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Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections.

Gaiser RA, Zomer AL, Wells JM, van Baarlen P.

Microbiol Resour Announc. 2019 Jun 6;8(23). pii: e00227-19. doi: 10.1128/MRA.00227-19.


Selection of antimicrobial frog peptides and temporin-1DRa analogs for treatment of bacterial infections based on their cytotoxicity and differential activity against pathogens.

Gaiser RA, Ayerra Mangado J, Mechkarska M, Kaman WE, van Baarlen P, Conlon JM, Wells JM.

Chem Biol Drug Des. 2019 May 18. doi: 10.1111/cbdd.13569. [Epub ahead of print]


Corrigendum: Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro.

Perdijk O, van Baarlen P, Fernandez-Gutierrez MM, van den Brink E, Schuren FHJ, Brugman S, Savelkoul HFJ, Kleerebezem M, van Neerven RJJ.

Front Immunol. 2019 Apr 10;10:762. doi: 10.3389/fimmu.2019.00762. eCollection 2019.


Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro.

Perdijk O, van Baarlen P, Fernandez-Gutierrez MM, van den Brink E, Schuren FHJ, Brugman S, Savelkoul HFJ, Kleerebezem M, van Neerven RJJ.

Front Immunol. 2019 Feb 12;10:94. doi: 10.3389/fimmu.2019.00094. eCollection 2019. Erratum in: Front Immunol. 2019 Apr 10;10:762.


KREAP: an automated Galaxy platform to quantify in vitro re-epithelialization kinetics.

Fernandez-Gutierrez MM, van Zessen DBH, van Baarlen P, Kleerebezem M, Stubbs AP.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy078.


Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity.

Venkatasubramanian PB, Toydemir G, de Wit N, Saccenti E, Martins Dos Santos VAP, van Baarlen P, Wells JM, Suarez-Diez M, Mes JJ.

Sci Rep. 2017 Jul 28;7(1):6778. doi: 10.1038/s41598-017-06355-0.


Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin.

Gaiser RA, Medema MH, Kleerebezem M, van Baarlen P, Wells JM.

Genome Announc. 2017 Jun 1;5(22). pii: e00453-17. doi: 10.1128/genomeA.00453-17.


Temporal Regulation of the Transformasome and Competence Development in Streptococcus suis.

Zaccaria E, Wels M, van Baarlen P, Wells JM.

Front Microbiol. 2016 Dec 20;7:1922. doi: 10.3389/fmicb.2016.01922. eCollection 2016.


Metabolic Context of the Competence-Induced Checkpoint for Cell Replication in Streptococcus suis.

Zaccaria E, Wells JM, van Baarlen P.

PLoS One. 2016 May 5;11(5):e0153571. doi: 10.1371/journal.pone.0153571. eCollection 2016.


A Zebrafish Larval Model to Assess Virulence of Porcine Streptococcus suis Strains.

Zaccaria E, Cao R, Wells JM, van Baarlen P.

PLoS One. 2016 Mar 21;11(3):e0151623. doi: 10.1371/journal.pone.0151623. eCollection 2016.


Identification of Commensal Species Positively Correlated with Early Stress Responses to a Compromised Mucus Barrier.

Sovran B, Lu P, Loonen LM, Hugenholtz F, Belzer C, Stolte EH, Boekschoten MV, van Baarlen P, Smidt H, Kleerebezem M, de Vos P, Renes IB, Wells JM, Dekker J.

Inflamm Bowel Dis. 2016 Apr;22(4):826-40. doi: 10.1097/MIB.0000000000000688.


IL-22-STAT3 pathway plays a key role in the maintenance of ileal homeostasis in mice lacking secreted mucus barrier.

Sovran B, Loonen LM, Lu P, Hugenholtz F, Belzer C, Stolte EH, Boekschoten MV, van Baarlen P, Kleerebezem M, de Vos P, Dekker J, Renes IB, Wells JM.

Inflamm Bowel Dis. 2015 Mar;21(3):531-42. doi: 10.1097/MIB.0000000000000319.


Live Faecalibacterium prausnitzii in an apical anaerobic model of the intestinal epithelial barrier.

Ulluwishewa D, Anderson RC, Young W, McNabb WC, van Baarlen P, Moughan PJ, Wells JM, Roy NC.

Cell Microbiol. 2015 Feb;17(2):226-40. doi: 10.1111/cmi.12360. Epub 2014 Oct 31.


Control of competence for DNA transformation in streptococcus suis by genetically transferable pherotypes.

Zaccaria E, van Baarlen P, de Greeff A, Morrison DA, Smith H, Wells JM.

PLoS One. 2014 Jun 26;9(6):e99394. doi: 10.1371/journal.pone.0099394. eCollection 2014.


WalK, the Path towards New Antibacterials with Low Potential for Resistance Development.

Velikova N, Bem AE, van Baarlen P, Wells JM, Marina A.

ACS Med Chem Lett. 2013 Sep 18;4(10):891-4. doi: 10.1021/ml400320s. eCollection 2013 Oct 10.


Carbohydrate availability regulates virulence gene expression in Streptococcus suis.

Ferrando ML, van Baarlen P, Orrù G, Piga R, Bongers RS, Wels M, De Greeff A, Smith HE, Wells JM.

PLoS One. 2014 Mar 18;9(3):e89334. doi: 10.1371/journal.pone.0089334. eCollection 2014.


The role of CRISPR-Cas systems in virulence of pathogenic bacteria.

Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J.

Microbiol Mol Biol Rev. 2014 Mar;78(1):74-88. doi: 10.1128/MMBR.00039-13. Review.


REG3γ-deficient mice have altered mucus distribution and increased mucosal inflammatory responses to the microbiota and enteric pathogens in the ileum.

Loonen LM, Stolte EH, Jaklofsky MT, Meijerink M, Dekker J, van Baarlen P, Wells JM.

Mucosal Immunol. 2014 Jul;7(4):939-47. doi: 10.1038/mi.2013.109. Epub 2013 Dec 18.


Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice.

El Aidy S, Derrien M, Aardema R, Hooiveld G, Richards SE, Dane A, Dekker J, Vreeken R, Levenez F, Doré J, Zoetendal EG, van Baarlen P, Kleerebezem M.

Benef Microbes. 2014 Mar;5(1):67-77. doi: 10.3920/BM2013.0018.


Gene expression analysis of peripheral cells for subclassification of pediatric inflammatory bowel disease in remission.

van Lierop PP, Swagemakers SM, de Bie CI, Middendorp S, van Baarlen P, Samsom JN, van Ijcken WF, Escher JC, van der Spek PJ, Nieuwenhuis EE.

PLoS One. 2013 Nov 18;8(11):e79549. doi: 10.1371/journal.pone.0079549. eCollection 2013.


Are bacteriophage defence and virulence two sides of the same coin in Campylobacter jejuni?

Louwen R, van Baarlen P.

Biochem Soc Trans. 2013 Dec;41(6):1475-81. doi: 10.1042/BST20130127. Review.


Vectorial secretion of interleukin-8 mediates autocrine signalling in intestinal epithelial cells via apically located CXCR1.

Rossi O, Karczewski J, Stolte EH, Brummer RJ, van Nieuwenhoven MA, Meijerink M, van Neerven JR, van Ijzendoorn SC, van Baarlen P, Wells JM.

BMC Res Notes. 2013 Oct 28;6:431. doi: 10.1186/1756-0500-6-431.


Omics approaches to study host-microbiota interactions.

van Baarlen P, Kleerebezem M, Wells JM.

Curr Opin Microbiol. 2013 Jun;16(3):270-7. doi: 10.1016/j.mib.2013.07.001. Epub 2013 Jul 23. Review.


Regulation of intestinal homeostasis and immunity with probiotic lactobacilli.

van Baarlen P, Wells JM, Kleerebezem M.

Trends Immunol. 2013 May;34(5):208-15. doi: 10.1016/ Epub 2013 Feb 26. Review.


Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon.

El Aidy S, Derrien M, Merrifield CA, Levenez F, Doré J, Boekschoten MV, Dekker J, Holmes E, Zoetendal EG, van Baarlen P, Claus SP, Kleerebezem M.

ISME J. 2013 Apr;7(4):743-55. doi: 10.1038/ismej.2012.142. Epub 2012 Nov 22.


A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome.

Louwen R, Horst-Kreft D, de Boer AG, van der Graaf L, de Knegt G, Hamersma M, Heikema AP, Timms AR, Jacobs BC, Wagenaar JA, Endtz HP, van der Oost J, Wells JM, Nieuwenhuis EE, van Vliet AH, Willemsen PT, van Baarlen P, van Belkum A.

Eur J Clin Microbiol Infect Dis. 2013 Feb;32(2):207-26. doi: 10.1007/s10096-012-1733-4. Epub 2012 Sep 4.


Campylobacter jejuni translocation across intestinal epithelial cells is facilitated by ganglioside-like lipooligosaccharide structures.

Louwen R, Nieuwenhuis EE, van Marrewijk L, Horst-Kreft D, de Ruiter L, Heikema AP, van Wamel WJ, Wagenaar JA, Endtz HP, Samsom J, van Baarlen P, Akhmanova A, van Belkum A.

Infect Immun. 2012 Sep;80(9):3307-18. doi: 10.1128/IAI.06270-11. Epub 2012 Jul 9.


The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation.

El Aidy S, Merrifield CA, Derrien M, van Baarlen P, Hooiveld G, Levenez F, Doré J, Dekker J, Holmes E, Claus SP, Reijngoud DJ, Kleerebezem M.

Gut. 2013 Sep;62(9):1306-14. doi: 10.1136/gutjnl-2011-301955. Epub 2012 Jun 21.


Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice.

El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, Doré J, Dekker J, Samsom JN, Nieuwenhuis EE, Kleerebezem M.

Mucosal Immunol. 2012 Sep;5(5):567-79. doi: 10.1038/mi.2012.32. Epub 2012 May 23.


Campylobacter bacteremia: a rare and under-reported event?

Louwen R, van Baarlen P, van Vliet AH, van Belkum A, Hays JP, Endtz HP.

Eur J Microbiol Immunol (Bp). 2012 Mar;2(1):76-87. doi: 10.1556/EuJMI.2.2012.1.11. Epub 2012 Mar 17. Review.


Host-recognition of pathogens and commensals in the mammalian intestine.

Rossi O, van Baarlen P, Wells JM.

Curr Top Microbiol Immunol. 2013;358:291-321. doi: 10.1007/82_2011_191. Review.


Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa.

Bron PA, van Baarlen P, Kleerebezem M.

Nat Rev Microbiol. 2011 Nov 21;10(1):66-78. doi: 10.1038/nrmicro2690. Review.


Modulation of Mucosal Immune Response, Tolerance, and Proliferation in Mice Colonized by the Mucin-Degrader Akkermansia muciniphila.

Derrien M, Van Baarlen P, Hooiveld G, Norin E, Müller M, de Vos WM.

Front Microbiol. 2011 Aug 1;2:166. doi: 10.3389/fmicb.2011.00166. eCollection 2011.


Epithelial crosstalk at the microbiota-mucosal interface.

Wells JM, Rossi O, Meijerink M, van Baarlen P.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4607-14. doi: 10.1073/pnas.1000092107. Epub 2010 Sep 8. Review.


Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways.

van Baarlen P, Troost F, van der Meer C, Hooiveld G, Boekschoten M, Brummer RJ, Kleerebezem M.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4562-9. doi: 10.1073/pnas.1000079107. Epub 2010 Sep 7.


Evolutionary relationships between Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici isolates inferred from mating type, elongation factor-1alpha and exopolygalacturonase sequences.

Lievens B, van Baarlen P, Verreth C, van Kerckhove S, Rep M, Thomma BP.

Mycol Res. 2009 Oct;113(Pt 10):1181-91. doi: 10.1016/j.mycres.2009.07.019. Epub 2009 Aug 11.


Genomics of plant-associated microbes.

van Baarlen P, Siezen RJ.

Microb Biotechnol. 2009 Jul;2(4):406-11. doi: 10.1111/j.1751-7915.2009.00127.x. No abstract available.


Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance.

van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJ, Brummer RJ, Kleerebezem M.

Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2371-6. doi: 10.1073/pnas.0809919106. Epub 2009 Feb 3.


Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo.

Troost FJ, van Baarlen P, Lindsey P, Kodde A, de Vos WM, Kleerebezem M, Brummer RJ.

BMC Genomics. 2008 Aug 5;9:374. doi: 10.1186/1471-2164-9-374.


The Cladosporium fulvum virulence protein Avr2 inhibits host proteases required for basal defense.

van Esse HP, Van't Klooster JW, Bolton MD, Yadeta KA, van Baarlen P, Boeren S, Vervoort J, de Wit PJ, Thomma BP.

Plant Cell. 2008 Jul;20(7):1948-63. doi: 10.1105/tpc.108.059394. Epub 2008 Jul 25.


Challenges in plant cellular pathway reconstruction based on gene expression profiling.

van Baarlen P, van Esse HP, Siezen RJ, Thomma BP.

Trends Plant Sci. 2008 Jan;13(1):44-50. Epub 2007 Dec 21. Review.


Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps?

van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BP.

FEMS Microbiol Rev. 2007 Apr;31(3):239-77. Epub 2007 Feb 26. Review.


Functional analysis of NLP genes from Botrytis elliptica.

Staats M, VAN Baarlen P, Schouten A, VAN Kan JA.

Mol Plant Pathol. 2007 Mar;8(2):209-14. doi: 10.1111/j.1364-3703.2007.00382.x.


Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.

van Baarlen P, van Belkum A, Thomma BP.

Drug Discov Today. 2007 Feb;12(3-4):167-73. Epub 2006 Dec 20. Review.


Histochemical and genetic analysis of host and non-host interactions of Arabidopsis with three Botrytis species: an important role for cell death control.

VAN Baarlen P, Woltering EJ, Staats M, VAN Kan JA.

Mol Plant Pathol. 2007 Jan;8(1):41-54. doi: 10.1111/j.1364-3703.2006.00367.x.


Positive selection in phytotoxic protein-encoding genes of Botrytis species.

Staats M, van Baarlen P, Schouten A, van Kan JA, Bakker FT.

Fungal Genet Biol. 2007 Jan;44(1):52-63. Epub 2006 Aug 28.


Induction of programmed cell death in lily by the fungal pathogen Botrytis elliptica.

VAN Baarlen P, Staats M, VAN Kan JA.

Mol Plant Pathol. 2004 Nov 1;5(6):559-74. doi: 10.1111/j.1364-3703.2004.00253.x.


Molecular phylogeny of the plant pathogenic genus Botrytis and the evolution of host specificity.

Staats M, van Baarlen P, van Kan JA.

Mol Biol Evol. 2005 Feb;22(2):333-46. Epub 2004 Oct 20.


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