Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype
    Gerritsen, J. ; Timmerman, H.M. ; Fuentes, S. ; Minnen, L.P. van; Panneman, H. ; Konstantinov, S.R. ; Rombouts, F.M. ; Gooszen, H.G. ; Akkermans, L.M.A. ; Smidt, H. ; Rijkers, G.T. - \ 2011
    Applied and Environmental Microbiology 77 (2011)21. - ISSN 0099-2240 - p. 7749 - 7756.
    severe acute-pancreatitis - ribosomal-rna - necrotizing pancreatitis - clinical-course - sequence data - overgrowth - gut - translocation - microbiota - cirrhosis
    Prophylactic probiotic therapy has shown beneficial effects in an experimental rat model for acute pancreatitis on the health status of the animals. Mechanisms by which probiotic therapy interferes with severity of acute pancreatitis and associated sepsis, however, are poorly understood. The aims of this study were to identify the probiotic-induced changes in the gut microbiota and to correlate these changes to disease outcome. Duodenum and ileum samples were obtained from healthy and diseased rats subjected to pancreatitis for 7 days and prophylactically treated with either a multispecies probiotic mixture or a placebo. Intestinal microbiota was characterized by terminal-restriction fragment length polymorphism (T-RFLP) analyses of PCR-amplified 16S rRNA gene fragments. These analyses showed that during acute pancreatitis the host-specific ileal microbiota was replaced by an “acute pancreatitis-associated microbiota.” This replacement was not reversed by administration of the probiotic mixture. An increase, however, was observed in the relative abundance of a novel bacterial phylotype most closely related to Clostridium lituseburense and referred to as commensal rat ileum bacterium (CRIB). Specific primers targeting the CRIB 16S rRNA gene sequence were developed to detect this phylotype by quantitative PCR. An ileal abundance of CRIB 16S rRNA genes of more than 7.5% of the total bacterial 16S rRNA gene pool was correlated with reduced duodenal bacterial overgrowth, reduced bacterial translocation to remote organs, improved pancreas pathology, and reduced proinflammatory cytokine levels in plasma. Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy.
    A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding
    Harlizius, B. ; Lopes, M.S. ; Duijvesteijn, N. ; Goor, L.H.P.V. van der; Haeringen, W.A. van; Panneman, H. ; Guimaraes, S.E.F. ; Merks, J.W.M. ; Knol, E.F. - \ 2011
    Journal of Animal Science 89 (2011)6. - ISSN 0021-8812 - p. 1661 - 1668.
    parentage exclusion - beef-cattle - snp markers - traceability - probability - population - selection - pedigree - number - impact
    In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (=90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was =5, the number of mismatches was =1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.
    Effect of pea, pea hulls, faba beans and faba bean hulls on the ileal microbial composition in weaned piglets
    Meulen, J. van der; Panneman, H. ; Jansman, A.J.M. - \ 2010
    Livestock Science 133 (2010)1-3. - ISSN 1871-1413 - p. 135 - 137.
    growing pigs - populations - colon - diets
    Grain legumes produced in Europe such as pea, faba beans and lupins are alternative vegetable protein sources for imported soy protein in animal feeds. These legume seeds contain constituents that are not digested and may act as a substrate for microbial fermentation in the gastrointestinal tract, thereby modulating the microbial population and affecting the microbial diversity. In this study the effect was evaluated of inclusion of pea and faba beans and their hull fractions in diets for piglets on the intestinal microbial population at the ileal level. A total of 72 piglets weaned at 28 days of age were fed a control diet based on soybean meal or diets with pea (250 g/kg), pea hulls (100 g/kg), faba beans (250 g/kg) or faba bean hulls (100 g/kg). All piglets were challenged orally with an enterotoxigenic Escherichia coli (ETEC) 7 days after weaning, except for half of the piglets fed the soybean meal diet that were inoculated with phosphate buffered saline. The piglets were sacrificed 21 days after weaning and ileal digesta samples were collected and analysed with a terminal restriction fraction length polymorphism based method of Microbial Community Profiling and Characterization. From 10 days after the challenge, there was no faecal excretion of ETEC in any of the piglets. There was a distinct different microbial profile in the piglets fed the diet with faba beans or faba bean hulls, showing a lower number of terminal restriction fragments (T-RFs) compared to the other treatments. Such an alteration in the ileal microflora composition by the use of different legume seeds or their hull fractions suggests a potential for the manipulation of intestinal microbial activity and thus in preventing or provoking intestinal disorders in piglets
    Fast response filter module with plug flow of filtrate for on-line sampling from submerged cultures of filamentous fungi
    Poulsen, B.R. ; Ruijter, G.J.G. ; Panneman, H. ; Iversen, J.J.L. ; Visser, J. - \ 2004
    Analytica Chimica Acta 510 (2004)2. - ISSN 0003-2670 - p. 203 - 212.
    column liquid-chromatography - aspergillus-niger - system - fermentation - metabolites - oxygen - inlet
    Automatic and accurate sampling is both convenient and sometimes necessary to obtain detailed information about cell cultures. We developed an autoclavable sampling system in which culture broth was pumped through an ultrafiltration cross-flow module with a novel filtrate collecting principle and a novel regulation of filter back pressure. Filtrate was collected from equal membrane filter areas through holes connected to channels with an even length to the collecting point, resulting in a near plug flow of filtrate and a reduction in the response time to 1 min (98% of full signal of the tracer molecule glucose). Constant pressure difference (0.3 bar) across the membrane filter (30 kDa cutoff value) and prevention of leakage was obtained by squeezing the tubing with culture broth between two flexible spring steel plates fixed at one corner (filtrate flow 1 ml min¿1). The large contact area allowed the tubing to open the passage more when pressure increased. Using this design of sampling system, the metabolite profiles of Aspergillus niger wild type and a phosphofructokinase overexpressing strain (three times wild type) were concluded to be indistinguishable by detailed monitoring of fast transients of substrates and products in batch culture and glucose pulse experiments. The combination of the fast response filter module and prevention of high pressure peaks with the flexible resistance to flow enables long-term (>5 days) and automatic monitoring of cultures of filamentous fungi or other microorganisms with fast changes in extracellular concentrations.
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