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Items: 1 to 50 of 103

1.

The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study.

Chermprapai S, Ederveen THA, Broere F, Broens EM, Schlotter YM, van Schalkwijk S, Boekhorst J, van Hijum SAFT, Rutten VPMG.

Vet Microbiol. 2019 Feb;229:90-99. doi: 10.1016/j.vetmic.2018.12.022. Epub 2018 Dec 21.

2.

Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11.

Dijkstra AR, Starrenburg MJC, Todt T, van Hijum SAFT, Hugenholtz J, Bron PA.

Front Microbiol. 2018 Oct 15;9:2418. doi: 10.3389/fmicb.2018.02418. eCollection 2018.

3.

Integrating glycomics and genomics uncovers SLC10A7 as essential factor for bone mineralization by regulating post-Golgi protein transport and glycosylation.

Ashikov A, Abu Bakar N, Wen XY, Niemeijer M, Rodrigues Pinto Osorio G, Brand-Arzamendi K, Hasadsri L, Hansikova H, Raymond K, Vicogne D, Ondruskova N, Simon MEH, Pfundt R, Timal S, Beumers R, Biot C, Smeets R, Kersten M, Huijben K; CDG group, Linders PTA, van den Bogaart G, van Hijum SAFT, Rodenburg R, van den Heuvel LP, van Spronsen F, Honzik T, Foulquier F, van Scherpenzeel M, Lefeber DJ; CDG group, Mirjam W, Han B, Helen M, Helen M, Peter VH, Jiddeke VK, Diego M, Lars M, Katja BH, Jozef H, Majid A, Kevin C, Johann TWN.

Hum Mol Genet. 2018 Sep 1;27(17):3029-3045. doi: 10.1093/hmg/ddy213.

PMID:
29878199
4.

The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.

Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ, Vehkala M, Knol MJ, Bootsma HJ, Välimäki N, Croucher NJ, Meis JF, Bentley S, van Hijum SAFT, Corander J, Zomer AL, Ferwerda G, de Jonge MI.

Clin Infect Dis. 2019 Jan 1;68(1):61-69. doi: 10.1093/cid/ciy417.

PMID:
29788414
5.

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses.

Ederveen THA, Ferwerda G, Ahout IM, Vissers M, de Groot R, Boekhorst J, Timmerman HM, Huynen MA, van Hijum SAFT, de Jonge MI.

Microbiome. 2018 Jan 11;6(1):10. doi: 10.1186/s40168-017-0395-y.

6.

Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis".

Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.

Clin Microbiol Rev. 2017 Nov 1;31(1). pii: e00082-17. doi: 10.1128/CMR.00082-17. Print 2018 Jan. No abstract available.

7.

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine.

Gerritsen J, Hornung B, Renckens B, van Hijum SAFT, Martins Dos Santos VAP, Rijkers GT, Schaap PJ, de Vos WM, Smidt H.

PeerJ. 2017 Sep 11;5:e3698. doi: 10.7717/peerj.3698. eCollection 2017.

8.

Gut microbiome in ADHD and its relation to neural reward anticipation.

Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT, Arias Vasquez A.

PLoS One. 2017 Sep 1;12(9):e0183509. doi: 10.1371/journal.pone.0183509. eCollection 2017.

9.

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.

Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.

Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17. Review. Erratum in: Clin Microbiol Rev. 2017 Nov 1;31(1):.

10.

Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis.

Rogier R, Ederveen THA, Boekhorst J, Wopereis H, Scher JU, Manasson J, Frambach SJCM, Knol J, Garssen J, van der Kraan PM, Koenders MI, van den Berg WB, van Hijum SAFT, Abdollahi-Roodsaz S.

Microbiome. 2017 Jun 23;5(1):63. doi: 10.1186/s40168-017-0278-2.

11.

Draft Genome Sequences of 24 Lactococcus lactis Strains.

Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SA, Bachmann H.

Genome Announc. 2017 Mar 30;5(13). pii: e01737-16. doi: 10.1128/genomeA.01737-16.

12.

Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.

Wels M, Backus L, Boekhorst J, Dijkstra A, Beerthuyzen M, Siezen RJ, Bachmann H, van Hijum SA.

Genome Announc. 2017 Mar 16;5(11). pii: e01739-16. doi: 10.1128/genomeA.01739-16.

13.

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data.

Mobegi FM, Cremers AJ, de Jonge MI, Bentley SD, van Hijum SA, Zomer A.

Sci Rep. 2017 Feb 16;7:42808. doi: 10.1038/srep42808.

14.

Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease.

Tunjungputri RN, Mobegi FM, Cremers AJ, van der Gaast-de Jongh CE, Ferwerda G, Meis JF, Roeleveld N, Bentley SD, Pastura AS, van Hijum SA, van der Ven AJ, de Mast Q, Zomer A, de Jonge MI.

MBio. 2017 Jan 17;8(1). pii: e01984-16. doi: 10.1128/mBio.01984-16.

15.

Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes.

Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken VACM, Mandemakers JJ, Zomer A, van Hijum SAFT, Netea MG, Murray M, van Crevel R, van Soolingen D.

Am J Respir Crit Care Med. 2017 Jun 1;195(11):1519-1527. doi: 10.1164/rccm.201605-1042OC.

16.

Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis.

Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA.

PLoS One. 2016 Dec 14;11(12):e0167944. doi: 10.1371/journal.pone.0167944. eCollection 2016.

17.

Reply to Meisel et al.

Zeeuwen PLJM, Boekhorst J, Ederveen THA, Kleerebezem M, Schalkwijk J, van Hijum SAFT, Timmerman HM.

J Invest Dermatol. 2017 Apr;137(4):961-962. doi: 10.1016/j.jid.2016.11.013. Epub 2016 Nov 22. No abstract available.

18.

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.

Urshev Z, Hajo K, Lenoci L, Bron PA, Dijkstra A, Alkema W, Wels M, Siezen RJ, Minkova S, van Hijum SA.

Genome Announc. 2016 Oct 6;4(5). pii: e01090-16. doi: 10.1128/genomeA.01090-16.

19.

Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin.

Zeeuwen PL, Ederveen TH, van der Krieken DA, Niehues H, Boekhorst J, Kezic S, Hanssen DA, Otero ME, van Vlijmen-Willems IM, Rodijk-Olthuis D, Falcone D, van den Bogaard EH, Kamsteeg M, de Koning HD, Zeeuwen-Franssen ME, van Steensel MA, Kleerebezem M, Timmerman HM, van Hijum SA, Schalkwijk J.

J Allergy Clin Immunol. 2017 Apr;139(4):1368-1371. doi: 10.1016/j.jaci.2016.09.017. Epub 2016 Oct 8. No abstract available.

20.

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).

Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R.

Stand Genomic Sci. 2016 Aug 24;11(1):52. doi: 10.1186/s40793-016-0172-8. eCollection 2016.

21.

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Martino ME, Bayjanov JR, Caffrey BE, Wels M, Joncour P, Hughes S, Gillet B, Kleerebezem M, van Hijum SA, Leulier F.

Environ Microbiol. 2016 Dec;18(12):4974-4989. doi: 10.1111/1462-2920.13455. Epub 2016 Aug 4.

PMID:
27422487
22.

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening.

Erkus O, de Jager VC, Geene RT, van Alen-Boerrigter I, Hazelwood L, van Hijum SA, Kleerebezem M, Smid EJ.

Int J Food Microbiol. 2016 Jul 2;228:1-9. doi: 10.1016/j.ijfoodmicro.2016.03.027. Epub 2016 Mar 25.

PMID:
27077825
23.

An In vitro Model for Bacterial Growth on Human Stratum Corneum.

van der Krieken DA, Ederveen TH, van Hijum SA, Jansen PA, Melchers WJ, Scheepers PT, Schalkwijk J, Zeeuwen PL.

Acta Derm Venereol. 2016 Nov 2;96(7):873-879. doi: 10.2340/00015555-2401.

24.

Draft Genome Sequence of Lactobacillus plantarum SF2A35B.

Bron PA, Lee IC, Backus L, van Hijum SA, Wels M, Kleerebezem M.

Genome Announc. 2016 Feb 25;4(1). pii: e01638-15. doi: 10.1128/genomeA.01638-15.

25.

Advances and perspectives in computational prediction of microbial gene essentiality.

Mobegi FM, Zomer A, de Jonge MI, van Hijum SA.

Brief Funct Genomics. 2017 Mar 1;16(2):70-79. doi: 10.1093/bfgp/elv063. Review.

PMID:
26857942
26.

Resequencing of the Lactobacillus plantarum Strain WJL Genome.

Martino ME, Bayjanov JR, Joncour P, Hughes S, Gillet B, Kleerebezem M, Siezen R, van Hijum SA, Leulier F.

Genome Announc. 2015 Nov 25;3(6). pii: e01382-15. doi: 10.1128/genomeA.01382-15.

27.

Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.

Wels M, Serrano LM, Eibrink BJ, Backus L, Bongers RS, Vriesendorp B, Siezen RJ, van Hijum SA, Meijer WC.

Genome Announc. 2015 Nov 25;3(6). pii: e01377-15. doi: 10.1128/genomeA.01377-15.

28.

Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877.

Martino ME, Bayjanov JR, Joncour P, Hughes S, Gillet B, Kleerebezem M, Siezen R, van Hijum SA, Leulier F.

Genome Announc. 2015 Nov 25;3(6). pii: e01370-15. doi: 10.1128/genomeA.01370-15.

29.

The post-vaccine microevolution of invasive Streptococcus pneumoniae.

Cremers AJ, Mobegi FM, de Jonge MI, van Hijum SA, Meis JF, Hermans PW, Ferwerda G, Bentley SD, Zomer AL.

Sci Rep. 2015 Oct 23;5:14952. doi: 10.1038/srep14952.

30.

Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.

Dingemanse C, Belzer C, van Hijum SA, Günthel M, Salvatori D, den Dunnen JT, Kuijper EJ, Devilee P, de Vos WM, van Ommen GB, Robanus-Maandag EC.

Carcinogenesis. 2015 Nov;36(11):1388-96. doi: 10.1093/carcin/bgv120. Epub 2015 Aug 29.

PMID:
26320104
31.

Microbial bioinformatics for food safety and production.

Alkema W, Boekhorst J, Wels M, van Hijum SA.

Brief Bioinform. 2016 Mar;17(2):283-92. doi: 10.1093/bib/bbv034. Epub 2015 Jun 16. Review.

32.

Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU.

Metselaar KI, den Besten HM, Boekhorst J, van Hijum SA, Zwietering MH, Abee T.

Front Microbiol. 2015 May 8;6:422. doi: 10.3389/fmicb.2015.00422. eCollection 2015.

33.
34.

CiVi: circular genome visualization with unique features to analyze sequence elements.

Overmars L, van Hijum SA, Siezen RJ, Francke C.

Bioinformatics. 2015 Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249. Epub 2015 Apr 24.

PMID:
25910699
35.

Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine.

Lamontanara A, Caggianiello G, Orrù L, Capozzi V, Michelotti V, Bayjanov JR, Renckens B, van Hijum SA, Cattivelli L, Spano G.

Genome Announc. 2015 Mar 12;3(2). pii: e00097-15. doi: 10.1128/genomeA.00097-15.

36.

The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition.

Cremers AJ, Zomer AL, Gritzfeld JF, Ferwerda G, van Hijum SA, Ferreira DM, Shak JR, Klugman KP, Boekhorst J, Timmerman HM, de Jonge MI, Gordon SB, Hermans PW.

Microbiome. 2014 Dec 15;2:44. doi: 10.1186/2049-2618-2-44. eCollection 2014.

37.

Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology.

Szalowska E, Tesfay HA, van Hijum SA, Kersten S.

BMC Genomics. 2014 Dec 15;15:1106. doi: 10.1186/1471-2164-15-1106.

38.

From microbial gene essentiality to novel antimicrobial drug targets.

Mobegi FM, van Hijum SA, Burghout P, Bootsma HJ, de Vries SP, van der Gaast-de Jongh CE, Simonetti E, Langereis JD, Hermans PW, de Jonge MI, Zomer A.

BMC Genomics. 2014 Nov 5;15:958. doi: 10.1186/1471-2164-15-958.

39.

Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness.

Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA.

Microb Cell Fact. 2014 Nov 4;13:148. doi: 10.1186/s12934-014-0148-6.

40.

Degenerate target sites mediate rapid primed CRISPR adaptation.

Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38. doi: 10.1073/pnas.1400071111. Epub 2014 Apr 7.

41.

Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains.

Schuurmans JM, van Hijum SA, Piet JR, Händel N, Smelt J, Brul S, ter Kuile BH.

Plasmid. 2014 Mar;72:1-8. doi: 10.1016/j.plasmid.2014.01.002. Epub 2014 Feb 10.

PMID:
24525238
42.

Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress.

Handtke S, Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum SA, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B.

PLoS One. 2014 Jan 20;9(1):e85625. doi: 10.1371/journal.pone.0085625. eCollection 2014.

43.

Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress.

Dijkstra AR, Setyawati MC, Bayjanov JR, Alkema W, van Hijum SA, Bron PA, Hugenholtz J.

Appl Environ Microbiol. 2014 Jan;80(2):603-11. doi: 10.1128/AEM.03434-13. Epub 2013 Nov 8.

44.

Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract.

van Bokhorst-van de Veen H, Smelt MJ, Wels M, van Hijum SA, de Vos P, Kleerebezem M, Bron PA.

Biotechnol J. 2013 Aug;8(8):895-904.

PMID:
24066356
45.

Multifactorial diversity sustains microbial community stability.

Erkus O, de Jager VC, Spus M, van Alen-Boerrigter IJ, van Rijswijck IM, Hazelwood L, Janssen PW, van Hijum SA, Kleerebezem M, Smid EJ.

ISME J. 2013 Nov;7(11):2126-36. doi: 10.1038/ismej.2013.108. Epub 2013 Jul 4.

46.

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.

Dutilh BE, Backus L, van Hijum SA, Tjalsma H.

Best Pract Res Clin Gastroenterol. 2013 Feb;27(1):85-99. doi: 10.1016/j.bpg.2013.03.008. Review.

PMID:
23768555
47.

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.

Ederveen TH, Overmars L, van Hijum SA.

PLoS One. 2013 May 10;8(5):e63523. doi: 10.1371/journal.pone.0063523. Print 2013.

48.

Explaining microbial phenotypes on a genomic scale: GWAS for microbes.

Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SA.

Brief Funct Genomics. 2013 Jul;12(4):366-80. doi: 10.1093/bfgp/elt008. Epub 2013 Apr 26. Review.

49.

Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.

Bayjanov JR, Starrenburg MJ, van der Sijde MR, Siezen RJ, van Hijum SA.

BMC Microbiol. 2013 Mar 26;13:68. doi: 10.1186/1471-2180-13-68.

50.

Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.

Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ.

PLoS One. 2013;8(3):e59239. doi: 10.1371/journal.pone.0059239. Epub 2013 Mar 19.

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