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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    Correction to: Rewiring of glucose metabolism defines trained immunity induced by oxidized low-density lipoprotein
    Keating, Samuel T. ; Groh, Laszlo ; Thiem, Kathrin ; Bekkering, Siroon ; Li, Yang ; Matzaraki, Vasiliki ; Heijden, Charlotte D.C.C. van der; Puffelen, Jelmer H. van; Lachmandas, Ekta ; Jansen, Trees ; Oosting, Marije ; Bree, L.C.J. de; Koeken, Valerie A.C.M. ; Moorlag, Simone J.C.F.M. ; Mourits, Vera P. ; Diepen, Janna van; Stienstra, Rinke ; Novakovic, Boris ; Stunnenberg, Hendrik G. ; Crevel, Reinout van; Joosten, Leo A.B. ; Netea, Mihai G. ; Riksen, Niels P. - \ 2020
    Journal of Molecular Medicine 98 (2020). - ISSN 0946-2716

    The correct name of the 17th Author is presented in this paper. In the paragraph “Metabolic analysis” of the Method section “an XFp Analyzer” should be changed to “an XFe96 Analyzer”.

    Rewiring of glucose metabolism defines trained immunity induced by oxidized low-density lipoprotein
    Keating, Samuel T. ; Groh, Laszlo ; Thiem, Kathrin ; Bekkering, Siroon ; Li, Yang ; Matzaraki, Vasiliki ; Heijden, Charlotte D.C.C. van der; Puffelen, Jelmer H. van; Lachmandas, Ekta ; Jansen, Trees ; Oosting, Marije ; Bree, L.C.J. de; Koeken, Valerie A.C.M. ; Moorlag, Simone J.C.F.M. ; Mourits, Vera P. ; Diepen, Janna van; Stienstra, Rinke ; Novakovic, Boris ; Stunnenberg, Hendrik G. ; Crevel, Reinout van; Joosten, Leo A.B. ; Netea, Mihai G. ; Riksen, Niels P. - \ 2020
    Journal of Molecular Medicine 98 (2020). - ISSN 0946-2716 - p. 819 - 831.
    Atherosclerosis - Cardiovascular disease - Diabetes complications - Glycolysis - Immunometabolism - Inflammation - Trained immunity

    Abstract: Stimulation of monocytes with microbial and non-microbial products, including oxidized low-density lipoprotein (oxLDL), induces a protracted pro-inflammatory, atherogenic phenotype sustained by metabolic and epigenetic reprogramming via a process called trained immunity. We investigated the intracellular metabolic mechanisms driving oxLDL-induced trained immunity in human primary monocytes and observed concomitant upregulation of glycolytic activity and oxygen consumption. In two separate cohorts of healthy volunteers, we assessed the impact of genetic variation in glycolytic genes on the training capacity of monocytes and found that variants mapped to glycolytic enzymes PFKFB3 and PFKP influenced trained immunity by oxLDL. Subsequent functional validation with inhibitors of glycolytic metabolism revealed dose-dependent inhibition of trained immunity in vitro. Furthermore, in vivo administration of the glucose metabolism modulator metformin abrogated the ability for human monocytes to mount a trained response to oxLDL. These findings underscore the importance of cellular metabolism for oxLDL-induced trained immunity and highlight potential immunomodulatory strategies for clinical management of atherosclerosis. Key messages: Brief stimulation of monocytes to oxLDL induces a prolonged inflammatory phenotype.This is due to upregulation of glycolytic metabolism.Genetic variation in glycolytic genes modulates oxLDL-induced trained immunity.Pharmacological inhibition of glycolysis prevents trained immunity.

    Outcome prediction of head and neck squamous cell carcinoma by MRI radiomic signatures
    Mes, Steven W. ; Velden, Floris H.P. van; Peltenburg, Boris ; Peeters, Carel F.W. ; Beest, Dennis E. te; Wiel, Mark A. van de; Mekke, Joost ; Mulder, Doriene C. ; Martens, Roland M. ; Castelijns, Jonas A. ; Pameijer, Frank A. ; Bree, Remco de; Boellaard, Ronald ; Leemans, C.R. ; Brakenhoff, Ruud H. ; Graaf, Pim de - \ 2020
    European Radiology (2020). - ISSN 0938-7994
    Factor analysis - Head and neck neoplasms - Magnetic resonance imaging - Prognosis

    Objectives: Head and neck squamous cell carcinoma (HNSCC) shows a remarkable heterogeneity between tumors, which may be captured by a variety of quantitative features extracted from diagnostic images, termed radiomics. The aim of this study was to develop and validate MRI-based radiomic prognostic models in oral and oropharyngeal cancer. Materials and Methods: Native T1-weighted images of four independent, retrospective (2005–2013), patient cohorts (n = 102, n = 76, n = 89, and n = 56) were used to delineate primary tumors, and to extract 545 quantitative features from. Subsequently, redundancy filtering and factor analysis were performed to handle collinearity in the data. Next, radiomic prognostic models were trained and validated to predict overall survival (OS) and relapse-free survival (RFS). Radiomic features were compared to and combined with prognostic models based on standard clinical parameters. Performance was assessed by integrated area under the curve (iAUC). Results: In oral cancer, the radiomic model showed an iAUC of 0.69 (OS) and 0.70 (RFS) in the validation cohort, whereas the iAUC in the oropharyngeal cancer validation cohort was 0.71 (OS) and 0.74 (RFS). By integration of radiomic and clinical variables, the most accurate models were defined (iAUC oral cavity, 0.72 (OS) and 0.74 (RFS); iAUC oropharynx, 0.81 (OS) and 0.78 (RFS)), and these combined models outperformed prognostic models based on standard clinical variables only (p < 0.001). Conclusions: MRI radiomics is feasible in HNSCC despite the known variability in MRI vendors and acquisition protocols, and radiomic features added information to prognostic models based on clinical parameters. Key Points: • MRI radiomics can predict overall survival and relapse-free survival in oral and HPV-negative oropharyngeal cancer. • MRI radiomics provides additional prognostic information to known clinical variables, with the best performance of the combined models. • Variation in MRI vendors and acquisition protocols did not influence performance of radiomic prognostic models.

    Vijf goudoogvliegjes nieuw voor de nederlandse fauna (Diptera: Chyromyidae)
    Bree, Elias de; Belgers, J.D.M. ; Weele, Ruud van der; Delfos, Alexander - \ 2019
    Nederlandse Faunistische Mededelingen 2019 (2019)53. - ISSN 0169-2453 - p. 135 - 142.
    Subgenomic flavivirus RNA binds the mosquito DEAD/H-box helicase ME31B and determines Zika virus transmission by Aedes aegypti
    Göertz, Giel P. ; Bree, Joyce W.M. van; Hiralal, Anwar ; Fernhout, Bas M. ; Steffens, Carmen ; Boeren, Sjef ; Visser, Tessa M. ; Vogels, Chantal B.F. ; Abbo, Sandra R. ; Fros, Jelke J. ; Koenraadt, Constantianus J.M. ; Oers, Monique M. van; Pijlman, Gorben P. - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)38. - ISSN 0027-8424 - p. 19136 - 19144.
    Aedes aegypti - Purification - RNA-affinity - Subgenomic flavivirus RNA - Transmission - Zika virus

    Zika virus (ZIKV) is an arthropod-borne flavivirus predominantly transmitted by Aedes aegypti mosquitoes and poses a global human health threat. All flaviviruses, including those that exclusively replicate in mosquitoes, produce a highly abundant, noncoding subgenomic flavivirus RNA (sfRNA) in infected cells, which implies an important function of sfRNA during mosquito infection. Currently, the role of sfRNA in flavivirus transmission by mosquitoes is not well understood. Here, we demonstrate that an sfRNA-deficient ZIKV (ZIKVΔSF1) replicates similar to wild-type ZIKV in mosquito cell culture but is severely attenuated in transmission by Ae. aegypti after an infectious blood meal, with 5% saliva-positive mosquitoes for ZIKVΔSF1 vs. 31% for ZIKV. Furthermore, viral titers in the mosquito saliva were lower for ZIKVΔSF1 as compared to ZIKV. Comparison of mosquito infection via infectious blood meals and intrathoracic injections showed that sfRNA is important for ZIKV to overcome the mosquito midgut barrier and to promote virus accumulation in the saliva. Next-generation sequencing of infected mosquitoes showed that viral small-interfering RNAs were elevated upon ZIKVΔSF1 as compared to ZIKV infection. RNA-affinity purification followed by mass spectrometry analysis uncovered that sfRNA specifically interacts with a specific set of Ae. aegypti proteins that are normally associated with RNA turnover and protein translation. The DEAD/H-box helicase ME31B showed the highest affinity for sfRNA and displayed antiviral activity against ZIKV in Ae. aegypti cells. Based on these results, we present a mechanistic model in which sfRNA sequesters ME31B to promote flavivirus replication and virion production to facilitate transmission by mosquitoes.

    Supplementation of fructooligosaccharides to suckling piglets affects intestinal microbiota colonization and immune development
    Schokker, Dirkjan ; Fledderus, Jan ; Jansen, Rutger ; Vastenhouw, Stephanie A. ; Bree, Freddy M. de; Smits, Mari A. ; Jansman, Alfons A.J.M. - \ 2018
    Journal of Animal Science 96 (2018)6. - ISSN 0021-8812 - p. 2139 - 2153.
    Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely dependent on available nutrients required for the specific microbial community structures to expand. It is currently not known what the specificities are of intestinal microbial community structures in relation to the programming of the intestinal mucosal immune system and development of the intestinal barrier function. The objective of the present study was to investigate the effects of a nutritional intervention on intestinal development of suckling piglets by daily oral administration of fructooligosaccharides (FOS) over a period of 12 d (days 2–14 of age). At the microbiota community level, a clear “bifidogenic” effect of the FOS administration was observed in the colon digesta at day 14. The former, however, did not translate into significant changes of local gene expression in the colonic mucosa. In the jejunum, significant changes were observed for microbiota composition at day 14, and microbiota diversity at day 25. In addition, significant differentially expressed gene sets in mucosal tissues of the jejunum were identified at both days 14 and 25 of age. At the age of 14 d, a lower activity of cell cycle–related processes and a higher activity of extracellular matrix processes were observed in the jejunal mucosa of piglets supplemented with FOS compared with control piglets. At day 25, the lower activity of immune-related processes in jejunal tissue was seen in piglets supplemented with FOS. Villi height and crypt depth in the jejunum were significantly different at day 25 between the experimental and control groups, where piglets supplemented with FOS had greater villi and deeper crypts. We conclude that oral FOS administration during the early suckling period of piglets had significant bifidogenic effects on the microbiota in the colon and on gene expression in the jejunal mucosa by thus far unknown mechanisms.
    Green Up The City! - Do urban greening initiatives lead to green gentrification in the Netherlands?
    Bree, J. de; Heijmans, M. ; Michailidi, E. ; Negru, R.M. ; Pelgrim, I. ; Smith, A. ; Jacobs, J. ; Haas, W. de; Wentink, C.Q. - \ 2018
    Towards a framework to access, compare and develop monitoring and evaluation of climate change adaptation in Europe
    Klostermann, J.E.M. ; Sandt, K. van de; Harley, M. ; Hilden, M. ; Leiter, T. ; Minnen, J. van; Pieterse, N. ; Bree, L. van - \ 2018
    Mitigation and Adaptation Strategies for Global Change 23 (2018)2. - ISSN 1381-2386 - p. 187 - 209.
    Adaptation is increasingly recognised as essential when dealing with the adverse impacts of climate change on societies, economies and the environment. However, there is insufficient information about the effectiveness of adaption policies, measures and actions. For this reason, the establishment of monitoring programmes is considered to be necessary. Such programmes can contribute to knowledge, learning and data to support adaptation governance. In the European Union (EU), member states are encouraged to develop National Adaptation Strategies (NASs). The NASs developed so far vary widely because of differing views, approaches and policies. A number of member states have progressed to monitoring and evaluating the implementation of their NAS. It is possible to identify key elements in these monitoring programmes that can inform the wider policy learning process. In this paper, four generic building blocks for creating a monitoring and evaluation programme are proposed: (1) definition of the system of interest, (2) selection of a set of indicators, (3) identification of the organisations responsible for monitoring and (4) definition of monitoring and evaluation procedures. The monitoring programmes for NAS in three member states—Finland, the UK and Germany—were analysed to show how these elements have been used in practice, taking into account their specific contexts. It is asserted that the provision of a common framework incorporating these elements will help other member states and organisations within them in setting up and improving their adaptation monitoring programmes.
    Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
    Byrne, Allison Q. ; Rothstein, Andrew P. ; Poorten, Thomas J. ; Erens, Jesse ; Settles, Matthew L. ; Rosenblum, Erica Bree - \ 2017
    University of California
    Fungi - swab - microfluidic multiplex PCR - Batrachochytrium dendrobatidis - Amphibians - Disease Biology - Ecological Genetics - genotype
    One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems. The most common non-invasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully-selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, non-invasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.
    Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
    Byrne, Allison Q. ; Rothstein, Andrew P. ; Poorten, Thomas J. ; Erens, Jesse ; Settles, Matthew L. ; Rosenblum, Erica Bree - \ 2017
    Molecular Ecology Resources 17 (2017)6. - ISSN 1755-098X - p. 1283 - 1292.
    Batrachochytrium dendrobatidis - genotype - microfluidic multiplex PCR - swab

    One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures have advanced our understanding of Bd phylogenetics, genomic architecture and mechanisms of virulence. However, pure cultures are laborious to obtain and whole-genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus, we still know little about the genetic diversity of Bd in natural systems. The most common noninvasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole-genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, noninvasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.

    Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development
    Schokker, D. ; Jansman, A.J.M. ; Veninga, Gosse ; Bruin, Naomi de; Vastenhouw, S.A. ; Bree, F.M. de; Bossers, A. ; Rebel, J.M.J. ; Smits, M.A. - \ 2017
    Wageningen University & Research
    chicken - gut - microbiota - gene expression - immune development
    Background Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa. Results We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8Â mg amoxicillin per bird per day) via the drinking water for a period of 24Â h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development. Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01+) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2Â weeks. Conclusion These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.
    Evaluation of a multiplex real-time PCR for detection of four bacterial agents commonly associated with bovine respiratory disease in bronchoalveolar lavage fluid
    Wisselink, H.J. ; Cornelissen, J.B.W.J. ; Wal, F.J. van der; Kooi, Bart ; Koene, M.G.J. ; Bossers, A. ; Smid, B. ; Bree, F.M. de; Antonis, A.F.G. - \ 2017
    BMC Veterinary Research 13 (2017)1. - ISSN 1746-6148
    Background
    Pasteurella multocida, Mannheimia haemolytica, Histophilus somni and Trueperella pyogenes are four bacterial agents commonly associated with bovine respiratory disease (BRD). In this study a bacterial multiplex real-time PCR (the RespoCheck PCR) was evaluated for the detection in bronchoalveolar lavage fluid (BALF) of these four bacterial agents.
    Results
    The analytical sensitivity of the multiplex real-time PCR assay determined on purified DNA and on bacterial cells of the four target pathogens was one to ten fg DNA/assay and 4 × 10−1 to 2 × 100 CFU/assay. The analytical specificity of the test was, as evaluated on a collection of 118 bacterial isolates, 98.3% for M. haemolytica and 100% for the other three target bacteria. A set of 160 BALF samples of calves originating from ten different herds with health problems related to BRD was examined with bacteriological methods and with the RespoCheck PCR. Using bacteriological examination as the gold standard, the diagnostic sensitivities and specificities of the four bacterial agents were respectively between 0.72 and 1.00 and between 0.70 and 0.99. Kappa values for agreement between results of bacteriological examination and PCRs were low for H. somni (0.17), moderate for P. multocida (0.52) and M. haemolytica (0.57), and good for T. pyogenes (0.79). The low and moderate kappa values seemed to be related to limitations of the bacteriological examination, this was especially the case for H. somni.
    Conclusion
    It was concluded that the RespoCheck PCR assay is a valuable diagnostic tool for the simultaneous detection of the four bacterial agents in BALF of calves.
    Indicators for Enteral Nutrition Use and Prophylactic Percutaneous Endoscopic Gastrostomy Placement in Patients with Head and Neck Cancer Undergoing Chemoradiotherapy
    Linden, Nina C. van der; Kok, Annemieke ; Leermakers-Vermeer, Marja J. ; Roos, Nicole M. de; Bree, Remco de; Cruijsen, Hester van; Terhaard, Chris H.J. - \ 2017
    Nutrition in Clinical Practice 32 (2017)2. - ISSN 0884-5336 - p. 225 - 232.
    chemoradiotherapy - enteral nutrition - gastrostomy - head and neck cancer - nutritional support - PEG tube

    Background: Chemoradiotherapy (CRT) is a major risk factor for malnutrition and dehydration in patients with head and neck cancer. Enteral support is often needed, and a percutaneous endoscopic gastrostomy (PEG) is frequently placed. Specific indicators for PEG placement remain unclear. This study retrospectively determined which factors contributed to enteral nutrition (EN) use and PEG placement in a large patient group to gain insight on potential indicators for PEG placement protocol creation. Methods: A retrospective chart review of 240 patients with head and neck cancer who underwent CRT in 2012-2015 was conducted. Lifestyle, oncological, treatment, and nutrition outcome characteristics were examined and compared between patients who used EN and those who did not, as well as between patients who received a PEG and those who did not. Results: In total, 195 patients used EN (via PEG or nasogastric tube). Multivariate analysis showed that nodal disease presence (P =.01) and bilateral neck irradiation (P =.01) were significantly related to EN use while increased age (P =.01), nodal disease presence (P =.02), reconstruction extent other than primary closure (P =.02), bilateral neck irradiation (P <.01), and an adapted intake consistency prior to treatment (P =.03) were significantly related to PEG placement. Conclusion: Important factors for EN usage and PEG placement consideration include nodal disease and planned bilateral neck irradiation. Results from this study in combination with existing literature can be taken into consideration in the design of a PEG placement protocol. A better understanding of predictive indicators to PEG placement should be explored in further prospective studies.

    Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases
    Cornelissen, Jan B.W.J. ; Bree, Freddy M. de; Wal, Fimme J. van der; Kooi, Engbert A. ; Koene, Miriam G.J. ; Bossers, Alex ; Smid, Bregtje ; Antonis, Adriaan F. ; Wisselink, Henk J. - \ 2017
    BMC Veterinary Research 13 (2017)1. - ISSN 1746-6148
    Bovine Mycoplasma - Bovine respiratory disease - M. bovirhinis - M. bovis - M. dispar - RespoCheck - Triplex PCR

    Background: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck Mycoplasma triplex real-time PCR are based on the V3/V4 region of the 16S rRNA gene of the three Mycoplasma species. Results: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M. dispar, and 30cfu/mL for M. bovis or M. bovirhinis. The analytical sensitivity of the RespoCheck Mycoplasma triplex real-time PCRwas, as determined on purified DNA, 10fg DNA per assay for M. dispar and 100fg fo rM. bovis and M. bovirhinis. The analytical specificity of the RespoCheck Mycoplasma triplex real-time PCR was, as determined by testing Mycoplasmas strains (n=17) and other bacterial strains (n=107), 100, 98.2 and 99.1% for M. bovis, M. dispar and M. bovirhinis respectively. The RespoCheck Mycoplasma triplex real-time PCR was compared with the PCR/DGGE analysis for M. bovis, M. dispar and M. bovirhinis respectively by testing 44 BALF samples from calves. Conclusion: In conclusion, the RespoCheck PCR assay can be a valuable tool for timely and accurate detection of three Mycoplasma species associated with in bovine respiratory disease.

    Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development
    Schokker, Dirkjan ; Jansman, Alfons J.M. ; Veninga, Gosse ; Bruin, Naomi de; Vastenhouw, Stephanie A. ; Bree, Freddy M. de; Bossers, Alex ; Rebel, Johanna M.J. ; Smits, Mari A. - \ 2017
    BMC Genomics 18 (2017). - ISSN 1471-2164 - 14 p.
    Background: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa.
    Results: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8 mg amoxicillin per bird per day) via the drinking water for a period of 24 h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development.
    Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01+) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2 weeks.
    Conclusion: These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.
    Effects of a high level of dietary zinc over different post weaning periods on intestinal microbiota and mucosal gene expression in piglets
    Jansman, A.J.M. ; Schokker, D. ; Gerritsen, R. ; Willems, E. ; Bree, F. de; Dekker, R.A. ; Smits, M.A. - \ 2016
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1001) - 48
    Effects of a high level of dietary zinc as model intervention on intestinal microbiota and mucosal gene expression in piglets
    Jansman, A.J.M. ; Schokker, D. ; Gerritsen, R. ; Bree, F. de; Hulst, M.M. ; Smits, M.A. - \ 2016
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1000) - 37
    Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme, and fish oil on immune competence related parameters of adult broiler
    Krimpen, M.M. van; Torki, M. ; Schokker, D. ; Lensing, M. ; Vastenhouw, S. ; Bree, F.M. de; Bossers, A. ; Bruijn, N. de; Jansman, A.J.M. ; Rebel, J.M.J. ; Smits, M.A. - \ 2016
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 977) - 50
    The purpose of this experiment was to evaluate the effects of five nutritional interventions, provided during d 14 – 28, including inclusion of a plant extract (quercetin); an insoluble fiber (oat hulls); a prebiotic (β- glucan); an anti-microbial protein (lysozyme), and ω-3 fatty acids from fish oil, on growth performance, composition of the intestinal microbiota, and morphology and gene expression of small intestine of broilers. Despite the different types of interventions, parameters related to immune competence were only marginally affected by the tested products. It seemed that in this study inclusion of oat hulls, and probably β-glucans, had perspective to improve immune competence. It is recommended to revaluate some of the tested interventions, especially dietary inclusion of oat hulls and β-glucans, in broilers starting from day-old onward.
    Effects of rye inclusion in diets on broiler performance, gut morphology and microbiota composition
    Krimpen, M.M. van; Torki, Mehran ; Borgijink, S.M. ; Schokker, D. ; Vastenhouw, S.A. ; Bree, F.M. de; Bossers, A. ; Fabri, T. ; Bruijn, Naomi de; Jansman, A.J.M. ; Rebel, J.M.J. ; Smits, M.A. ; Emous, R.A. van - \ 2016
    - p. 65 - 65.
    It has been hypothesized that dietary inclusion of rye would increase viscosity of intestinal
    digesta, consequently resulting in an effect on nutrient absorption, gut wall morphology,
    composition of microbiota, and immunity-related processes in the gut wall, and it might be a
    helpful model ingredient to investigate the negative effects of nutrition on immune competence
    parameters of the birds. In this experiment the effects of dietary inclusion of three levels (0, 5,
    and 10%) of rye between 14 and 28 days of age on gut health, digesta microbiota composition,
    expression of genes in the small intestinal tissue and performance in broilers were investigated.
    A total of 960 day-old male Ross 308 chicks were allocated to 24 pens (40 birds per pen).
    Inclusion of 10% rye in the diet did not affect feed intake, but decreased body weight gain, and
    increased feed conversion ratio. Litter quality was inversely related to the level of rye inclusion
    in the diet. Providing rye-rich diets resulted in increased jejunal villus height and crypt depth
    during the first week of provision, whereas the villus-crypt ratio was not affected. During the
    second week of the experiment, however, the level of rye inclusion had no effect on jejunal
    gut morphology. Inclusion of rye into the diet did not affect the number and size of jejunal
    goblet cells. Dietary inclusion of rye did not affect the diversity of the jejunal microbiota,
    as determined by the Shannon index, although specific microbial strains were affected by
    rye inclusion. Lactobacillus species made about 75-80% of the jejunal microbiota, and rye
    inclusion resulted in an exchange between the different lactobacillus species. At d28, the share
    of Lactobacillus reuteri, Staphylococcus saporphyticus and Aerococcaceae in the microbiota in jejunal digesta decreased with increasing dietary rye. Dietary rye inclusion affected expression of genes in the small intestinal tissue involved in cell cycle processes of the epithelial cells, including proliferation, differentiation, motility, and survival, as well as in the complement and coagulation cascade. At 28 d of age, effects were more pronounced in birds fed the 10% rye diet, compared to birds fed the 5% rye diet. In conclusion, inclusion of 5% or 10% rye to the grower diet of broilers have limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue; however, were affected by dietary rye inclusion level.
    An unrecognized species of the Culicoides obsoletus complex feeding on livestock in the Netherlands
    Meiswinkel, R. ; Bree, F.M. de; Vries, Ruth de; Elbers, A.R.W. - \ 2015
    Veterinary Parasitology 207 (2015)3-4. - ISSN 0304-4017 - p. 324 - 328.
    In studies on Culicoides attacking livestock in the Netherlands, we chanced upon a species of the Obsoletus complex that we do not recognize, but whose dark wing pattern is distinctive. Nine cytochrome c oxidase (CO1) sequences of our so-called ‘dark obsoletus’ support its status as a separate species, the sequences differing significantly from those representing Culicoides obsoletus (Meigen) (90–91% homology) and Culicoides scoticus Downes & Kettle (87–88% homology). In the last decade, several research groups in Europe have encountered ‘mystery species’ related to C. obsoletus and in some instances have made their sequences for various genetic loci available in GenBank. These include a CO1 series submitted from Sweden in 2012 (annotated as ‘obsoletus 01, 02, or 03 MA-2012′) and of which some share a 99% identity with our sequences for ‘dark obsoletus’. Without doubt, the series from the Netherlands, along with a portion of the Swedish submissions, together represent a single species (‘dark obsoletus’). Whether this species is referable to the Russian Culicoides gornostaevae Mirzaeva recorded recently from Norway, Sweden and Poland, and based solely upon the external morphology of the male, is not clear. The presence in Western Europe of multiple undescribed species related to C. obsoletus means that the taxonomy of this important vector complex is not fully resolved; consequently, we know little about these cryptic species with regard to seasonality, geographic range and host preference. This is undesirable given that Culicoides-borne arboviruses causing disease in livestock are moving more regularly out of the tropics and spreading north into temperate latitudes.
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