropic regulator cody. Applied and environmental microbiology, 86(8), Article 2937. https://doi.org/10.1128/AEM.02937-19

Zhao, X., Li, Z., & Kuipers, O. P. (2020). Mimicry of a Non-ribosomally Produced Antimicrobial, Brevicidine, by Ribosomal Synthesis and Post-translational Modification. Cell Chemical Biology, 27(10), 1262-1271. https://doi.org/10.1016/j.chembiol.2020.07.005

van Tilburg, A. Y., van Heel, A. J., Stülke, J., de Kok, N. A. W., Rueff, A.-S., & Kuipers, O. P. (2020). MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics. ACS Synthetic Biology, 9(7), 1833-1842. Article acssynbio.0c00194. https://doi.org/10.1021/acssynbio.0c00194

Li, Z., de Vries, R. H., Chakraborty, P., Song, C., Zhao, X., Scheffers, D.-J., Roelfes, G., & Kuipers, O. P. (2020). Novel modifications of nonribosomal peptides from Brevibacillus laterosporus MG64 and investigation of their mode of action. Applied and environmental microbiology, 86(24), 1-14. Article e01981-20. https://doi.org/10.1128/AEM.01981-20

Chen, J., van Heel, A. J., & Kuipers, O. P. (2020). Subcellular Localization and Assembly Process of the Nisin Biosynthesis Machinery in Lactococcus lactis. mBio, 11(6), 1-22. Article e02825-20. https://doi.org/10.1128/mBio.02825-20

Vaishampayan, A., Ahmed, R., Wagner, O., de Jong, A., Haag, R., Kok, J., & Grohmann, E. (2021). Transcriptomic analysis of stress response to novel antimicrobial coatings in a clinical MRSA strain. Materials science & engineering c-Biomimetic and supramolecular systems, 119, Article 111578. https://doi.org/10.1016/j.msec.2020.111578

Huang, C., & Kok, J. (2020). Editing of the proteolytic system of Lactococcus lactis increases its bioactive potential. Applied and environmental microbiology, 86(18), Article e01319. https://doi.org/10.1128/AEM.01319-20

Papadimitriou, K., Kline, K., Renault, P., & Kok, J. (2020). Editorial: Omics and Systems Approaches to Study the Biology and Applications of Lactic Acid Bacteria. Frontiers in Microbiology, 11, Article 1786. https://doi.org/10.3389/fmicb.2020.01786

van Tatenhove-Pel, R. J., Hernandez-Valdes, J. A., Teusink, B., Kuipers, O. P., Fischlechner, M., & Bachmann, H. (2020). Microdroplet screening and selection for improved microbial production of extracellular compounds. Current Opinion in Biotechnology, 61, 72-81. https://doi.org/10.1016/j.copbio.2019.10.007

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. (2019). Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evolutionary Biology, 19(1), Article 15. https://doi.org/10.1186/s12862-018-1331-x

Marcelli, B., de Jong, A., Karsens, H., Janzen, T., Kok, J., & Kuipers, O. P. (2019). A specific sugar moiety in the Lactococcus lactis cell wall pellicle is required for infection by CHPC971, a member of the rare 1706 phage species. Applied and environmental microbiology, 85(19), Article e01224-19. https://doi.org/10.1128/AEM.01224-19

Perez, M., Calles-Enríquez, M., Del Rio, B., Redruello, B., de Jong, A., Kuipers, O. P., Kok, J., Martin, M. C., Ladero, V., Fernandez, M., & Alvarez, M. A. (2019). Construction and characterization of a double mutant of Enterococcus faecalis that does not produce biogenic amines. Scientific Reports, 9(1), Article 16881. https://doi.org/10.1038/s41598-019-53175-5

Kasuga, G., Tanaka, M., Harada, Y., Nagashima, H., Yamato, T., Wakimoto, A., Arakawa, K., Ito, Y., Kawai, Y., Kok, J., & Masuda, T. (2019). Homologous expression and characterization of gassericin T and gassericin S, a novel class IIb bacteriocin produced by LA327. Applied and environmental microbiology, 85(6), Article e02815-18. https://doi.org/10.1128/AEM.02815-18

Omony, J., de Jong, A., Kok, J., & van Hijum, S. A. F. T. (2019). Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network. PLoS ONE, 14(5), Article e0214868. https://doi.org/10.1371/journal.pone.0214868

van der Meulen, S. B., Hesseling-Meinders, A., de Jong, A., & Kok, J. (2019). The protein regulator ArgR and the sRNA derived from the 3'-UTR region of its gene, ArgX, both regulate the arginine deiminase pathway in Lactococcus lactis. PLoS ONE, 14(6), Article e0218508. https://doi.org/10.1371/journal.pone.0218508

Tarazanova, M., Starrenburg, M., Todt, T., van Hijum, S., Kok, J., & Bachmann, H. (2019). Transcriptional response of Lactococcus lactis during bacterial emulsification. PLoS ONE, 14(7), Article e0220048. https://doi.org/10.1371/journal.pone.0220048

Bron, P. A., Marcelli, B., Mulder, J., van der Els, S., Morawska, L. P., Kuipers, O. P., Kok, J., & Kleerebezem, M. (2019). Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria. Current Opinion in Biotechnology, 56, 61-68. https://doi.org/10.1016/j.copbio.2018.09.004

Tarazanova, M., Huppertz, T., Kok, J., & Bachmann, H. (2018). Altering textural properties of fermented milk by using surface-engineered Lactococcus lactis. Microbial Biotechnology, 11(4), 770-780. https://doi.org/10.1111/1751-7915.13278

Vaishampayan, A., de Jong, A., Wight, D. J., Kok, J., & Grohmann, E. (2018). A Novel Antimicrobial Coating Represses Biofilm and Virulence-Related Genes in Methicillin-Resistant Staphylococcus aureus. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00221

van Heel, A. J., de Jong, A., Song, C., Viel, J. H., Kok, J., & Kuipers, O. P. (2018). BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 46(W1), W278-W281. https://doi.org/10.1093/nar/gky383

Solopova, A., Bachmann, H., Teusink, B., Kok, J., & Kuipers, O. P. (2018). Further Elucidation of Galactose Utilization in MG1363. Frontiers in Microbiology, 9, Article 1803. https://doi.org/10.3389/fmicb.2018.01803

Tarazanova, M., Huppertz, T., Kok, J., & Bachmann, H. (2018). Influence of lactococcal surface properties on cell retention and distribution in cheese curd. International Dairy Journal, 85, 73-78. https://doi.org/10.1016/j.idairyj.2018.05.003

Siroli, L., Braschi, G., de Jong, A., Kok, J., Patrignani, F., & Lanciotti, R. (2018). Transcriptomic approach and membrane fatty acid analysis to study the response mechanisms of Escherichia coli to thyme essential oil, carvacrol, 2-(E)-hexanal and citral exposure. Journal of Applied Microbiology, 125(5), 1308-1320. Article jam.14048. https://doi.org/10.1111/jam.14048

Clauss-Lendzian, E., Vaishampayan, A., de Jong, A., Landau, U., Meyer, C., Kok, J., & Grohmann, E. (2018). Stress response of a clinical Enterococcus faecalis isolate subjected to a novel antimicrobial surface coating. Microbiological Research, 207, 53-64. https://doi.org/10.1016/j.micres.2017.11.006

Tarazanova, M., Huppertz, T., Beerthuyzen, M., van Schalkwijk, S., Janssen, P., Wels, M., Kok, J., & Bachmann, H. (2017). Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates. Frontiers in Microbiology, 8, Article 1691. https://doi.org/10.3389/fmicb.2017.01691

Solopova, A., Kok, J., & Kuipers, O. P. (2017). Disruption of a transcriptional repressor by an IS-element integration leads to the activation of a novel silent cellobiose transporter in Lactococcus lactis MG1363. Applied and environmental microbiology, 83(23), Article e01279-17. https://doi.org/10.1128/AEM.01279-17

van der Meulen, S. B., de Jong, A., & Kok, J. (2017). Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs. Frontiers in Microbiology, 8, Article 1704. https://doi.org/10.3389/fmicb.2017.01704

Visweswaran, G. R. R., Kurek, D., Szeliga, M., Pastrana, F. R., Kuipers, O. P., Kok, J., & Buist, G. (2017). Expression of prophage-encoded endolysins contributes to autolysis of Lactococcus lactis. Applied Microbiology and Biotechnology, 101(3), 1099-1110. https://doi.org/10.1007/s00253-016-7822-z

van Gijtenbeek, L. A., & Kok, J. (2017). Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Frontiers in Microbiology, 8, Article 1161. https://doi.org/10.3389/fmicb.2017.01161

Kok, J., van Gijtenbeek, L. A., de Jong, A., van der Meulen, S. B., Solopova, A., & Kuipers, O. P. (2017). The evolution of gene regulation research in Lactococcus lactis. FEMS Microbiology Reviews, 41(Supp_1), S220-S243. https://doi.org/10.1093/femsre/fux028

Perez, M., Ladero, V., del Rio, B., Redruello, B., de Jong, A., Kuipers, O., Kok, J., Martin, M. C., Fernandez, M., & Alvarez, M. A. (2017). The Relationship among Tyrosine Decarboxylase and Agmatine Deiminase Pathways in Enterococcus faecalis. Frontiers in Microbiology, 8, 1-9. Article 2107. https://doi.org/10.3389/fmicb.2017.02107

Solopova, A., Formosa-Dague, C., Courtin, P., Furlan, S., Veiga, P., Péchoux, C., Armalyte, J., Sadauskas, M., Kok, J., Hols, P., Dufrêne, Y. F., Kuipers, O. P., Chapot-Chartier, M.-P., & Kulakauskas, S. (2016). Regulation of cell wall plasticity by nucleotide metabolism in Lactococcus lactis. The Journal of Biological Chemistry, 291(21), 11323-11336. https://doi.org/10.1074/jbc.M116.714303

Papadimitriou, K., Alegría, Á., Bron, P. A., de Angelis, M., Gobbetti, M., Kleerebezem, M., Lemos, J. A., Linares, D. M., Ross, P., Stanton, C., Turroni, F., van Sinderen, D., Varmanen, P., Ventura, M., Zúñiga, M., Tsakalidou, E., & Kok, J. (2016). Stress Physiology of Lactic Acid Bacteria. Microbiology and Molecular Biology Reviews, 80(3), 837-890. https://doi.org/10.1128/MMBR.00076-15

van der Meulen, S. B., de Jong, A., & Kok, J. (2016). Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biology, 13(3), 353-366. https://doi.org/10.1080/15476286.2016.1146855

Perez, M., Ladero, V., Del Rio, B., Redruello, B., Jong, de, A., Kuipers, O. P., Kok, J., Martin, M. C., Fernandez, M., & Alvarez, M. A. (2016). Transcriptome profiling of TDC cluster deletion mutant of Enterococcus faecalis V583. Genomics Data, 9, 67-69. https://doi.org/10.1016/j.gdata.2016.06.012

Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Branco dos Santos, F., Giera, M., Fusetti, F., de Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P., & Teusink, B. (2015). Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect? Molecular Microbiology, 97(1), 77-92. https://doi.org/10.1111/mmi.13012

de Jong, A., van der Meulen, S., Kuipers, O. P., & Kok, J. (2015). T-REx: Transcriptome analysis webserver for RNA-seq Expression data. BMC Genomics, 16(1), Article 663. https://doi.org/10.1186/s12864-015-1834-4

Solopova, A., van Gestel, J., Weissing, F. J., Bachmann, H., Teusink, B., Kok, J., & Kuipers, O. P. (2014). Bet-hedging during bacterial diauxic shift. Proceedings of the National Academy of Science of the United States of America, 111(20), 7427-7432. https://doi.org/10.1073/pnas.1320063111

C. Abrantes, M., Kok, J., & de Fatima Silva Lopes, M. (2014). Enterococcus faecalis zinc-responsive proteins mediate bacterial defence against zinc overload, lysozyme and oxidative stress. Microbiology, 160(12), 2755-2762. https://doi.org/10.1099/mic.0.080341-0

Visweswaran, G. R. R., Leenhouts, K., van Roosmalen, M., Kok, J., & Buist, G. (2014). Exploiting the peptidoglycan-binding motif, LysM, for medical and industrial applications. Applied Microbiology and Biotechnology, 98(10), 4331-4345. https://doi.org/10.1007/s00253-014-5633-7

Kok, J., Johansen, E., Kleerebezem, M., & Teusink, B. (2014). Lactic Acid Bacteria: embarking on 30 more years of research. Microbial Cell Factories, 13(Suppl 1), Article l1. https://doi.org/10.1186/1475-2859-13-S1-I1

Puri, P., Eckhardt, T. H., Franken, L. E., Fusetti, F., Stuart, M. C. A., Boekema, E. J., Kuipers, O. P., Kok, J., & Poolman, B. (2014). Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization. Molecular Microbiology, 91(2), 394-407. https://doi.org/10.1111/mmi.12468

Visweswaran, G. R. R., Steen, A., Leenhouts, K., Szeliga, M., Ruban, B., Hesseling-Meinders, A., Dijkstra, B. W., Kuipers, O. P., Kok, J., & Buist, G. (2013). AcmD, a homolog of the major autolysin AcmA of Lactococcus lactis, binds to the cell wall and contributes to cell separation and autolysis. PLoS ONE, 8(8), Article e72167. https://doi.org/10.1371/journal.pone.0072167

van Heel, A. J., de Jong, A., Montalban-Lopez, M., Kok, J., & Kuipers, O. P. (2013). BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Research, 41(W1), W448-W453. https://doi.org/10.1093/nar/gkt391

Overkamp, W., Beilharz, K., Weme, R. D. O., Solopova, A., Karsens, H., Kovacs, A. T., Kok, J., Kuipers, O. P., & Veening, J.-W. (2013). Benchmarking Various Green Fluorescent Protein Variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for Live Cell Imaging. Applied and environmental microbiology, 79(20), 6481-6490. https://doi.org/10.1128/AEM.02033-13

Abrantes, M. C., Kok, J., & Lopes, M. D. F. (2013). EfaR Is a Major Regulator of Enterococcus faecalis Manganese Transporters and Influences Processes Involved in Host Colonization and Infection. Infection and Immunity, 81(3), 935-944. https://doi.org/10.1128/IAI.06377-11

Steele, J., Broadbent, J., & Kok, J. (2013). Perspectives on the contribution of lactic acid bacteria to cheese flavor development. Current Opinion in Biotechnology, 24(2), 135-141. https://doi.org/10.1016/j.copbio.2012.12.001

de Jong, A., Hansen, M. E., Kuipers, O. P., Kilstrup, M., & Kok, J. (2013). The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk. PLoS ONE, 8(1), Article e53085. https://doi.org/10.1371/journal.pone.0053085

Eckhardt, T. H., Skotnicka, D., Kok, J., & Kuipers, O. P. (2013). Transcriptional Regulation of Fatty Acid Biosynthesis in Lactococcus lactis. Journal of Bacteriology, 195(5), 1081-1089. https://doi.org/10.1128/JB.02043-12

Visweswaran, G. R. R., Dijkstra, B. W., & Kok, J. (2012). A genetically engineered protein domain binding to bacterial murein, archaeal pseudomurein, and fungal chitin cell wall material. Applied Microbiology and Biotechnology, 96(3), 729-737. https://doi.org/10.1007/s00253-012-3871-0

Solopova, A., Bachmann, H., Teusink, B., Kok, J., Neves, A. R., & Kuipers, O. P. (2012). A Specific Mutation in the Promoter Region of the Silent cel Cluster Accounts for the Appearance of Lactose-Utilizing Lactococcus lactis MG1363. Applied and environmental microbiology, 78(16), 5612-5621. https://doi.org/10.1128/AEM.00455-12

Price, C. E., Zeyniyev, A., Kuipers, O. P., & Kok, J. (2012). From meadows to milk to mucosa - adaptation of Streptococcus and Lactococcus species to their nutritional environments. FEMS Microbiology Reviews, 36(5), 949-971. https://doi.org/10.1111/j.1574-6976.2011.00323.x

Tariq, M., Bruijs, C., Kok, J., & Krom, B. P. (2012). Link between Culture Zeta Potential Homogeneity and Ebp in Enterococcus faecalis. Applied and environmental microbiology, 78(7), 2282-2288. https://doi.org/10.1128/AEM.07618-11

de Jong, A., Pietersma, H., Cordes, M., Kuipers, O. P., & Kok, J. (2012). PePPER: a webserver for prediction of prokaryote promoter elements and regulons. BMC Genomics, 13(1), Article 299. https://doi.org/10.1186/1471-2164-13-299

Honda, H., Nagaoka, S., Kawai, Y., Kemperman, R., Kok, J., Yamazaki, Y., Tateno, Y., Kitazawa, H., & Saito, T. (2012). Purification and characterization of two phospho-β-galactosidases, LacG1 and LacG2, from Lactobacillus gasseri ATCC33323T. The Journal of General and Applied Microbiology, 58(1), 11-17. https://doi.org/10.2323/jgam.58.11

Roces, C., Pérez, V., Campelo, A. B., Blanco, D., Kok, J., Kuipers, O. P., Rodríguez, A., & Martínez, B. (2012). The putative lactococcal extracytoplasmic function anti-sigma factor llmg2447 determines resistance to the cell wall-active bacteriocin lcn972. Antimicrobial Agents and Chemotherapy, 56(11), 5520-5527. https://doi.org/10.1128/AAC.01206-12

Puri, P., Eckhardt, T., Franken, L., Fusetti, F., Stuart, M., Boekema, E., Kok, J., Kuipers, O., & Poolman, B. (2012). YfiA is necessary and sufficient for dimerization and inactivation of ribosomes in Lactococcus lactis. Molecular Biology of the Cell, 23, 1695.

Visweswaran, G. R. R., Dijkstra, B. W., & Kok, J. (2011). A minimum of three motifs is essential for optimal binding of pseudomurein cell wall-binding domain of Methanothermobacter thermautotrophicus. PLoS ONE, 6(6), Article 21582. https://doi.org/10.1371/journal.pone.0021582

de Jong, A., Kok, J., & Kuipers, O. (2011). Data resources and mining tools for reconstructing gene networks in Lactococcus lactis. Japanese Journal of Lactic Acid Bacteria, 22(1), 3-14.

Pinto, J. P. C., Kuipers, O. P., Marreddy, R. K. R., Poolman, B., & Kok, J. (2011). Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR. PLoS ONE, 6(7), Article 21873. https://doi.org/10.1371/journal.pone.0021873

Kabuki, T., Kawai, Y., Uenishi, H., Seto, Y., Kok, J., Nakajima, H., & Saito, T. (2011). Gene cluster for biosynthesis of thermophilin 1277-a lantibiotic produced by Streptococcus thermophilus SBT1277, and heterologous expression of TepI, a novel immunity peptide. Journal of Applied Microbiology, 110(3), 641-649. https://doi.org/10.1111/j.1365-2672.2010.04914.x

Abrantes, M. C., Lopes, M. D. F., & Kok, J. (2011). Impact of manganese, copper and zinc ions on the transcriptome of the nosocomial pathogen Enterococcus faecalis V583. PLoS ONE, 6(10), Article e26519. https://doi.org/10.1371/journal.pone.0026519

Rigottier-Gois, L., Alberti, A., Houel, A., Taly, J.-F., Palcy, P., Manson, J., Pinto, D., Matos, R. C., Carrilero, L., Montero, N., Tariq, M., Karsens, H., Repp, C., Kropec, A., Budin-Verneuil, A., Benachour, A., Sauvageot, N., Bizzini, A., Gilmore, M. S., ... Serror, P. (2011). Large-Scale Screening of a Targeted Enterococcus faecalis Mutant Library Identifies Envelope Fitness Factors. PLoS ONE, 6(12), Article 29023. https://doi.org/10.1371/journal.pone.0029023

Visweswaran, G. R. R., Dijkstra, B. W., & Kok, J. (2011). Murein and pseudomurein cell wall binding domains of bacteria and archaea-a comparative view. Applied Microbiology and Biotechnology, 92(5), 921-928. https://doi.org/10.1007/s00253-011-3637-0

Pinto, J. P. C., Zeyniyev, A., Karsens, H., Trip, H., Lolkema, J. S., Kuipers, O. P., & Kok, J. (2011). pSEUDO, a Genetic Integration Standard for Lactococcus lactis. Applied and environmental microbiology, 77(18), 6687-6690. https://doi.org/10.1128/AEM.05196-11

Campelo, A. B., Gaspar, P., Roces, C., Rodriguez, A., Kok, J., Kuipers, O. P., Neves, A. R., & Martinez, B. (2011). The Lcn972 Bacteriocin-Encoding Plasmid pBL1 Impairs Cellobiose Metabolism in Lactococcus lactis. Applied and environmental microbiology, 77(21), 7576-7585. https://doi.org/10.1128/AEM.06107-11

Hill, C., Kleerebezem, M., & Kok, J. (2011). The proceedings of the Tenth Symposium on Lactic Acid Bacteria. Microbial Cell Factories, 10((Suppl. 1) : S1), S1-S1. https://doi.org/10.1186/1475-2859-10-S1-S1

de Jong, A., van Heel, A. J., Kok, J., & Kuipers, O. P. (2010). BAGEL2: Mining for bacteriocins in genomic data. Nucleic Acids Research, 38, W647-W651. https://doi.org/10.1093/nar/gkq365

Linares, D. M., Kok, J., & Poolman, B. (2010). Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies. Journal of Bacteriology, 192(21), 5806 - 5812. https://doi.org/10.1128/JB.00533-10

Chikindas, M., Emond, E., Haandrikman, A. J., Kok, J., Leenhouts, K., Pandian, S., Venema, G., & Venema, K. (2010). Heterologous Processing and Export of the Bacteriocins Pediocin PA-1 and Lactococcin A in Lactococcus Lactis: A Study with Leader Exchange. Probiotics and Antimicrobial Proteins, 2(2), 66-76. https://doi.org/10.1007/s12602-009-9023-x

Neves, A. R., Pool, W., Solopova, A., Kok, J., Santos, H., & Kuipers, O. P. (2010). Towards Enhanced Galactose Utilization by Lactococcus lactis. Applied and environmental microbiology, 76(21), 7048 - 7060. https://doi.org/10.1128/AEM.01195-10

Visweswaran, G. R. R., Dijkstra, B. W., & Kok, J. (2010). Two Major Archaeal Pseudomurein Endoisopeptidases: PeiW and PeiP. Archaea-An international microbiological journal, 2010(3), 1-4. Article 480492. https://doi.org/10.1155/2010/480492

Castro, R., Neves, A. R., Fonseca, L. L., Pool, W. A., Kok, J., Kuipers, O. P., & Santos, H. (2009). Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease. Molecular Microbiology, 71(3), 795-806. https://doi.org/10.1111/j.1365-2958.2008.06564.x

Kawai, Y., Kusnadi, J., Kemperman, R., Kok, J., Ito, Y., Endo, M., Arakawa, K., Uchida, H., Nishimura, J., Kitazawa, H., & Saito, T. (2009). DNA Sequencing and Homologous Expression of a Small Peptide Conferring Immunity to Gassericin A, a Circular Bacteriocin Produced by Lactobacillus gasseri LA39. Applied Environmental Microbiology, 75(5), 1324-1330. https://doi.org/10.1128/AEM.02485-08

Kramer, N. E., Hasper, H. E., van den Bogaard, P. T. C., Morath, S., de Kruijff, B., Hartung, T., Smid, E. J., Breukink, E., Kok, J., & Kuipers, O. P. (2008). Increased D-alanylation of lipoteichoic acid and a thickened septum are main determinants in the nisin resistance mechanism of Lactococcus lactis. Microbiology-Sgm, 154(6), 1755-1762. https://doi.org/10.1099/mic.0.2007/015412-0

Buist, G., Steen, A., Kok, J., & Kuipers, O. P. (2008). LysM, a widely distributed protein motif for binding to (peptido)glycans. Molecular Microbiology, 68(4), 838-847. https://doi.org/10.1111/j.1365-2958.2008.06211.x

Steen, A., Buist, G., Kramer, N. E., Jalving, R., Benus, G. F. J. D., Venema, G., Kuipers, O. P., & Kok, J. (2008). Reduced lysis upon growth of Lactococcus lactis on galactose is a consequence of decreased binding of the autolysin AcmA. Applied Environmental Microbiology, 74(15), 4671-4679. https://doi.org/10.1128/AEM.00103-08

van Hijum, S. A. F. T., Baerends, R. J. S., Zomer, A. L., Karsens, H. A., Martin-Requena, V., Trelles, O., Kok, J., & Kuipers, O. P. (2008). Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. Bmc Bioinformatics, 9(93), Article 93. https://doi.org/10.1186/1471-2105-9-93

Larsen, R., van Hijum, S. A. F. T., Martinussen, J., Kuipers, O. P., & Kok, J. (2008). Transcriptome analysis of the Lactococcus lactis ArgR and AhrC Regulons. Applied and environmental microbiology, 74(15), 4768-4771. https://doi.org/10.1128/AEM.00117-08

Martinez, B., Zomer, A. L., Rodriguez, A., Kok, J., & Kuipers, O. P. (2007). Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the lactococcal two-component system CesSR. Molecular Microbiology, 64(2), 473-486. https://doi.org/10.1111/j.1365-2958.2007.05668.x

Ventura, M., Zomer, A., Canchaya, C., O'Connell-Motherway, M., Kuipers, O., Turroni, F., Ribbera, A., Foroni, E., Buist, G., Wegmann, U., Shearman, C., Gasson, M. J., Fitzgerald, G. F., Kok, J., van Sinderen, D., & O’Connell-Motherway, M. (2007). Comparative analyses of prophage-like elements present in two Lactococcus lactis strains. Applied Environmental Microbiology, 73(23), 7771-7780. https://doi.org/10.1128/AEM.01273-07

Wegmann, U., O'Connell-Motherwy, M., Zomer, A., Buist, G., Shearman, C., Canchaya, C., Ventura, M., Goesmann, A., Gasson, M. J., Kuipers, O. P., van Sinderen, D., & Kok, J. (2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp cremoris MG1363. Journal of Bacteriology, 189(8), 3256-3270. https://doi.org/10.1128/JB.01768-06

Reviriego, C., Fernandez, L., Kuipers, O. P., Kok, J., & Rodriguez, J. M. (2007). Enhanced production of pediocin PA-1 in wild nisin- and non-nisin-producing Lactococcus lactis strains of dairy origin. International Dairy Journal, 17(5), 574-577. https://doi.org/10.1016/j.idairyj.2006.05.013

Steen, A., van Schalkwijk, S., Buist, G., Twigt, M., Szeliga, M., Meijer, W., Kuipers, O. P., Kok, J., & Hugenholtz, J. (2007). Lytr, a phage-derived amidase is most effective in induced lysis of Lactococcus lactis compared with other lactococcal amidases and glucosaminidases. International Dairy Journal, 17(8), 926-936. https://doi.org/10.1016/j.idairyj.2006.12.007

Veiga, P., Bulbarela-Sampieri, C., Furlan, S., Maisons, A., Chapot-Chartier, M.-P., Erkelenz, M., Mervelet, P., Noirot, P., Frees, D., Kuipers, O. P., Kok, J., Gruss, A., Buist, G., & Kulakauskas, S. (2007). SpxB regulates O-acetylation-dependent resistance of Lactococcus lactis peptidoglycan to hydrolysis. The Journal of Biological Chemistry, 282(27), 19342-19354. https://doi.org/10.1074/jbc.M611308200

Zomer, A. L., Buist, G., Larsen, R., Kok, J., & Kuipers, O. P. (2007). Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp cremoris MG1363. Journal of Bacteriology, 189(4), 1366-1381. https://doi.org/10.1128/JB.01013-06

Lulko, A. T., Buist, G., Kok, J., & Kuipers, O. P. (2007). Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes. Journal of Molecular Microbiology and Biotechnology, 12(1-2), 82-95. https://doi.org/10.1159/000096463

de Jong, A., van Hijum, S. A. F. T., Bijlsma, J. J. E., Kok, J., & Kuipers, O. P. (2006). BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Research, 34, W273-W279. https://doi.org/10.1093/nar/gkl237

Kenny, JG., Leach, S., de la Hoz, AB., Venema, G., Kok, J., Fitzgerald, GF., Nauta, A., Alonso, JC., van Sinderen, D., Kenny, J. G., Hoz, A. B. D. L., Fitzgerald, G. F., & Alonso, J. C. (2006). Characterization of the lytic-lysogenic switch of the lactococcal bacteriophage Tuc2009. Virology, 347(2), 434-446. https://doi.org/10.1016/j.virol.2005.11.041

Buist, G., Ridder, A. N. J. A., Kok, J., & Kuipers, O. P. (2006). Different subcellular locations of secretome components of Gram-positive bacteria. Microbiology-Sgm, 152(10), 2867-2874. https://doi.org/10.1099/mic.0.29113-0

Larsen, R., Kloosterman, TG., Kok, J., & Kuipers, OP. (2006). GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis. Journal of Bacteriology, 188(13), 4978-4982. https://doi.org/10.1128/JB.00025-06

Gutierrez, J., Larsen, R., Cintas, L. M., Kok, J., & Hernandez, P. E. (2006). High-level heterologous production and functional expression of the sec-dependent enterocin P from Enterococcus faecium P13 in Lactococcus lactis. Applied Microbiology and Biotechnology, 72(1), 41-51. https://doi.org/10.1007/s00253-005-0233-1

den Hengst, CD., Groeneveld, M., Kuipers, OP., Kok, J., & Hengst, C. D. D. (2006). Identification and functional characterization of the Lactococcus lactis CodY-regulated branched-chain amino acid permease BcaP (CtrA). Journal of Bacteriology, 188(9), 3280-3289. https://doi.org/10.1128/JB.188.9.3280-3289.2006