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Microbial biogeography of drinking water: Patterns in phylogenetic diversity across space and time

Roeselers, G. (author), Coolen, J. (author), van der Wielen, P.W. (author), Jaspers, M.C. (author), Atsma, A. (author), de Graaf, B. (author), Schuren, F. (author)

In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high-throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water...

article 2015

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A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria

Boesten, R.J. (author), Schuren, F.H.J. (author), de Vos, W.M. (author), TNO Kwaliteit van Leven (author)

A genomic DNA-based microarray was constructed containing over 6000 randomly cloned genomic fragments of approximately 1-2 kb from six mammalian intestinal Bifidobacterium spp. including B. adolescentis, B. animalis, B. bifidum, B. catenulatum, B. longum and B. pseudolongum. This Bifidobacterium Mixed-Species (BMS) microarray was used to...

article 2009

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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

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Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing

Kovatcheva-Datchary, P. (author), Egert, M. (author), Maathuis, A. (author), Rajilić-Stojanović, M. (author), de Graaf, A.A. (author), Smidt, H. (author), de Vos, W.M. (author), Venema, K. (author), TNO Kwaliteit van Leven (author)

Summary Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under...

article 2009

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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

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Increased infiltration of Chlamydophila pneumoniae in the vessel wall of human veins after perfusion

Kupreishvili, K. (author), ter Weeme, M. (author), Morré, S.A. (author), van den Brule, A.J.C. (author), Huybregts, M.A.J.M. (author), Quax, P.H.A. (author), ten Velden, J. (author), van Hinsbergh, V.W.M. (author), Stooker, W. (author), Eijsman, L. (author), Niessen, H.W.M. (author), TNO Kwaliteit van Leven (author)

Background: Several studies have suggested an association between Chlamydophila pneumoniae (Cp) infection and atherosclerosis. A recent study detected Cp DNA in the saphenous vein of 12% of all patients before bypass grafting and in 38% of failed grafts. We used a system in which human veins were perfused with autologous blood under arterial...

article 2008

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Pyrosequencinq analysis of the oral microflora of healthy adults

Keijser, B.J.F. (author), Zaura, E. (author), Huse, S.M. (author), van der Vossen, J.M.B.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), ten Gate, J.M. (author), Crielaard, W. (author), TNO Kwaliteit van Leven (author)

A good definition of commensal microflora and an understanding of its relation to health are essential in preventing and combating disease. We hypothesized that the species richness of human oral microflora is underestimated. Saliva and supragingival plaque were sampled from 71 and 98 healthy adults, respectively. Amplieons from the V6...

article 2008

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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

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Functional analysis of three plasmids from Lactobacillus plantarum

TNO Kwaliteit van Leven (author), van Kranenburg, R. (author), Golic, N. (author), Bongers, R. (author), Leer, R.J. (author), de Vos, W.M. (author), Siezen, R.J. (author), Kleerebezem, M. (author)

Lactobacillus plantarum WCFS1 harbors three plasmids, pWCFS101, pWCFS102, and pWCFS103, with sizes of 1,917, 2,365, and 36,069 bp, respectively. The two smaller plasmids are of unknown function and contain replication genes that are likely to function via the rolling-circle replication mechanism. The host range of the p WCFS101 replicon includes...

article 2005

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Glucan synthesis in the genus Lactobacillus: Isolation and characterization of glucansucrase genes, enzymes and glucan products from six different strains

Kralj, S. (author), van Geel-Schutten, G.H. (author), Dondorff, M.M.G. (author), Kirsanovs, S. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)

Members of the genera Streptococcus and Leuconostoc synthesize various α-glucans (dextran, alternan and mutan). In Lactobacillus, until now, the only glucosyltransferase (GTF) enzyme that has been characterized is gtfA of Lactobacillus reuteri 121, the first GTF enzyme synthesizing a glucan (reuteran) that contains mainly α-(1 → 4) linkages...

article 2004

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Biochemical and molecular characerization of a levansucrase from Lactobacillus reuteri

van Hijum, S.A.F.T. (author), Szalowska, E. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)

Lactobacillus reuteri strain 121 employs a fructosyltransferase (FTF) to synthesize a fructose polymer [a fructan of the levan type, with β(2→6) linkages] from sucrose or raffinose. Purification of this FTF (a levansucrase), and identification of peptide amino acid sequences, allowed isolation of the first Lactobacillus levansucrase gene (lev),...

article 2004

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DNA analysis of the genes encoding acidocin LF221 A and acidocin LF221 B, two bacteriocins produced by Lactobacillus gasseri LF221

Majhenič, A.Č. (author), Venema, K. (author), Allison, G.E. (author), Matijašić, B.B. (author), Rogelj, I. (author), Klaenhammer, T.R. (author), TNO Voeding (author)

Lactobacillus gasseri LF221, an isolate from the feces of a child, produces two bacteriocins. Standard procedures for molecular techniques were used to locate, clone and sequence the fragments of LF221 chromosomal DNA carrying the acidocin LF221 A and B structural genes, respectively. Sequencing analysis revealed the gene of acidocin LF221 A to...

article 2004

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Role of bacterial virulence proteins in Agrobacterium-mediated transformation of Aspergillus awamori

Michielse, C.B. (author), Ram, A.F.J. (author), Hooykaas, P.J.J. (author), van den Hondel, C.A.M.J.J. (author), TNO Voeding (author)

The Agrobacterium-mediated transformation of Aspergillus awamori was optimized using defined co-cultivation conditions, which resulted in a reproducible and efficient transformation system. Optimal co-cultivation conditions were used to study the role of Agrobacterium tumefaciens virulence proteins in T-DNA transfer. This study revealed that...

article 2004

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A PCR-based method for identification of bifidobacteria from the human alimentary tract at the species level

Venema, K. (author), Maathuis, A.J.H. (author), TNO Voeding (author)

A polymerase chain reaction (PCR)-based method was developed for the identification of isolates of Bifidobacterium at the species level. Using two Bifidobacterium-specific primers directed against the 16S ribosomal gene (Bif164 and Bif662), a PCR product was obtained from the type strains of 12 different bifidobacterial species that have been...

article 2003

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Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium

Berry, A. (author), Janssens, D. (author), Hümbelin, M. (author), Jore, J.P.M. (author), Hoste, B. (author), Cleenwerck, I. (author), Vancanneyt, M. (author), Bretzel, W. (author), Mayer, A.F. (author), Lopez-Ulibarri, R. (author), Shanmugam, B. (author), Swings, J. (author), Pasamontes, L. (author)

A comprehensive taxonomic re-evaluation was performed on the marine, zeaxanthin-producing bacterium formerly classified as [Flavobacterium] sp. strain R-1512 (ATCC 21588). This strain, together with two other previously described marine isolates, [Flavobacterium] strain R-1506 and Paracoccus sp. strain MBIC 3966, were found to comprise a new...

article 2003

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Molecular Evidence for Dissemination of Unique Campylobacter jejuni Clones in Curaçao, Netherlands Antilles

Duim, B. (author), Godschalk, P.C.R. (author), van den Braak, N. (author), Dingle, K.E. (author), Dijkstra, J.R. (author), Leyde, E. (author), van der Plas, J. (author), Colles, F.M. (author), Endtz, H.P. (author), Wagenaar, J.A. (author), Maiden, M.C.J. (author), van Belkum, A. (author)

Campylobacter jejuni isolates (n = 234) associated with gastroenteritis and the Guillain-Barré syndrome (GBS) in the island of Curaçao, Netherlands Antilles, and collected from March 1999 to March 2000 were investigated by a range of molecular typing techniques. Data obtained by pulsed-field gel electrophoresis (PFGE), amplified fragment length...

article 2003

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Effects of tylosin on bacterial mucolysis, Clostridium perfringens colonization, and intestinal barrier function in a chick model of necrotic enteritis

TNO Animal Nutrition (author), Collier, C.T. (author), van der Klis, J.D. (author), Deplancke, B. (author), Anderson, D.B. (author), Gaskins, H.R. (author)

Necrotic enteritis (NE) is a worldwide poultry disease caused by the alpha toxin-producing bacterium Clostridium perfringens. Disease risk factors include concurrent coccidial infection and the dietary use of cereal grains high in nonstarch polysaccharides (NSP), such as wheat, barley, rye, and oats. Outbreaks of NE can be prevented or treated...

article 2003

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Staphylococcus aureus resistance to human defensins and evasion of neutrophil killing via the novel virulence factor MprF is based on modification of membrane lipids with L-lysine

Peschel, A. (author), Jack, R.W. (author), Otto, M. (author), Collins, L.V. (author), Staubitz, P. (author), Nicholson, G. (author), Kalbacher, H. (author), Nieuwenhuizen, W.F. (author), Jung, G. (author), Tarkowski, A. (author), van Kessel, K.P.M. (author), van Strijp, J.A.G. (author)

Defensins, antimicrobial peptides of the innate immune system, protect human mucosal epithelia and skin against microbial infections and are produced in large amounts by neutrophils. The bacterial pathogen Staphylococcus aureus is insensitive to defensins by virtue of an unknown resistance mechanism. We describe a novel staphylococcal gene, mprF...

article 2001

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Complement-resistant Moraxella catarrhalis forms a genetically distinct lineage within the species

Verduin, C.M. (author), Kools-Sijmons, M. (author), van der Plas, J. (author), Vlooswijk, J. (author), Tromp, M. (author), van Dijk, H. (author), Banks, J. (author), verbrugh, H. (author), van Belkum, A. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Moraxella catarrhalis is a bacterial species that has been implicated in 15^20% of all cases of otitis media in the USA and the complementresistantvariant of M. catarrhalis has been considered particularly pathogenic. A collection of geographically diverse, complement-sensitive (n = 28) and -resistant strains (n = 47) of M. catarrhalis was...

article 2000

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Establishing a campylobacter-free pig population through a top-down approach

Weijtens, M.J.B.M. (author), Urlings, H.A.P. (author), van der Plas, J. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Fattening pigs are often infected with campylobacter. To eliminate campylobacter from the pig population, a top-down approach, involving the breeding and reproduction farms, seems appropriate. In order to investigate the effectiveness of a top-down approach, sows' faeces from the following farms were analysed for the presence of campylobacter:...

article 2000