Details about all my publications and my citations can be found on Google Scholar .
My Linkedin page can be found here: https://www.linkedin.com/in/aldertzomer
Publications
2024
Scholarly publications
Dec, M., Zomer, A., Webster, J., Nowak, T., Stępień-Pyśniak, D., & Urban-Chmiel, R. (2024). Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in <i>Erysipelothrix rhusiopathiae</i> Strains from Domestic Geese in Poland. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms25094638
Perez, C. S., Jongh, R. D., Jonkergouw, R., Pelayo, P., Balskus, E. P., Zomer, A., & Strijbis, K. (2024). Prevotella timonensis degrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities. (pp. 1-26). bioRxiv. https://doi.org/10.1101/2024.01.09.574844
2023
Scholarly publications
Rubio-Garcia, A., Zomer, A. L., Guo, R., Rossen, J. W. A., van Zeijl, J. H., Wagenaar, J. A., & Luiken, R. E. C. (2023). Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation. PLoS One, 18(12 December), 1-19. Article e0295072. https://doi.org/10.1371/journal.pone.0295072
https://dspace.library.uu.nl/bitstream/handle/1874/434933/journal.pone.0295072.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/434933/journal.pone.0295072.pdf?sequence=1
Rattigan, R., Wajda, L., Vlasblom, A. A., Wolfe, A., Zomer, A. L., Duim, B., Wagenaar, J. A., & Lawlor, P. G. (2023). Safety Evaluation of an Intranasally Applied Cocktail of Lactococcus lactis Strains in Pigs. Animals, 13(22), Article 3442. https://doi.org/10.3390/ani13223442
D'Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., Zomer, A., Lopes, M. B., Ibrahimi, E., Gruca, A., Nechyporenko, A., Frohme, M., Klammsteiner, T., Pau, E. C. S., Marcos-Zambrano, L. J., Hron, K., Pio, G., Simeon, A., Suharoschi, R., ... Claesson, M. J. (2023). Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action. Frontiers in Microbiology, 14, Article 1257002. https://doi.org/10.3389/fmicb.2023.1257002
Stege, P. B., Hordijk, J., Sandholt, A. K. S., Zomer, A. L., Viveen, M. C., Rogers, M. R. C., Salomons, M., Wagenaar, J. A., Mughini-Gras, L., Willems, R. J. L., & Paganelli, F. L. (2023). Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiology spectrum, 11(4), Article e0006323. https://doi.org/10.1128/spectrum.00063-23
van der Graaf-van Bloois, L., Chen, H., Wagenaar, J. A., & Zomer, A. L. (2023). Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping. Microbial genomics, 9(5), Article 001007. https://doi.org/10.1099/mgen.0.001007
IJsseldijk, L. L., Begeman, L., Duim, B., Gröne, A., Kik, M. J. L., Klijnstra, M. D., Lakemeyer, J., Leopold, M. F., Munnink, B. B. O., Ten Doeschate, M., van Schalkwijk, L., Zomer, A., der Graaf-van Bloois, L. V., & Broens, E. M. (2023). Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021. Emerging Infectious Diseases, 29(4), 835-838. https://doi.org/10.3201/eid2904.221698
Theelen, M. J. P., Luiken, R. E. C., Wagenaar, J. A., Sloet van Oldruitenborgh-Oosterbaan, M. M., Rossen, J. W. A., Schaafstra, F. J. W. C., van Doorn, D. A., & Zomer, A. L. (2023). Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome. Microbiome, 11(1), Article 33. https://doi.org/10.1186/s40168-023-01465-6
van der Graaf-van Bloois, L., Duim, B., Looft, T., Veldman, K. T., Zomer, A. L., & Wagenaar, J. A. (2023). Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution. Microbial genomics, 9(3), Article 000934. https://doi.org/10.1099/mgen.0.000934
Naing, S. Y., Duim, B., Broens, E. M., Schweitzer, V., Zomer, A., van der Graaf-van Bloois, L., van der Meer, C., Stellingwerff, L., Fluit, A. C., & Wagenaar, J. A. (2023). Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus coagulans. Microbiology spectrum, 11(2), Article e0467022. https://doi.org/10.1128/spectrum.04670-22
Bloomfield, S. J., Zomer, A. L., O'grady, J., Kay, G. L., Wain, J., Janecko, N., Palau, R., & Mather, A. E. (2023). Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiology, 110, 1-12. Article 104162. https://doi.org/10.1016/j.fm.2022.104162
Weerdenburg, E., Davies, T., Morrow, B., Zomer, A. L., Hermans, P., Go, O., Spiessens, B., van den Hoven, T., van Geet, G., Aitabi, M., DebRoy, C., Dudley, E. G., Bonten, M., Poolman, J., & Geurtsen, J. (2023). Global Distribution of O Serotypes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Collected From the Blood of Patients With Bacteremia Across Multiple Surveillance Studies. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 76(3), E1236-E1243. https://doi.org/10.1093/cid/ciac421
2022
Scholarly publications
Wegener, A., Duim, B., van der Graaf-van Bloois, L., Zomer, A. L., Visser, C. E., Spaninks, M., Timmerman, A. J., Wagenaar, J. A., & Broens, E. M. (2022). Within-Household Transmission and Bacterial Diversity of Staphylococcus pseudintermedius. Pathogens, 11(8), 1-6. Article 850. https://doi.org/10.3390/pathogens11080850
Speksnijder, D. C., Hopman, N. E. M., Kusters, N. E., Timmerman, A., Swinkels, J. M., Penterman, P. A. A., Krömker, V., Bradley, A. J., Botteldoorn, N., Gehring, R., & Zomer, A. L. (2022). Potential of ESBL-producing Escherichia coli selection in bovine feces after intramammary administration of first generation cephalosporins using in vitro experiments. Scientific Reports, 12(1), 1-10. Article 15083. https://doi.org/10.1038/s41598-022-15558-z
Moreno-Indias, I., Zomer, A. L., Gómez-Cabrero, D., & Claesson, M. J. (2022). Editorial: Microbiome and Machine Learning. Frontiers in Microbiology, 13, Article 964921. https://doi.org/10.3389/fmicb.2022.964921
Geurtsen, J., de Been, M., Weerdenburg, E., Zomer, A., McNally, A., & Poolman, J. (2022). Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiology Reviews, 46(6), 1-30. Article fuac031. https://doi.org/10.1093/femsre/fuac031
Middendorf, P. S., Jacobs-Reitsma, W. F., Zomer, A. L., den Besten, H. M. W., & Abee, T. (2022). Comparative Analysis of L-Fucose Utilization and Its Impact on Growth and Survival of Campylobacter Isolates. Frontiers in Microbiology, 13, 1-12. Article 872207. https://doi.org/10.3389/fmicb.2022.872207
Naing, S. Y., Hordijk, J., Duim, B., Broens, E., van der Graaf - van Bloois, L., Rossen, J. W. A., Robben, J., Leendertse, M., Wagenaar, J., & Zomer, A. (2022). Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. Pathogens, 11(2), 1-14. Article 123. https://doi.org/10.3390/pathogens11020123
2021
Scholarly publications
van der Graaf-van Bloois, L., Wagenaar, J. A., & Zomer, A. L. (2021). RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning. Microbial genomics, 7(11), 1-11. Article 000683. https://doi.org/10.1099/mgen.0.000683
Heikema, A. P., Strepis, N., Horst-Kreft, D., Huynh, S., Zomer, A., Kelly, D. J., Cooper, K. K., & Parker, C. T. (2021). Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated Campylobacter jejuni serotype HS:19. Microbial genomics, 7(11), 1-18. Article 000660. https://doi.org/10.1099/mgen.0.000660
Wegener, A., Broens, E. M., van der Graaf-van Bloois, L., Zomer, A. L., Visser, C. E., van Zeijl, J., van der Meer, C., Kusters, J. G., Friedrich, A. W., Kampinga, G. A., Sips, G. J., Smeets, L., van Kerckhoven, M. E. J., Timmerman, A. J., Wagenaar, J. A., & Duim, B. (2021). Absence of Host-Specific Genes in Canine and Human Staphylococcus pseudintermedius as Inferred from Comparative Genomics. Antibiotics, 10(7), 1-10. Article 854. https://doi.org/10.3390/antibiotics10070854
Patel, S., Vlasblom, A. A., Verstappen, K. M., Zomer, A. L., Fluit, A. C., Rogers, M. R. C., Wagenaar, J. A., Claesson, M. J., & Duim, B. (2021). Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets. mSystems, 6(4), 1-15. Article e00152-21. https://doi.org/10.1128/mSystems.00152-21
Theelen, M., Luiken, R., Wagenaar, J., Sloet van Oldruitenborgh - Oosterbaan, M., Rossen, J. W. A., Schaafstra, FJWC., van Doorn, D., & Zomer, A. (2021). Short- and long-term effect of hospitalization and oral trimethoprim-sulfadiazine administration on the faecal microbiota and resistome in horses. Poster session presented at ECCMID 2021, Austria.
Theelen, M., Luiken, R., Roelfsema, E., Wagenaar, J., Sloet van Oldruitenborgh - Oosterbaan, M., Rossen, J. W. A., & Zomer, A. (2021). Temporal changes in the fecal microbiota and its functional capacity of ponies developing insulin dysregulation. Poster session presented at ACVIM Forum 2021, United States.
Theelen, M. J. P., Luiken, R. E. C., Wagenaar, J. A., Sloet van Oldruitenborgh-Oosterbaan, M. M., Rossen, J. W. A., & Zomer, A. L. (2021). The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors. Animals, 11(6), 1-17. Article 1762. https://doi.org/10.3390/ani11061762
Moreno-Indias, I., Lahti, L., Nedyalkova, M., Elbere, I., Roshchupkin, G., Adilovic, M., Aydemir, O., Bakir-Gungor, B., Santa Pau, E. C., D’Elia, D., Desai, M. S., Falquet, L., Gundogdu, A., Hron, K., Klammsteiner, T., Lopes, M. B., Marcos-Zambrano, L. J., Marques, C., Mason, M., ... Claesson, M. J. (2021). Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology, 12, Article 635781. https://doi.org/10.3389/fmicb.2021.635781
Duim, B., van der Graaf-van Bloois, L., Timmerman, A., Wagenaar, J. A., Flipse, J., Wallinga, J., Bloembergen, P., Miller, W. G., & Zomer, A. L. (2021). Complete Genome Sequence of a Clinical Campylobacter Isolate Identical to a Novel Campylobacter Species. Microbiology Resource Announcements, 10(7), 1-3. Article e00721. https://doi.org/10.1128/MRA.00721-20
Mughini-Gras, L., Pijnacker, R., Coipan, C., Mulder, A. C., Veludo, A. F., de Rijk, S., van Hoek, A. H. A. M., Buij, R., Muskens, G., Koene, M., Veldman, K., Duim, B., Graaf-van Bloois, L. V. D., van der Weijden, C., Kuiling, S., Verbruggen, A., van der Giessen, J., Opsteegh, M., van der Voort, M., ... Franz, E. (2021). Sources and transmission routes of campylobacteriosis: a combined analysis of genome and exposure data. Journal of Infection, 82(2), 216-226. https://doi.org/10.1016/j.jinf.2020.09.039
2020
Scholarly publications
van Bloois, L. V. D. G., Wagenaar, J. A., & Zomer, A. L. (2020). RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning. (pp. 1-17). bioRxiv. https://doi.org/10.1101/2020.07.31.230631
https://dspace.library.uu.nl/bitstream/handle/1874/419991/2020.07.31.230631v2.full.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/419991/2020.07.31.230631v2.full.pdf?sequence=1
Speksnijder, D., Zomer, A., Timmerman, A., & Kusters, N. (2020). The use of cephapirin and cefalonium containing intramammary injectors for mastitis treatment in dairy cattle and selection of ESBL producing Enterobacteriaceae: End report of a series of studies commissioned by Merck Animal Health International.
Flipse, J., Duim, B., Wallinga, J. A., de Wijkerslooth, L. R. H., Graaf-van Bloois, L. V. D., Timmerman, A. J., Zomer, A. L., Veldman, K. T., Wagenaar, J. A., & Bloembergen, P. (2020). A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans. Pathogens, 9(12), Article 1003. https://doi.org/10.3390/pathogens9121003
Theelen, M. J. P., Wagenaar, J. A., Oosterbaan, M. M., Rossen, J. W. A., Schaafstra, FJWC., van Doorn, D. A., & Zomer, A. L. (2020). Short- and long-term effect of hospitalization and oral trimethoprim-sulfadiazine administration on the fecal microbiome. Abstract from ECEIM Congress 2020.
Hoekstra, J., Zomer, A. L., Rutten, V. P. M. G., Benedictus, L., Stegeman, A., Spaninks, M. P., Bennedsgaard, T. W., Biggs, A., De Vliegher, S., Mateo, D. H., Huber-Schlenstedt, R., Katholm, J., Kovács, P., Krömker, V., Lequeux, G., Moroni, P., Pinho, L., Smulski, S., Supré, K., ... Koop, G. (2020). Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis. Scientific Reports, 10(1), Article 18172. https://doi.org/10.1038/s41598-020-75179-2
Mulder, A. C., Franz, E., de Rijk, S., Versluis, M. A. J., Coipan, C., Buij, R., Müskens, G., Koene, M., Pijnacker, R., Duim, B., Bloois, L. V. D. G. V., Veldman, K., Wagenaar, J. A., Zomer, A. L., Schets, F. M., Blaak, H., & Mughini-Gras, L. (2020). Tracing the animal sources of surface water contamination with Campylobacter jejuni and Campylobacter coli. Water Research, 187, Article 116421. https://doi.org/10.1016/j.watres.2020.116421
Arenas, J., Zomer, A., Harders-Westerveen, J., Bootsma, H. J., De Jonge, M. I., Stockhofe-Zurwieden, N., Smith, H. E., & De Greeff, A. (2020). Identification of conditionally essential genes for Streptococcus suis infection in pigs. Virulence, 11(1), 446-464. https://doi.org/10.1080/21505594.2020.1764173
Castellanos, L. R., van der Graaf-van Bloois, L., Donado-Godoy, P., Veldman, K., Duarte, F., Acuña, M. T., Jarquín, C., Weill, F.-X., Mevius, D. J., Wagenaar, J. A., Hordijk, J., & Zomer, A. L. (2020). Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America. Emerging Infectious Diseases, 26(6), 1164-1173. https://doi.org/10.3201/eid2606.191121
Gilbert, M. J., IJsseldijk, L. L., Rubio-García, A., Gröne, A., Duim, B., Rossen, J., Zomer, A. L., & Wagenaar, J. A. (2020). After the bite: bacterial transmission from grey seals ( Halichoerus grypus ) to harbour porpoises ( Phocoena phocoena ). Royal Society Open Science, 7(5), Article 192079. https://doi.org/10.1098/rsos.192079
Ryan, F. J., Ahern, A. M., Fitzgerald, R. S., Laserna-Mendieta, E. J., Power, E. M., Clooney, A. G., O’Donoghue, K. W., McMurdie, P. J., Iwai, S., Crits-Christoph, A., Sheehan, D., Moran, C., Flemer, B., Zomer, A. L., Fanning, A., O’Callaghan, J., Walton, J., Temko, A., Stack, W., ... Claesson, M. J. (2020). Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nature Communications, 11(1), Article 1512. https://doi.org/10.1038/s41467-020-15342-5
IBESS group (2020). Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity. BMC Genomics, 21(1), Article 138. https://doi.org/10.1186/s12864-020-6555-7
Rozwandowicz, M., Hordijk, J., Bossers, A., Zomer, A., Wagenaar, J. A., Mevius, D. J., & Brouwer, M. S. M. (2020). Incompatibility and phylogenetic relationship of I-complex plasmids. Plasmid, 109, Article 102502. https://doi.org/10.1016/j.plasmid.2020.102502
2019
Scholarly publications
Kooyman, F. N. J., Wagenaar, J. A., & Zomer, A. (2019). Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes. Microbial genomics, 5(12). https://doi.org/10.1099/mgen.0.000302
Gaiser, R. A., Zomer, A. L., Wells, J. M., & van Baarlen, P. (2019). Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections. Microbiology Resource Announcements, 8(23), Article e00227-19. https://doi.org/10.1128/mra.00227-19
Gilbert, M. J., Duim, B., Zomer, A. L., & Wagenaar, J. A. (2019). Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles. Frontiers in Microbiology, 10, Article 1086. https://doi.org/10.3389/fmicb.2019.01086
Castellanos, L. R., van der Graaf-van Bloois, L., Donado-Godoy, P., Mevius, D. J., Wagenaar, J. A., Hordijk, J., & Zomer, A. (2019). Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring blaCMY-2 and blaSHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries. Antimicrobial Agents and Chemotherapy, 63(7), Article e02546-18. https://doi.org/10.1128/AAC.02546-18
Sleutjens, J., Meijer, D., Meregalli, P. G., Bakker, L., Wagenaar, J. A., Duim, B., & Zomer, A. (2019). Zoonotic Endocarditis in a Man, the Netherlands. Emerging Infectious Diseases, 25(1), 180-182. https://doi.org/10.3201/eid2501.181029
Wegener, A. C. H., Broens, E. M., Zomer, A. L., van Bloois, L., Timmerman, A. J., Wagenaar, J. A., & Duim, B. (2019). Comparison and dynamics of resistance gene content in canine and human Staphylococcus pseudintermedius. Poster session presented at KNVM Spring meeting.
Cremers, A. J. H., Mobegi, F. M., van der Gaast-de Jongh, C. E., van Weert, M., van Opzeeland, F. J., Vehkala, M., Knol, M. J., Bootsma, H. J., Välimäki, N., Croucher, N. J., Meis, J. F., Bentley, S. D., van Hijum, S. A. F. T., Corander, J., Zomer, A. L., Ferwerda, G., & de Jonge, M. I. (2019). The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease. Clinical Infectious Diseases, 68(1), 61-69. https://doi.org/10.1093/cid/ciy417
2018
Scholarly publications
Duim, B., Wegener, A. C. H., Zomer, A. L., Spaninks, M. P., Wagenaar, J. A., & Broens, E. M. (2018). Phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius detected with whole genome sequencing. Poster session presented at ECCMID 2018.
Wegener, A. C. H., Broens, E. M., Zomer, A. L., Timmerman, A. J., Wagenaar, J. A., & Duim, B. (2018). Genomic comparisons of antimicrobial resistance in canine and human S. pseudintermedius. Poster session presented at Challenges and new concepts in Antibiotics Research conference.
Castellanos, L. R., van der Graaf-van Bloois, L., Donado-Godoy, P., León, M., Clavijo, V., Arévalo, A., Bernal, J. F., Mevius, D. J., Wagenaar, J. A., Zomer, A., & Hordijk, J. (2018). Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant in the Colombian Poultry Chain. Frontiers in Microbiology, 9, Article 2431. https://doi.org/10.3389/fmicb.2018.02431
Theelen, M. J. P., Wagenaar, J. A., Oosterbaan, M. M., Rossen, J. W., & Zomer, A. L. (2018). The effect of air exposure on the stability of the microbiome in faecal samples collected from horses (ECEIM Congress 2018). Poster session presented at ECEIM Congress 2018, Ghent, Belgium.
Theelen, M. J. P., Wagenaar, J. A., Oosterbaan, M. M., Rossen, J. W., & Zomer, A. L. (2018). Factors affecting the faecal microbiome of horses and ponies (ECEIM Congress 2018). Poster session presented at ECEIM Congress 2018, Ghent, Belgium.
Wegener, A., Broens, E. M., Zomer, A., Spaninks, M., Wagenaar, J. A., & Duim, B. (2018). Comparative genomics of phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius of canine origin. Veterinary Microbiology, 225, 125-131. https://doi.org/10.1016/j.vetmic.2018.09.013
Kiers, D., Wielockx, B., Peters, E., van Eijk, L. T., Gerretsen, J., John, A., Janssen, E., Groeneveld, R., Peters, M., Damen, L., Meneses, A. M., Krüger, A., Langereis, J. D., Zomer, A. L., Blackburn, M. R., Joosten, L. A., Netea, M. G., Riksen, N. P., van der Hoeven, J. G., ... Kox, M. (2018). Short-Term Hypoxia Dampens Inflammation in vivo via Enhanced Adenosine Release and Adenosine 2B Receptor Stimulation. EBioMedicine, 33, 144-156. https://doi.org/10.1016/j.ebiom.2018.06.021
Cuperus, T., Kraaij, M. D., Zomer, A. L., van Dijk, A., & Haagsman, H. P. (2018). Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2. PLoS One, 13(6), Article e0198188. https://doi.org/10.1371/journal.pone.0198188
Zomer, A., Otsuka, N., Hiramatsu, Y., Kamachi, K., Nishimura, N., Ozaki, T., Poolman, J. T., & Geurtsen, J. (2018). Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines. Microbial genomics, 4(5). https://doi.org/10.1099/mgen.0.000180
Gilbert, M. J., Duim, B., van der Graaf-van Bloois, L., Wagenaar, J. A., & Zomer, A. L. (2018). Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation. Genome Biology and Evolution, 10(3), 716-722. https://doi.org/10.1093/gbe/evy048
Gilbert, M. J., Zomer, A. L., Timmerman, A. J., Spaninks, M. P., Rubio García, A., Rossen, J. W. A., Duim, B., & Wagenaar, J. A. (2018). Campylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina). International Journal of Systematic and Evolutionary Microbiology, 68, 1787-1794. https://doi.org/10.1099/ijsem.0.002742
Lavelle, K., Murphy, J., Fitzgerald, B., Lugli, G. A., Zomer, A., Neve, H., Ventura, M., Franz, C. M., Cambillau, C., van Sinderen, D., & Mahony, J. (2018). A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant. Applied and Environmental Microbiology, 84(10), Article e02855-17. https://doi.org/10.1128/AEM.02855-17
van Beek, L. L. F., Gouw, D. D., Eleveld, M. J., Bootsma, H. J., de Jonge, M. I., Mooi, F. R., Zomer, A. A., & Diavatopoulos, D. A. (2018). Adaptation of Bordetella pertussis to the respiratory tract. Journal of Infectious Diseases, 217(12), 1987-1996. https://doi.org/10.1093/infdis/jiy125
van der Maten, E., van den Broek, B., de Jonge, M. I., Rensen, K. J. W., Eleveld, M. J., Zomer, A. L., Cremers, A. J. H., Ferwerda, G., de Groot, R., Langereis, J. D., & van der Flier, M. (2018). Streptococcus pneumoniae PspC-subgroup prevalence in invasive disease and difference in contribution to complement evasion. Infection and Immunity, 86(4), Article e00010-18. https://doi.org/10.1128/IAI.00010-18
2017
Scholarly publications
Wegener, A. C. H., Broens, E. M., Zomer, A. L., Spaninks, M. P., Wagenaar, J. A., & Duim, B. (2017). Comparative genomics of phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius. Poster session presented at veterinary science day 2017, Bunnik.
Wegener, A. C. H., Broens, E. M., Zomer, A. L., Spaninks, M. P., Wagenaar, J. A., & Duim, B. (2017). Comparative genomics of phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius. Poster session presented at KNVM Spring meeting.
Bottacini, F., Zomer, A., Milani, C., Ferrario, C., Lugli, G. A., Egan, M., Ventura, M., & van Sinderen, D. (2017). Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003. BMC Genomics, 18(1), Article 991. https://doi.org/10.1186/s12864-017-4387-x
Ahout, I. M. L., Brand, K. H., Zomer, A., van den Hurk, W. H., Schilders, G., Brouwer, M. L., Neeleman, C., de Groot, R., & Ferwerda, G. (2017). Prospective observational study in two Dutch hospitals to assess the performance of inflammatory plasma markers to determine disease severity of viral respiratory tract infections in children. BMJ Open, 7(6), Article e014596. https://doi.org/10.1136/bmjopen-2016-014596
Kuipers, K., Jong, W. S. P., van der Gaast-de Jongh, C. E., Houben, D., van Opzeeland, F., Simonetti, E., van Selm, S., de Groot, R., Koenders, M. I., Azarian, T., Pupo, E., van der Ley, P., Langereis, J. D., Zomer, A., Luirink, J., & de Jonge, M. I. (2017). Th17-Mediated Cross Protection against Pneumococcal Carriage by Vaccination with a Variable Antigen. Infection and Immunity, 85(10), Article E00281-17. https://doi.org/10.1128/IAI.00281-17
https://dspace.library.uu.nl/bitstream/handle/1874/360918/Infect._Immun._2017_Kuipers_.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/360918/Infect._Immun._2017_Kuipers_.pdf?sequence=1
Gilbert, M. J., Duim, B., Timmerman, A. J., Zomer, A. L., & Wagenaar, J. A. (2017). Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host. Scientific Reports, 7, Article 8387. https://doi.org/10.1038/s41598-017-09091-7
Koppenaal, H., Groenendijk, F., van den Berge, M., Verkade, E., Verduin, K., Zomer, A. L., Duim, B., Wagenaar, J. A., Tijsma, A. S. L., Spierenburg, M. A. H., & Te Wierik, M. J. M. (2017). Een uitbraak met Campylobacter fetus na het eten van rauwmelkse schapenkaas: Hoe traceer je de bron van een uitbraak? Nederlands Tijdschrift voor Geneeskunde, 161, Article D1704.
https://dspace.library.uu.nl/bitstream/handle/1874/360917/d1704.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/360917/d1704.pdf?sequence=1
Capel, E., Barnier, J.-P., Zomer, A. L., Bole-Feysot, C., Nussbaumer, T., Jamet, A., Lécuyer, H., Euphrasie, D., Virion, Z., Frapy, E., Pélissier, P., Join-Lambert, O., Rattei, T., Bourdoulous, S., Nassif, X., & Coureuil, M. (2017). Peripheral blood vessels are a niche for blood-borne meningococci. Virulence, 8(8), 1808-1819. https://doi.org/10.1080/21505594.2017.1391446
Vries, S. P. W. D., Gupta, S., Baig, A., Wright, E., Wedley, A., Jensen, A. N., Lora, L. L., Humphrey, S., Skovgård, H., Macleod, K., Pont, E., Wolanska, D. P., L'Heureux, J., Mobegi, F. M., Smith, D. G. E., Everest, P., Zomer, A., Williams, N., Wigley, P., ... Grant, A. J. (2017). Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models. Scientific Reports, 7(1), Article 1251. https://doi.org/10.1038/s41598-017-01133-4
Rozwandowicz, M., Brouwer, M. S. M., Zomer, A. L., Bossers, A., Harders, F., Mevius, D. J., Wagenaar, J. A., & Hordijk, J. (2017). Plasmids of distinct IncK lineages show compatible phenotypes. Antimicrobial Agents and Chemotherapy, 61(3), Article e01954-16. https://doi.org/10.1128/AAC.01954-16
Mobegi, F. M., Cremers, A. J. H., de Jonge, M. I., Bentley, S. D., van Hijum, S. A. F. T., & Zomer, A. (2017). Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. Scientific Reports, 7, Article 42808. https://doi.org/10.1038/srep42808
Tunjungputri, R. N., Mobegi, F. M., Cremers, A. J., van der Gaast-de Jongh, C. E., Ferwerda, G., Meis, J. F., Roeleveld, N., Bentley, S. D., Pastura, A. S., van Hijum, S. A. F. T., van der Ven, A. J., de Mast, Q., Zomer, A., & de Jonge, M. I. (2017). Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. mBio, 8(1), Article e01984-16 . https://doi.org/10.1128/mBio.01984-16
Nebenzahl-Guimaraes, H., van Laarhoven, A., Farhat, M. R., Koeken, V. A., Mandemakers, J., Zomer, A., van Hijum, S. A., Netea, M. G., Murray, M., van Crevel, R., & van Soolingen, D. (2017). Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. American Journal of Respiratory and Critical Care Medicine, 195(11), 1519-1527. https://doi.org/10.1164/rccm.201605-1042OC
Mobegi, F. M., Zomer, A., de Jonge, M. I., & van Hijum, S. A. F. T. (2017). Advances and perspectives in computational prediction of microbial gene essentiality. Briefings in Functional Genomics, 16(2), 70-79. https://doi.org/10.1093/bfgp/elv063
https://dspace.library.uu.nl/bitstream/handle/1874/350110/Advances.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/350110/Advances.pdf?sequence=1
2016
Scholarly publications
Broens, E. M., de Laat, J., Zomer, A. L., Wagenaar, J. A., & Duim, B. (2016). Staphylococcus schleiferi: a single species or two separate subspecies?. Poster session presented at ECCMID.
Duim, B., Zomer, A. L., de Laat, J., Wagenaar, J. A., & Broens, E. M. (2016). Classification of Staphylococcus schleiferi Subspecies Using Whole Genome Comparisons. Poster session presented at ASM-Microbe.
Jong, V. L., Ahout, I. M. L., van den Ham, H.-J., Jans, J., Zaaraoui-Boutahar, F., Zomer, A., Simonetti, E., Bijl, M. A., Brand, H. K., van IJcken, W. F. J., de Jonge, M. I., Fraaij, P. L., de Groot, R., Osterhaus, A. D. M. E., Eijkemans, M. J., Ferwerda, G., & Andeweg, A. C. (2016). Transcriptome assists prognosis of disease severity in respiratory syncytial virus infected infants. Scientific Reports, 6, Article 36603. https://doi.org/10.1038/srep36603
Capel, E., Zomer, A. L., Nussbaumer, T., Bole, C., Izac, B., Frapy, E., Meyer, J., Bouzinba-Ségard, H., Bille, E., Jamet, A., Cavau, A., Letourneur, F., Bourdoulous, S., Rattei, T., Nassif, X., & Coureuil, M. (2016). Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. MBio [E], 7(4), Article e01173-16. https://doi.org/10.1128/mBio.01173-16
Gilbert, M. J., Miller, W. G., Yee, E., Kik, M., Zomer, A. L., Wagenaar, J. A., & Duim, B. (2016). Comparative genomics of Campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts. Genome Biology and Evolution, 8(9), 3022-3029. https://doi.org/10.1093/gbe/evw218
van der Graaf-van Bloois, L., Duim, B., Miller, W. G., Forbes, K. J., Wagenaar, J. A., & Zomer, A. (2016). Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production. BMC Genomics, 17, Article 713. https://doi.org/10.1186/s12864-016-3058-7
Gilbert, M. J., Miller, W. G., Yee, E., Zomer, A. L., van der Graaf-van Bloois, L., Fitzgerald, C., Forbes, K. J., Méric, G., Sheppard, S. K., Wagenaar, J. A., & Duim, B. (2016). Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. Genome Biology and Evolution, 8(6), 2006-2019. https://doi.org/10.1093/gbe/evw146
Graaf-van Bloois, L. V. D., Miller, W. G., Yee, E., Gorkiewicz, G., Forbes, K. J., Zomer, A. L., Wagenaar, J. A., & Duim, B. (2016). Campylobacter fetus Subspecies Contain Conserved Type IV Secretion Systems on Multiple Genomic Islands and Plasmids. PLoS One, 11(4), Article e0152832. https://doi.org/10.1371/journal.pone.0152832
Murphy, J., Bottacini, F., Mahony, J., Kelleher, P., Neve, H., Zomer, A., Nauta, A., & van Sinderen, D. (2016). Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Scientific Reports, 6, Article 21345. https://doi.org/10.1038/srep21345
Kuipers, K., Gallay, C., Martínek, V., Rohde, M., Martínková, M., van der Beek, S. L., Jong, W. S. P., Venselaar, H., Zomer, A., Bootsma, H., Veening, J.-W., & de Jonge, M. I. (2016). Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. Molecular Microbiology, 101(1), 12-26. https://doi.org/10.1111/mmi.13312
Other output
Zomer, A. L., & Poolman, J. T. (2016). Meningitis b vaccine. (Patent No. WO 2016083583 A1).
2015
Scholarly publications
Zomer, A. L., Duim, B., Broens, E. M., Rossen, J. W. A., Leendertse, M., Wagenaar, J. A., & Hordijk, J. (2015). Genomic epidemiology of multiple Acinetobacter baumannii outbreaks in a veterinary intensive care unit. Poster session presented at KNVM Spring meeting.
Cremers, A. J. H., Mobegi, F. M., de Jonge, M. I., van Hijum, S. A. F. T., Meis, J. F., Hermans, P. W. M., Ferwerda, G., Bentley, S. D., & Zomer, A. L. (2015). The post-vaccine microevolution of invasive Streptococcus pneumoniae. Scientific Reports, 5, Article 14952. https://doi.org/10.1038/srep14952
2014
Scholarly publications
de Gouw, D., Serra, D. O., de Jonge, M. I., Hermans, P. W., Wessels, H. J., Zomer, A., Yantorno, O. M., Diavatopoulos, D. A., & Mooi, F. R. (2014). The vaccine potential of Bordetella pertussis biofilm-derived membrane proteins. Emerging Microbes and Infections [E], 3(8), e58. https://doi.org/10.1038/emi.2014.58
Cremers, A. J., Zomer, A. L., Gritzfeld, J. F., Ferwerda, G., van Hijum, S. A., Ferreira, D. M., Shak, J. R., Klugman, K. P., Boekhorst, J., Timmerman, H. M., de Jonge, M. I., Gordon, S. B., & Hermans, P. W. (2014). The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. Microbiome, 2, 44. https://doi.org/10.1186/2049-2618-2-44
Short, K. R., Vissers, M., de Kleijn, S., Zomer, A. L., Kedzierska, K., Grant, E., Reading, P. C., Hermans, P. W. M., Ferwerda, G., & Diavatopoulos, D. A. (2014). Bacterial lipopolysaccharide inhibits influenza virus infection of human macrophages and the consequent induction of CD8+ T cell immunity. Journal of Innate Immunity, 6(2), 129-139. https://doi.org/10.1159/000353905
Mobegi, F. M., van Hijum, S. A., Burghout, P., Bootsma, H. J., de Vries, S. P., Jongh, C. E. V. D. G., Simonetti, E., Langereis, J. D., Hermans, P. W., de Jonge, M. I., & Zomer, A. (2014). From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-958
de Gouw, D., Hermans, P. W. M., Bootsma, H. J., Zomer, A., Heuvelman, K., Diavatopoulos, D. A., & Mooi, F. R. (2014). Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally. PLoS One, 9(1), e84523. https://doi.org/10.1371/journal.pone.0084523
Bottacini, F., O'Connell Motherway, M., Kuczynski, J., O'Connell, K. J., Serafini, F., Duranti, S., Milani, C., Turroni, F., Lugli, G. A., Zomer, A., Zhurina, D., Riedel, C., Ventura, M., & van Sinderen, D. (2014). Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics, 15, 170. https://doi.org/10.1186/1471-2164-15-170
O'Connell, K. J., Motherway, M. OC., Liedtke, A., Fitzgerald, G. F., Paul Ross, R., Stanton, C., Zomer, A., & van Sinderen, D. (2014). Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. Applied and Environmental Microbiology, 80(12), 3604-14. https://doi.org/10.1128/AEM.00130-14
Wilson, C. M., Loach, D., Lawley, B., Bell, T., Sims, I. M., O'Toole, P. W., Zomer, A., & Tannock, G. W. (2014). Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach. Applied and Environmental Microbiology, 80(19), 6104-13. https://doi.org/10.1128/AEM.01876-14
Gouw, D. D., Jonge, M. I. D., Hermans, P. W. M., Wessels, H. J. C. T., Zomer, A., Berends, A., Pratt, C., Berbers, G. A., Mooi, F. R., & Diavatopoulos, D. A. (2014). Proteomics-identified Bvg-activated autotransporters protect against bordetella pertussis in a mouse model. PLoS One, 9(8), e105011. https://doi.org/10.1371/journal.pone.0105011
van den Kieboom, C. H., Ahout, I. M. L., Zomer, A., Brand, K. H., de Groot, R., Ferwerda, G., & de Jonge, M. I. (2014). Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection. European Respiratory Journal. https://doi.org/10.1183/09031936.00085614
Verhagen, L. M., de Jonge, M. I., Burghout, P., Schraa, K., Spagnuolo, L., Mennens, S., Eleveld, M. J., van der Gaast-de Jongh, C. E., Zomer, A., Hermans, P. W. M., & Bootsma, H. J. (2014). Genome-wide identification of genes essential for the survival of Streptococcus pneumoniae in human saliva. PLoS One, 9(2), Article e89541. https://doi.org/10.1371/journal.pone.0089541
2013
Scholarly publications
de Vries, S. P. W., Burghout, P., Langereis, J. D., Zomer, A., Hermans, P. W. M., & Bootsma, H. J. (2013). Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions. Molecular Microbiology, 87(1), 14-29. https://doi.org/10.1111/mmi.12081
Short, K. R., Reading, P. C., Brown, L. E., Pedersen, J., Gilbertson, B., Job, E. R., Edenborough, K. M., Habets, M. N., Zomer, A., Hermans, P. W. M., Diavatopoulos, D. A., & Wijburg, O. L. (2013). Influenza-induced inflammation drives pneumococcal otitis media. Infection and Immunity, 81(3), 645-52. https://doi.org/10.1128/IAI.01278-12
Burghout, P., Zomer, A., van der Gaast-de Jongh, C. E., Janssen-Megens, E. M., Françoijs, K.-J., Stunnenberg, H. G., & Hermans, P. W. M. (2013). Streptococcus pneumoniae folate biosynthesis responds to environmental CO2 levels. Journal of Bacteriology, 195(7), 1573-1582. https://doi.org/10.1128/JB.01942-12
Verhagen, L. M., Zomer, A., Maes, M., Villalba, J. A., Del Nogal, B., Eleveld, M., van Hijum, S. A., de Waard, J. H., & Hermans, P. W. (2013). A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children. BMC Genomics, 14, Article 74. https://doi.org/10.1186/1471-2164-14-74
Ainsworth, S., Zomer, A., de Jager, V., Bottacini, F., van Hijum, S. A. F. T., Mahony, J., & van Sinderen, D. (2013). Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. Genome Announcements, 1(1), Article 119-12. https://doi.org/10.1128/genomeA.00119-12
Langereis, J. D., Zomer, A., Stunnenberg, H. G., Burghout, P., & Hermans, P. W. M. (2013). Nontypeable Haemophilus influenzae carbonic anhydrase is important for environmental and intracellular survival. Journal of Bacteriology, 195(12), 2737-2746. https://doi.org/10.1128/JB.01870-12
Ainsworth, S., Zomer, A., Mahony, J., & van Sinderen, D. (2013). Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied and Environmental Microbiology, 79(16), 4786-98. https://doi.org/10.1128/AEM.01197-13
Johnston, C., Caymaris, S., Zomer, A., Bootsma, H. J., Prudhomme, M., Granadel, C., Hermans, P. W. M., Polard, P., Martin, B., & Claverys, J.-P. (2013). Natural genetic transformation generates a population of merodiploids in Streptococcus pneumoniae. PLoS Genetics, 9(9), e1003819. https://doi.org/10.1371/journal.pgen.1003819
de Stoppelaar, S. F., Bootsma, H. J., Zomer, A., Roelofs, J. J. T. H., Hermans, P. W. M., van 't Veer, C., & van der Poll, T. (2013). Streptococcus pneumoniae serine protease HtrA, but not SFP or PrtA, is a major virulence factor in pneumonia. PLoS One, 8(11), e80062. https://doi.org/10.1371/journal.pone.0080062
2012
Scholarly publications
Ruiz, L., Zomer, A., O'Connell-Motherway, M., van Sinderen, D., & Margolles, A. (2012). Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics. Applied and Environmental Microbiology, 78(4), 1123-31. https://doi.org/10.1128/AEM.06060-11
Ruiz, L., O'Connell-Motherway, M., Zomer, A., de los Reyes-Gavilán, C. G., Margolles, A., & van Sinderen, D. (2012). A bile-inducible membrane protein mediates bifidobacterial bile resistance. Microbial Biotechnology, 5(4), 523-35. https://doi.org/10.1111/j.1751-7915.2011.00329.x
Fanning, S., Hall, L. J., Cronin, M., Zomer, A., MacSharry, J., Goulding, D., Motherway, M. OC., Shanahan, F., Nally, K., Dougan, G., & van Sinderen, D. (2012). Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proceedings of the National Academy of Sciences of the United States of America, 109(6), 2108-13. https://doi.org/10.1073/pnas.1115621109
Alvarez-Martin, P., Fernández, M., O'Connell-Motherway, M., O'Connell, K. J., Sauvageot, N., Fitzgerald, G. F., MacSharry, J., Zomer, A., & van Sinderen, D. (2012). A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 78(15), 5258-69. https://doi.org/10.1128/AEM.00804-12
Zomer, A., Burghout, P., Bootsma, H. J., Hermans, P. W. M., & van Hijum, S. A. F. T. (2012). ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. PLoS One, 7(8), e43012. https://doi.org/10.1371/journal.pone.0043012
Zomer, A., de Vries, S. P. W., Riesbeck, K., Meinke, A. L., Hermans, P. W. M., & Bootsma, H. J. (2012). Genome sequence of Moraxella catarrhalis RH4, an isolate of seroresistant lineage. Journal of Bacteriology, 194(24), 6969. https://doi.org/10.1128/JB.01833-12
2011
Scholarly publications
Ventura, M., Margolles, A., Turroni, F., Zomer, A., Clara, G., & van Sinderen, D. (2011). Stress Responses of Bifidobacteria: Stress Responses of Lactic Acid Bacteria. In Stress Responses of Lactic Acid Bacteria (pp. 323-347). Springer US.
Zhurina, D., Zomer, A., Gleinser, M., Brancaccio, V. F., Auchter, M., Waidmann, M. S., Westermann, C., van Sinderen, D., & Riedel, C. U. (2011). Complete genome sequence of Bifidobacterium bifidum S17. Journal of Bacteriology, 193(1), 301-2. https://doi.org/10.1128/JB.01180-10
Pokusaeva, K., O'Connell-Motherway, M., Zomer, A., Macsharry, J., Fitzgerald, G. F., & van Sinderen, D. (2011). Cellodextrin utilization by bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 77(5), 1681-90. https://doi.org/10.1128/AEM.01786-10
O'Connell Motherway, M., Zomer, A., Leahy, S. C., Reunanen, J., Bottacini, F., Claesson, M. J., O'Brien, F., Flynn, K., Casey, P. G., Munoz, J. A. M., Kearney, B., Houston, A. M., O'Mahony, C., Higgins, D. G., Shanahan, F., Palva, A., de Vos, W. M., Fitzgerald, G. F., Ventura, M., ... van Sinderen, D. (2011). Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proceedings of the National Academy of Sciences of the United States of America, 108(27), 11217-22. https://doi.org/10.1073/pnas.1105380108
Cronin, M., Zomer, A., Fitzgerald, G. F., & van Sinderen, D. (2011). Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioengineered Bugs, 3(3), 157-67. https://doi.org/10.4161/bbug.18985
2010
Scholarly publications
Sánchez, B., Ruiz, L., van Sinderen, D., Margolles, A., & Zomer, A. L. (2010). Acid and Bile Resistance and Stress. In B. Mayo, & D. V. Sinderen (Eds.), Bifidobacteria: Genomics and Molecular Aspects (pp. 71). Caister Academic press, Norfolk (UK). http://www.horizonpress.com/bifidobacteria
Turroni, F., Foroni, E., O'Connell Motherway, M., Bottacini, F., Giubellini, V., Zomer, A., Ferrarini, A., Delledonne, M., Zhang, Z., van Sinderen, D., & Ventura, M. (2010). Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Applied and Environmental Microbiology, 76(10), 3206-19. https://doi.org/10.1128/AEM.02938-09
Pokusaeva, K., Neves, A. R., Zomer, A., O'Connell-Motherway, M., MacSharry, J., Curley, P., Fitzgerald, G. F., & van Sinderen, D. (2010). Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Microbial Biotechnology, 3(3), 311-23. https://doi.org/10.1111/j.1751-7915.2009.00152.x
Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.-H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., Delledonne, M., Henrissat, B., Coutinho, P., Oggioni, M., Fitzgerald, G. F., Mills, D., Margolles, A., Kelly, D., van Sinderen, D., & Ventura, M. (2010). Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proceedings of the National Academy of Sciences of the United States of America, 107(45), 19514-9. https://doi.org/10.1073/pnas.1011100107
Zomer, A., & van Sinderen, D. (2010). Intertwinement of stress response regulons in Bifidobacterium breve UCC2003. Benef Microbes, 1(2), 100-102. https://doi.org/10.4161/gmic.1.2.11477
2009
Scholarly publications
Pokusaeva, K., O'Connell-Motherway, M., Zomer, A., Fitzgerald, G. F., & van Sinderen, D. (2009). Characterization of two novel alpha-glucosidases from Bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 75(4), 1135-43. https://doi.org/10.1128/AEM.02391-08
Ventura, M., Turroni, F., Lima-Mendez, G., Foroni, E., Zomer, A., Duranti, S., Giubellini, V., Bottacini, F., Horvath, P., Barrangou, R., Sela, D. A., Mills, D. A., & van Sinderen, D. (2009). Comparative analyses of prophage-like elements present in bifidobacterial genomes. Applied and Environmental Microbiology, 75(21), 6929-36. https://doi.org/10.1128/AEM.01112-09
Ventura, M., Turroni, F., Zomer, A., Foroni, E., Giubellini, V., Bottacini, F., Canchaya, C., Claesson, M. J., He, F., Mantzourani, M., Mulas, L., Ferrarini, A., Gao, B., Delledonne, M., Henrissat, B., Coutinho, P., Oggioni, M., Gupta, R. S., Zhang, Z., ... van Sinderen, D. (2009). The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genetics, 5(12), e1000785. https://doi.org/10.1371/journal.pgen.1000785
Zomer, A., Fernandez, M., Kearney, B., Fitzgerald, G. F., Ventura, M., & van Sinderen, D. (2009). An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. Journal of Bacteriology, 191(22), 7039-49. https://doi.org/10.1128/JB.00897-09
2008
Scholarly publications
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. https://doi.org/10.1186/1471-2105-9-93
2007
Scholarly publications
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), 1366-81. https://doi.org/10.1128/JB.01013-06
Wegmann, U., O'Connell-Motherway, 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), 3256-70. https://doi.org/10.1128/JB.01768-06
Martínez, B., Zomer, A. L., Rodríguez, 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), 473-86. 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. (2007). Comparative analyses of prophage-like elements present in two Lactococcus lactis strains. Applied and Environmental Microbiology, 73(23), 7771-80. https://doi.org/10.1128/AEM.01273-07
2005
Scholarly publications
Kok, J., Buist, G., Zomer, A. L., van Hijum, S. A. F. T., & Kuipers, O. P. (2005). Comparative and functional genomics of lactococci. FEMS Microbiology Reviews, 29(3), 411-33. https://doi.org/10.1016/j.femsre.2005.04.004
van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2005). Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Research, 33(Web Server issue), W560-6. https://doi.org/10.1093/nar/gki356
2003
Scholarly publications
Steen, A., Buist, G., Leenhouts, K. J., El Khattabi, M., Grijpstra, F., Zomer, A. L., Venema, G., Kuipers, O. P., & Kok, J. (2003). Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents. Journal of Biological Chemistry, 278(26), 23874-81. https://doi.org/10.1074/jbc.M211055200
van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2003). Projector: automatic contig mapping for gap closure purposes. Nucleic Acids Research, 31(22), e144.
2002
Scholarly publications
Kuipers, O. P., de Jong, A., Baerends, R. J. S., van Hijum, S. A. F. T., Zomer, A. L., Karsens, H. A., den Hengst, C. D., Kramer, N. E., Buist, G., & Kok, J. (2002). Transcriptome analysis and related databases of Lactococcus lactis. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 82(1-4), 113-22.