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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    Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status : The NU-AGE 1-year dietary intervention across five European countries
    Ghosh, Tarini Shankar ; Rampelli, Simone ; Jeffery, Ian B. ; Santoro, Aurelia ; Neto, Marta ; Capri, Miriam ; Giampieri, Enrico ; Jennings, Amy ; Candela, Marco ; Turroni, Silvia ; Zoetendal, Erwin G. ; Hermes, Gerben D.A. ; Elodie, Caumon ; Brugere, Corinne Malpuech ; Pujos-Guillot, Estelle ; Berendsen, Agnes M. ; Groot, Lisette C.P.G.M. De; Feskens, Edith J.M. ; Kaluza, Joanna ; Pietruszka, Barbara ; Bielak, Marta Jeruszka ; Comte, Blandine ; Maijo-Ferre, Monica ; Nicoletti, Claudio ; Vos, Willem M. de; Fairweather-Tait, Susan ; Cassidy, Aedin ; Brigidi, Patrizia ; Franceschi, Claudio ; O'Toole, Paul W. - \ 2020
    Gut 69 (2020)7. - ISSN 0017-5749
    ageing - diet - enteric bacterial microflora - inflammation - intestinal bacteria

    Objective: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty. Design: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet). Results: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks. Conclusion: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.

    AGINFRA PLUS: Running Crop Simulations on the D4Science Distributed e-Infrastructure
    Knapen, M.J.R. ; Lokers, R.M. ; Candela, L. ; Janssen, S.J.C. - \ 2020
    In: Environmental Software Systems. - Springer (IFIP Advances in Information and Communication Technology ) - ISBN 9783030398149 - p. 81 - 89.
    Virtual Research Environments (VREs) bridge the gap between the compute and storage infrastructure becoming available as the ‘cloud’, and the needs of researchers for tools supporting open science and analytics on ever larger datasets. In the AGINFRA PLUS project such a VRE, based on the D4Science platform, was examined to improve and test its capabilities for running large numbers of crop simulations at field level, based on the WOFOST-WISS model and Dutch input datasets from the AgroDataCube. Using the gCube DataMiner component of the VRE, and based on the Web Processing Service standard, a system has been implemented that can run such workloads successfully on an available cluster, and with good performance, providing summarized results to agronomists for further analysis. The methods used and the resulting implementation are briefly described in this paper. Overall the approach seems viable and opening the door to many follow-up implementation opportunities and further research. Some of them are indicated in more detail in the conclusions.
    Using Virtual Research Environments in Agro-Environmental Research
    Lokers, R.M. ; Knapen, M.J.R. ; Candela, L. ; Hoek, S.B. ; Meijninger, W.M.L. - \ 2020
    In: Environmental Software Systems. - Springer (IFIP Advances in Information and Communication Technology ) - ISBN 9783030398149
    Tackling some of the grand global challenges, agro-environmental research has turned more and more into an international venture, where distributed research teams work together to solve complex research questions. Moreover, the interdisciplinary character of these challenges requires that a large diversity of different data sources and information is combined in new, innovative ways. There is a pressing need to support researchers with environments that allow them to efficiently work together and co-develop research. As research is often data-intensive, and big data becomes a common part of a lot of research, such environments should also offer the resources, tools and workflows that allow to process data at scale if needed. Virtual research environments (VRE), which combine working in the Cloud, with collaborative functions and state of the art data science tools, can be a potential solution. In the H2020 AGINFRA+ project, the usability of the VREs has been explored for use cases around agro-climatic modelling. The implemented pilot application for crop growth modelling has successfully shown that VREs can support distributed research teams in co-development, helps them to adopt open science and that the VRE’s cloud computing facilities allow large scale modelling applications.
    A mediterranean diet mix has chemopreventive effects in a murine model of colorectal cancer modulating apoptosis and the gut microbiota
    Piazzi, Giulia ; Prossomariti, Anna ; Baldassarre, Maurizio ; Montagna, Claudio ; Vitaglione, Paola ; Fogliano, Vincenzo ; Biagi, Elena ; Candela, Marco ; Brigidi, Patrizia ; Balbi, Tiziana ; Munarini, Alessandra ; Belluzzi, Andrea ; Pariali, Milena ; Bazzoli, Franco ; Ricciardiello, Luigi - \ 2019
    Frontiers in Oncology 9 (2019)MAR. - ISSN 2234-943X
    Chemoprevention - Colorectal cancer - Mediterranean diet - Microbiota - Omega-3

    Objectives: Unhealthy dietary patterns have been associated with colorectal cancer (CRC) onset while Mediterranean Diet (MD) has been proposed for CRC prevention. This study evaluated the effect of a Mediterranean Diet Mix (MD-MIX) on colonic tumors development in A/J mice fed a low-fat (LFD) or a high-fat western diet (HFWD), and injected with the procarcinogen azoxymethane (AOM). Materials and Methods: Forty A/J male mice were randomly assigned into four feeding arms (10 mice/arm; LFD, LFD-MD-MIX, HFWD, HFWD-MD-MIX) to be treated with AOM. Ten mice were exposed to the diets alone (Healthy LFD and Healthy HFWD) to be used as control. Tumor incidence and multiplicity were evaluated at sacrifice. Mucosal fatty acid content and urinary phenolic compounds were assayed by mass spectrometry. Apoptosis was evaluated by TUNEL assay and gene expression markers. Cell proliferation was evaluated by Ki67 immunohistochemistry. Microbiota composition was assessed at different time points by 16S RNA sequencing. Results: A tumor incidence of 100% was obtained in AOM-treated mice. The MD-MIX supplementation was able to reduce the number of colonic lesions in both LFD and HFWD-fed mice and to induce apoptosis, in particular in the LFD-MD-MIX arm. Moreover, a preventive effect on low-grade dysplasia and macroscopical lesions (>1 mm) development was found in HFWD-fed mice together with a regulation of the AOM-driven intestinal dysbiosis. Conclusions: MD-MIX was able to counteract CRC development in mice under different dietary backgrounds through the regulation of apoptosis and gut microbiota.

    Serving scientists in agri-food area by virtual research environments
    Ballis, A. ; Boizet, A. ; Candela, L. ; Castelli, D. ; Fernandez, E. ; Filter, M. ; Gunther, T. ; Kakaletris, G. ; Karampiperis, P. ; Katris, D. ; Knapen, M.J.R. ; Lokers, R.M. ; Penev, L. ; Sipos, G. ; Zervas, P. - \ 2018
    In: Proceedings - IEEE 14th International Conference on eScience. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9781538691564 - p. 405 - 406.
    Agro-climatic modelling - E-Infrastructure - Food Safety - Food Security - Virtual Research Environment

    Agri-food research calls for changes in the practices dealing with data collection, collation, processing and analytics, and publishing thus to fully benefit from and contribute to the Open Science movement. One of the major issues faced by the agri-food researchers is the fragmentation of the 'assets' that can be exploited when performing research tasks, e.g. data of interest are heterogeneous and scattered across several repositories, the tools exploited by modellers are diverse and often rely on local computing environments, the publishing practices are various and rarely aim at making available the 'whole story' with datasets, processes, workflows. This paper presents the AGINFRA+ endeavour to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the access to and use of the 'assets' of interest and promote collaboration.

    Re-evaluating the role of bacteria in gerbera vase life
    Schouten, Rob E. ; Verdonk, Julian C. ; Meeteren, Uulke van - \ 2018
    Postharvest Biology and Technology 143 (2018). - ISSN 0925-5214 - p. 1 - 12.
    Antimicrobial compounds - Elongation - Temperature - Transpiration - Water uptake
    The relation between bacteria numbers in vase water and vase life of gerbera cut flowers has recently been challenged because of reported negative effects of bactericidal compounds. This relation is investigated using two types of experiments that do not rely on antimicrobial compounds. The first type controls vase water temperature (4, 15, 22 or 28 °C) independently from air temperature (15, 22 or 28 °C) to investigate whether fresh weight behavior for two mini gerbera cultivars (‘Okidoki’ and ‘Kimsey’) is affected by bacterial growth and leaking of soluble sugars in the vase water, or by senescence of the flower head. Fresh weight loss, when compared at constant water temperatures, was higher at higher air temperatures. At higher water temperatures and constant air temperatures fresh weight loss was not higher, although bacterial levels were high enough to expect water uptake issues. Also sugar consumption in the vase water depended on water temperature. This indicates that senescence was the main reason for the decline in fresh weight for these flowers, not bacterial growth. The second type of experiments was based on adding predetermined levels of bacteria (0, 103 or 105 CFU mL−1) and sugars (0.1% glucose or 0.2% sucrose) into vase water of flowers of three large-bloomed (‘Carambole’, ‘Candela’ and ‘Iceberg’) cultivars harvested with closed stem-ends and had their scapes sterilized before the start of vase life. When bacteria were added varying types of responses were observed. ‘Carambole’ flowers showed lower water uptake and lower transpiration and, early scape bending. Petal wilting was observed for ‘Candela’ flowers. ‘Carambole’ flowers showed higher scape sugar leakage levels in the vase water while ‘Candela’ flowers had higher scape firmness. ‘Iceberg’ flowers were also affected by bacteria, resulting in early scape bending, although sugar levels in the vase water were low. Furthermore, adding sucrose and/or bacteria in the vase water of one ‘Iceberg’ and one ‘Carambole’ flower in the same flask resulted in later scape bending for ‘Iceberg’ flowers compared to having two ‘Carambole’ or two ‘Iceberg’ flowers. The results indicate that bacteria interactions with gerbera flowers depend strongly on genotype.
    Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure
    Amaral, Rafael ; Badia, Rosa M. ; Blanquer, Ignacio ; Braga-Neto, Ricardo ; Candela, Leonardo ; Castelli, Donatella ; Flann, Christina ; Giovanni, Renato De; Gray, William A. ; Jones, Andrew ; Lezzi, Daniele ; Pagano, Pasquale ; Perez-Canhos, Vanderlei ; Quevedo, Francisco ; Rafanell, Roger ; Rebello, Vinod ; Sousa-Baena, Mariane S. ; Torres, Erik - \ 2015
    Concurrency Computation 27 (2015)2. - ISSN 1532-0626 - p. 376 - 394.
    biodiversity - cloud - data infrastructure - ecological niche modelling - taxonomy - virtual research environments

    SummaryEUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity research by integrating open access data and user-friendly tools widely available in Brazil and Europe. The project deploys the EU-Brazil Hybrid Data Infrastructure that allows the sharing of hardware, software and data on-demand. This infrastructure provides access to several integrated services and resources to seamlessly aggregate taxonomic, biodiversity and climate data, used by processing services implementing checklist cross-mapping and ecological niche modelling. A Virtual Research Environment was created to provide users with a single entry point to processing and data resources. This article describes the architecture, demonstration use cases and some experimental results and validation.

    Eicosapentaenoic acid free fatty acid prevents and suppresses colonic neoplasia in colitis-associated colorectal cancer acting on Notch signaling and gut microbiota
    Piazzi, G. ; Argenio, G. D'; Prossomariti, A. ; Lembo, V. ; Mazzone, G. ; Candela, M. ; Biagi, E. ; Brigidi, P. ; Vitaglione, P. ; Fogliano, V. ; Angelo and others, L. D' - \ 2014
    International Journal of Cancer 135 (2014)9. - ISSN 0020-7136 - p. 2004 - 2013.
    inflammatory-bowel-disease - dietary fish-oil - intestinal microbiota - mouse model - docosahexaenoic acid - mice - sodium - cells - differentiation - chemoprevention
    Inflammatory bowel diseases are associated with increased risk of developing colitis-associated colorectal cancer (CAC). Epidemiological data show that the consumption of ¿-3 polyunsaturated fatty acids (¿-3 PUFAs) decreases the risk of sporadic colorectal cancer (CRC). Importantly, recent data have shown that eicosapentaenoic acid-free fatty acid (EPA-FFA) reduces polyp formation and growth in models of familial adenomatous polyposis. However, the effects of dietary EPA-FFA are unknown in CAC. We tested the effectiveness of substituting EPA-FFA, for other dietary fats, in preventing inflammation and cancer in the AOM-DSS model of CAC. The AOM-DSS protocols were designed to evaluate the effect of EPA-FFA on both initiation and promotion of carcinogenesis. We found that EPA-FFA diet strongly decreased tumor multiplicity, incidence and maximum tumor size in the promotion and initiation arms. Moreover EPA–FFA, in particular in the initiation arm, led to reduced cell proliferation and nuclear ß-catenin expression, whilst it increased apoptosis. In both arms, EPA-FFA treatment led to increased membrane switch from ¿-6 to ¿-3 PUFAs and a concomitant reduction in PGE2 production. We observed no significant changes in intestinal inflammation between EPA-FFA treated arms and AOM-DSS controls. Importantly, we found that EPA-FFA treatment restored the loss of Notch signaling found in the AOM-DSS control and resulted in the enrichment of Lactobacillus species in the gut microbiota. Taken together, our data suggest that EPA-FFA is an excellent candidate for CRC chemoprevention in CAC.
    Maintenance of a healthy trajectory of the intestinal microbiome during aging: A dietary approach
    Candela, M. ; Biagi, E. ; Brigidi, P. ; O'Toole, P.W. ; Vos, W.M. de - \ 2014
    Mechanisms of Ageing and Development 136-137 (2014). - ISSN 0047-6374 - p. 70 - 75.
    gut microbiota - fecal microbiota - immune-system - elderly-patients - human longevity - age - disease - immunosenescence - intervention - enterotypes
    Sharing an intense transgenomic metabolism with the host, the intestinal microbiota is an essential factor for several aspects of the human physiology. However, several age-related factors, such as changes diet, lifestyle, inflammation and frailty, force the deterioration of this intestinal microbiota-host mutualistic interaction, compromising the possibility to reach longevity. In this scenario, the NU-AGE project involves the development of dietary interventions specifically tailored to the maintenance of a healthy trajectory of the intestinal microbiome, counteracting all processes connected to the pathophysiology of the human aging
    BIO_SOS´ EODHaM System towards an operational Habitat Monitoring Service
    Manakos, I. ; Bollanos, S. ; Stutte, J. ; Blonda, P. ; Kosmidou, V. ; Petrou, Z. ; Mücher, C.A. ; Lucas, R. ; Dimopoulos, P. ; Jongman, R.H.G. ; Nagendra, H. ; Iasillo, D. ; Arnaud, A. ; Mairota, P. ; Honrado, J. ; Schioppa, E.P. ; Durieux, L. ; Candela, L. ; Inglada, J. - \ 2013
    Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians
    Biagi, E. ; Nylund, L. ; Candela, M. ; Ostan, R. ; Bucci, L. ; Pini, E. ; Nikkïla, J. ; Monti, D. ; Satokari, R.M. ; Franceschi, C. ; Brigidi, P. ; Vos, W.M. de - \ 2010
    PLoS ONE 5 (2010)5. - ISSN 1932-6203 - 14 p.
    ribosomal-rna gene - real-time pcr - butyrate-producing bacteria - fecal microbiota - eubacterium-limosum - human feces - human longevity - human colon - t-cells - age
    BACKGROUND: Age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections. METHODOLOGY/PRINCIPAL FINDINGS: By using the Human Intestinal Tract Chip (HITChip) and quantitative PCR of 16S rRNA genes of Bacteria and Archaea, we explored the age-related differences in the gut microbiota composition among young adults, elderly, and centenarians, i.e subjects who reached the extreme limits of the human lifespan, living for over 100 years. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment in facultative anaerobes, notably pathobionts. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammatory status, also known as inflammageing, as determined by a range of peripheral blood inflammatory markers. This may be explained by a remodelling of the centenarians' microbiota, with a marked decrease in Faecalibacterium prauznitzii and relatives, symbiotic species with reported anti-inflammatory properties. As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians. CONCLUSIONS/SIGNIFICANCE: We provide evidence for the fact that the ageing process deeply affects the structure of the human gut microbiota, as well as its homeostasis with the host's immune system. Because of its crucial role in the host physiology and health status, age-related differences in the gut microbiota composition may be related to the progression of diseases and frailty in the elderly population
    Summary and general conclusions/outcomes on the role and fate of sugars in human nutrition and health
    Arola, L. ; Luisa Bonet, M. ; Delzenne, N.M. ; Dugal, M. ; Gomez-Candela, C. ; Huyghebaert, A. ; Laville, M. ; Lingstrom, P. ; Livingstone, B. ; Palou, A. ; Pico, C. ; Sanders, T. ; Schaafsma, G. ; Baak, M.A. van; Loveren, C. van; Schothorst, E.M. van - \ 2009
    Obesity Reviews 10 (2009)S1. - ISSN 1467-7881 - p. 55 - 58.
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