document

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

van der Veer, C. (author), Hertzberger, R.Y. (author), Bruisten, S.M. (author), Tytgat, H.L.P. (author), Swanenburg, J. (author), de Kat Angelino-Bart, A. (author), Schuren, F. (author), Molenaar, D. (author), Reid, G. (author), de Vries, H. (author), Kort, R. (author)

Background: A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal...

article 2019

document

Rapid and reliable discrimination between Shigella species and Escherichia coli using MALDI-TOF mass spectrometry

Paauw, A. (author), Jonker, D. (author), Roeselers, G. (author), Heng, J.M.E. (author), Mars-Groenendijk, R.H. (author), Trip, H. (author), Molhoek, E.M. (author), Jansen, H.J. (author), van der Plas, J. (author), de Jong, A.L. (author), Majchrzykiewicz-Koehorst, J.A. (author), Speksnijder, A.G.C.L. (author)

E. coli-. Shigella species are a cryptic group of bacteria in which the Shigella species are distributed within the phylogenetic tree of E. coli. The nomenclature is historically based and the discrimination of these genera developed as a result of the epidemiological need to identify the cause of shigellosis, a severe disease caused by Shigella...

article 2015

document

Differential modulation by Akkermansia muciniphila and faecalibacterium prausnitzii of host peripheral lipid metabolism and histone acetylation in mouse gut organoids

Lukovac, S. (author), Belzer, C. (author), Pellis, L. (author), Keijser, B.J. (author), de Vos, W.M. (author), Montijn, R.C. (author), Roeselers, G. (author)

The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids. We have explored the transcriptional...

article 2014

document

Genome Analysis of Legionella pneumophila Strains Using a Mixed-Genome Microarray

Euser, S.M. (author), Nagelkerke, N.J. (author), Schuren, F. (author), Jansen, R. (author), den Boer, J.W. (author)

Background: Legionella, the causative agent for Legionnaires' disease, is ubiquitous in both natural and man-made aquatic environments. The distribution of Legionella genotypes within clinical strains is significantly different from that found in environmental strains. Developing novel genotypic methods that offer the ability to distinguish...

article 2012

document

Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14

Koopman, F. (author), Wierckx, N. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author), TNO Kwaliteit van Leven (author)

The toxic fermentation inhibitors in lignocellulosic hydrolysates pose significant problems for the production of second-generation biofuels and biochemicals. Among these inhibitors, 5-(hydroxymethyl) furfural (HMF) and furfural are specifically notorious. In this study, we describe the complete molecular identification and characterization of...

article 2010

document

Establishment of oxidative D-xylose metabolism in Pseudomonas putida S12

Meijnen, J.P. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author)

The oxidative D-xylose catabolic pathway of Caulobacter crescentus, encoded by the xylXABCD operon, was expressed in the gram-negative bacterium Pseudomonas putida S12. This engineered transformant strain was able to grow on D-xylose as a sole carbon source with a biomass yield of 53% (based on g [dry weight] g D-xylose-1) and a maximum growth...

article 2009

document

Metabolic flux analysis of a phenol producing mutant of Pseudomonas putida S12: Verification and complementation of hypotheses derived from transcriptomics

Wierckx, N. (author), Ruijssenaars, H.J. (author), de Winde, J.H. (author), Schmid, A. (author), Blank, L.M. (author), TNO Kwaliteit van Leven (author)

The physiological effects of genetic and transcriptional changes observed in a phenol producing mutant of the solvent-tolerant Pseudomonas putida S12 were assessed with metabolic flux analysis. The upregulation of a malate/lactate dehydrogenase encoding gene could be connected to a flux increase from malate to oxaloacetate. A mutation in the...

article 2009

document

Performance and population analysis of a non-sterile trickle bed reactor inoculated with caldicellulosiruptor saccharolyticus, a thermophilic hydrogen producer

van Groenestijn, J.W. (author), Geelhoed, J.S. (author), Goorissen, H.P. (author), Meesters, K.P.M. (author), Stams, A.J.M. (author), Claassen, P.A.M. (author), TNO Kwaliteit van Leven (author)

Non-axenic operation of a 400 L trickle bed reactor inoculated with the thermophile Caldicellulosiruptor saccharolyticus, yielded 2.8 molH 2mol hexose converted. The reactor was fed with a complex medium with sucrose as the main substrate, continuously flushed with nitrogen gas, and operated at 73°C. The volumetric productivity was 22 mmolH2(L...

article 2009

document

Identification of resistance and virulence factors in an epidemic Enterobacter hormaechei outbreak strain

Paauw, A. (author), Caspers, M.P.M. (author), Leverstein-van Hall, M.A. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Verhoef, J. (author), Fluit, A.C. (author), TNO Kwaliteit van Leven (author)

Bacterial strains differ in their ability to cause hospital outbreaks. Using comparative genomic hybridization, Enterobacter cloacae complex isolates were studied to identify genetic markers specific for Enterobacter cloacae complex outbreak strains. No outbreak-specific genes were found that were common in all investigated outbreak strains....

article 2009

document

Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor

Weelink, S.A.B. (author), Tan, N.C.G. (author), ten Broeke, H. (author), van den Kieboom, C. (author), van Doesburg, W. (author), Langenhoff, A.A.M. (author), Gerritse, J. (author), Junca, H. (author), Stams, A.J.M. (author), TNO Bouw en Ondergrond (author)

A bacterium, strain BC, was isolated from a benzene-degrading chlorate-reducing enrichment culture. Strain BC degrades benzene in conjunction with chlorate reduction. Cells of strain BC are short rods that are 0.6 μm wide and 1 to 2 μm long, are motile, and stain gram negative. Strain BC grows on benzene and some other aromatic compounds with...

article 2008

document

Lactobacillus casei Shirota does not decrease the food allergic response to peanut extract in Brown Norway rats

de Jonge, J.D. (author), Ezendam, J. (author), Knippels, L.M.J. (author), Penninks, A.H. (author), Pieters, R. (author), van Loveren, H. (author), TNO Kwaliteit van Leven (author)

Probiotics are claimed to beneficially affect the immune system and their involvement in allergy prevention is being investigated extensively. However, the efficacy of probiotics in allergy prevention remains controversial. We investigated whether the probiotic Lactobacillus casei Shirota (LcS) could modulate the food allergic response against...

article 2008

document

Bioproduction of p-hydroxybenzoate from renewable feedstock by solvent-tolerant Pseudomonas putida S12

Verhoef, S. (author), Ruijssenaars, H.J. (author), de Bont, J.A.M. (author), Wery, J. (author), TNO Kwaliteit van Leven (author)

Pseudomonas putida strain S12palB1 was constructed that produces p-hydroxybenzoate from renewable carbon sources via the central metabolite l-tyrosine. P. putida S12palB1 was based on the platform strain P. putida S12TPL3, which has an optimised carbon flux towards l-tyrosine. Phenylalanine ammonia lyase (Pal) was introduced for the conversion...

article 2007

document

Dynamics in prophage content of invasive and noninvasive M1 and M28 Streptococcus pyogenes isolates in the Netherlands from 1959 to 1996

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Beitsma, M.M. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Invasive group A streptococcal (GAS) disease reemerged in The Netherlands in the late 1980s. To seek an explanation for this resurgence, the genetic compositions of 22 M1 and 19 M28 GAS strains isolated in The Netherlands between 1960s and the mid-1990s were analyzed by using a mixed-genome DNA microarray. During this four-decade period, M1 and...

article 2007

document

Determination of the relationship between group A streptococcal genome content, M type, and toxic shock syndrome by a mixed genome microarray

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Fluit, A.C. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Group A streptococci (GAS), or Streptococcus pyogenes, are associated with a remarkable variety of diseases, ranging from superficial infections to life-threatening diseases such as toxic-shock-like syndrome (TSS). GAS strains belonging to M types M1 and M3 are associated with TSS. This study aims to obtain insight into the gene profiles...

article 2007

document

Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

Ballerstedt, H. (author), Volkers, R.J.M. (author), Mars, A.E. (author), Hallsworth, J.E. (author), Santos, V.A.M.D. (author), Puchalka, J. (author), van Duuren, J. (author), Eggink, G. (author), Timmis, K.N. (author), de Bont, J.A.M. (author), Wery, J. (author), TNO Kwaliteit van Leven (author)

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas...

article 2007

document

Physiological and phylogenetic characterization of a stable benzene-degrading, chlorate-reducing microbial community

Weelink, S.A.B. (author), Tan, N.C.G. (author), ten Broeke, H. (author), van Doesburg, W. (author), Langenhoff, A.A.M. (author), Gerritse, J. (author), Stams, A.J.M. (author), TNO Bouw en Ondergrond (author)

A stable anoxic enrichment culture was obtained that degraded benzene with chlorate as an electron acceptor. The benzene degradation rate was 1.65 mM benzene per day, which is similar to reported aerobic benzene degradation rates but 20-1650 times higher than reported for anaerobic benzene degradation. Denaturing gradient gel electrophoresis of...

article 2007

document

Intragastric immunization with recombinant Lactobacillus casei expressing flagellar antigen confers antibody-independent protective immunity against Salmonella enterica serovar Enteritidis

Kajikawa, A. (author), Satoh, E. (author), Leer, R.J. (author), Yamamoto, S. (author), Igimi, S. (author), TNO Kwaliteit van Leven (author)

A recombinant Lactobacillus casei expressing a flagellar antigen from Salmonella enterica serovar Enteritidis was constructed and evaluated as a mucosal vaccine. Intragastric immunization of the recombinant strain conferred protective immunity against Salmonella infection in mice. This immunization did not result in antigen-specific antibody in...

article 2007

document

Towards understanding molecular modes of probiotic action

Marco, M.L. (author), Pavan, S. (author), Kleerebezem, M. (author), TNO Kwaliteit van Leven (author)

The possibility that certain microorganisms might be beneficial to human health is highlighted by the numerous consumer products containing probiotic bacteria. Probiotics are typically administered in food that, following entry into the gastro-intestinal tract, results in measurable health-promoting effects. Although there is a growing list of...

article 2006

document

Evaluation of the antibacterial spectrum of drosocin analogues

Bikker, F.J. (author), Kaman-van Zanten, W.E. (author), de Vries-van de Ruit, A.M.B.C. (author), Voskamp-Visser, I. (author), van Hooft, P.A.V. (author), Mars-Groenendijk, R.H. (author), de Visser, P.C. (author), Noort, D. (author), TNO Defensie en Veiligheid (author)

Drosocin is a 19-mer, cationic antimicrobial peptide from Drosophila melanogaster. The aim of the study was to examine the antibacterial spectrum of unglycosylated drosocin analogues. Furthermore, the amino acid sequence of DnaK, drosocin's intracellular target, from susceptible species was aligned and studied for sequence homology. From this a...

article 2006

document

Rational transformation of Lactobacillus reuteri 121 reuteransucrase into a dextransucrase

Kralj, S. (author), van Geel-Schutten, G.H. (author), Faber, E.J. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Kwaliteit van Leven (author)

Glucansucrase or glucosyltransferase (GTF) enzymes of lactic acid bacteria display high sequence similarity but catalyze synthesis of different α-glucans (e.g., dextran, mutan, alternan, and reuteran) from sucrose. The variations in glucosidic linkage specificity observed in products of different glucansucrase enzymes appear to be based on...

article 2005