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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    Enduring Behavioral Effects Induced by Birth by Caesarean Section in the Mouse
    Morais, Livia H. ; Golubeva, Anna V. ; Moloney, Gerard M. ; Moya-Pérez, Angela ; Ventura-Silva, Ana Paula ; Arboleya, Silvia ; Bastiaanssen, Thomaz F.S. ; O'Sullivan, Orla ; Rea, Kieran ; Borre, Yuliya ; Scott, Karen A. ; Patterson, Elaine ; Cherry, Paul ; Stilling, Roman ; Hoban, Alan E. ; Aidy, Sahar El; Sequeira, Ana M. ; Beers, Sasja ; Moloney, Rachel D. ; Renes, Ingrid B. ; Wang, Shugui ; Knol, Jan ; Ross, R.P. ; O'Toole, Paul W. ; Cotter, Paul D. ; Stanton, Catherine ; Dinan, Timothy G. ; Cryan, John F. - \ 2020
    Current Biology 30 (2020)19. - ISSN 0960-9822 - p. 3761 - 3774.e6.
    behavior - Caesarean section - co-housing - gut-brain axis - microbiota - microbiota gut-brain axis - prebiotics - probiotics

    Birth by Caesarean (C)-section impacts early gut microbiota colonization and is associated with an increased risk of developing immune and metabolic disorders. Moreover, alterations of the microbiome have been shown to affect neurodevelopmental trajectories. However, the long-term effects of C-section on neurobehavioral processes remain unknown. Here, we demonstrated that birth by C-section results in marked but transient changes in microbiome composition in the mouse, in particular, the abundance of Bifidobacterium spp. was depleted in early life. Mice born by C-section had enduring social, cognitive, and anxiety deficits in early life and adulthood. Interestingly, we found that these specific behavioral alterations induced by the mode of birth were also partially corrected by co-housing with vaginally born mice. Finally, we showed that supplementation from birth with a Bifidobacterium breve strain, or with a dietary prebiotic mixture that stimulates the growth of bifidobacteria, reverses selective behavioral alterations in C-section mice. Taken together, our data link the gut microbiota to behavioral alterations in C-section-born mice and suggest the possibility of developing adjunctive microbiota-targeted therapies that may help to avert long-term negative consequences on behavior associated with C-section birth mode.

    The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate!
    Dulio, Valeria ; Koschorreck, Jan ; Bavel, Bert van; Brink, Paul van den; Hollender, Juliane ; Munthe, John ; Schlabach, Martin ; Aalizadeh, Reza ; Agerstrand, Marlene ; Ahrens, Lutz ; Allan, Ian ; Alygizakis, Nikiforos ; Barcelo, Damia ; Bohlin-Nizzetto, Pernilla ; Boutroup, Susanne ; Brack, Werner ; Bressy, Adèle ; Christensen, Jan H. ; Cirka, Lubos ; Covaci, Adrian ; Derksen, Anja ; Deviller, Geneviève ; Dingemans, Milou M.L. ; Engwall, Magnus ; Fatta-Kassinos, Despo ; Gago-Ferrero, Pablo ; Hernández, Félix ; Herzke, Dorte ; Hilscherová, Klára ; Hollert, Henner ; Junghans, Marion ; Kasprzyk-Hordern, Barbara ; Keiter, Steffen ; Kools, Stefan A.E. ; Kruve, Anneli ; Lambropoulou, Dimitra ; Lamoree, Marja ; Leonards, Pim ; Lopez, Benjamin ; López de Alda, Miren ; Lundy, Lian ; Makovinská, Jarmila ; Marigómez, Ionan ; Martin, Jonathan W. ; McHugh, Brendan ; Miège, Cécile ; O’Toole, Simon ; Perkola, Noora ; Polesello, Stefano ; Posthuma, Leo ; Rodriguez-Mozaz, Sara ; Roessink, Ivo ; Rostkowski, Pawel ; Ruedel, Heinz ; Samanipour, Saer ; Schulze, Tobias ; Schymanski, Emma L. ; Sengl, Manfred ; Tarábek, Peter ; Hulscher, Dorien Ten; Thomaidis, Nikolaos ; Togola, Anne ; Valsecchi, Sara ; Leeuwen, Stefan van; Ohe, Peter von der; Vorkamp, Katrin ; Vrana, Branislav ; Slobodnik, Jaroslav - \ 2020
    Environmental Sciences Europe 32 (2020)1. - ISSN 2190-4707
    Chemical risk assessment and prioritisation - Contaminants of emerging concern - Effect-based methods - Environmental monitoring - High-resolution mass spectrometry - Non-target screening - NORMAN network - Suspect screening

    The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU. The plan is to bring chemical risk assessors and managers together with scientists to accelerate method development and the production of necessary data and knowledge, and to facilitate the transition to next-generation evidence-based risk assessment, a non-toxic environment and the European Green Deal. The NORMAN Network is an independent, well-established and competent network of more than 80 organisations in the field of emerging substances and has enormous potential to contribute to the implementation of the PARC partnership. NORMAN stands ready to provide expert advice to PARC, drawing on its long experience in the development, harmonisation and testing of advanced tools in relation to chemicals of emerging concern and in support of a European Early Warning System to unravel the risks of contaminants of emerging concern (CECs) and close the gap between research and innovation and regulatory processes. In this commentary we highlight the tools developed by NORMAN that we consider most relevant to supporting the PARC initiative: (i) joint data space and cutting-edge research tools for risk assessment of contaminants of emerging concern; (ii) collaborative European framework to improve data quality and comparability; (iii) advanced data analysis tools for a European early warning system and (iv) support to national and European chemical risk assessment thanks to harnessing, combining and sharing evidence and expertise on CECs. By combining the extensive knowledge and experience of the NORMAN network with the financial and policy-related strengths of the PARC initiative, a large step towards the goal of a non-toxic environment can be taken.

    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.

    Potentially modifiable determinants of malnutrition in older adults: A systematic review
    O'Keeffe, M. ; Kelly, M. ; O'Herlihy, E. ; O'Toole, P.W. ; Kearney, P.M. ; Timmons, S. ; O'shea, E. ; Stanton, C. ; Hickson, M. ; Rolland, Y. ; Sulmont Rossé, C. ; Issanchou, S. ; Maitre, I. ; Stelmach-Mardas, M. ; Nagel, G. ; Flechtner-Mors, M. ; Wolters, M. ; Hebestreit, A. ; Groot, L. De; De Rest, O. Van; Teh, R. ; Peyron, M.A. ; Dardevet, D. ; Papet, I. ; Schindler, K. ; Streicher, M. ; Torbahn, G. ; Kiesswetter, E. ; Visser, M. ; Volkert, D. ; O'Connor, E.M. - \ 2019
    Clinical Nutrition 38 (2019)6. - ISSN 0261-5614 - p. 2477 - 2498.
    Background & aims: Malnutrition in older adults results in significant personal, social, and economic burden. To combat this complex, multifactorial issue, evidence-based knowledge is needed on the modifiable determinants of malnutrition. Systematic reviews of prospective studies are lacking in this area; therefore, the aim of this systematic review was to investigate the modifiable determinants of malnutrition in older adults. Methods: A systematic approach was taken to conduct this review. Eight databases were searched. Prospective cohort studies with participants of a mean age of 65 years or over were included. Studies were required to measure at least one determinant at baseline and malnutrition as outcome at follow-up. Study quality was assessed using a modified version of the Quality in Prognosis Studies (QUIPS) tool. Pooling of data in a meta-analysis was not possible therefore the findings of each study were synthesized narratively. A descriptive synthesis of studies was used to present results due the heterogeneity of population source and setting, definitions of determinants and outcomes. Consistency of findings was assessed using the schema: strong evidence, moderate evidence, low evidence, and conflicting evidence. Results: Twenty-three studies were included in the final review. Thirty potentially modifiable determinants across seven domains (oral, psychosocial, medication and care, health, physical function, lifestyle, eating) were included. The majority of studies had a high risk of bias and were of a low quality. There is moderate evidence that hospitalisation, eating dependency, poor self-perceived health, poor physical function and poor appetite are determinants of malnutrition. Moderate evidence suggests that chewing difficulties, mouth pain, gum issues co-morbidity, visual and hearing impairments, smoking status, alcohol consumption and physical activity levels, complaints about taste of food and specific nutrient intake are not determinants of malnutrition. There is low evidence that loss of interest in life, access to meals and wheels, and modified texture diets are determinants of malnutrition. Furthermore, there is low evidence that psychological distress, anxiety, loneliness, access to transport and wellbeing, hunger and thirst are not determinants of malnutrition. There appears to be conflicting evidence that dental status, swallowing, cognitive function, depression, residential status, medication intake and/or polypharmacy, constipation, periodontal disease are determinants of malnutrition. Conclusion: There are multiple potentially modifiable determinants of malnutrition however strong robust evidence is lacking for the majority of determinants. Better prospective cohort studies are required. With an increasingly ageing population, targeting modifiable factors will be crucial to the effective treatment and prevention of malnutrition.
    Miscanthus biochar had limited effects on soil physical properties, microbial biomass, and grain yield in a four-year field experiment in Norway
    O’toole, Adam ; Moni, Christophe ; Weldon, Simon ; Schols, Anne ; Carnol, Monique ; Bosman, Bernard ; Rasse, Daniel P. - \ 2018
    Agriculture 8 (2018)11. - ISSN 2077-0472
    Biochar - Miscanthus - Norway

    The application of biochar to soils is a promising technique for increasing soil organic C and offsetting GHG emissions. However, large-scale adoption by farmers will likely require the proof of its utility to improve plant growth and soil quality. In this context, we conducted a four-year field experiment between October 2010 to October 2014 on a fertile silty clay loam Albeluvisol in Norway to assess the impact of biochar on soil physical properties, soil microbial biomass, and oat and barley yield. The following treatments were included: Control (soil), miscanthus biochar 8 t C ha−1 (BC8), miscanthus straw feedstock 8 t C ha−1 (MC8), and miscanthus biochar 25 t C ha−1 (BC25). Average volumetric water content at field capacity was significantly higher in BC25 when compared to the control due to changes in BD and total porosity. The biochar amendment had no effect on soil aggregate (2–6 mm) stability, pore size distribution, penetration resistance, soil microbial biomass C and N, and basal respiration. Biochar did not alter crop yields of oat and barley during the four growing seasons. In order to realize biochar’s climate mitigation potential, we suggest future research and development efforts should focus on improving the agronomic utility of biochar in engineered fertilizer and soil amendment products.

    Publisher Correction : Enterotypes in the landscape of gut microbial community composition
    Costea, Paul I. ; Hildebrand, Falk ; Arumugam, Manimozhiyan ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O’Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2018
    Nature Microbiology 3 (2018). - ISSN 2058-5276
    In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
    Selected aspects of the human gut microbiota
    Ventura, Marco ; O’Toole, Paul W. ; Vos, Willem M. de; Sinderen, Douwe van - \ 2018
    Cellular and Molecular Life Sciences 75 (2018)1. - ISSN 1420-682X - p. 81 - 82.
    Diet & health - Gut commensals - Microbiome - Microbiota - Probiotic

    The gut microbiota represents a highly complex assembly of microbes, which interact with each other and with their host. These interactions have various implications in terms of health and disease, and this multi-author review issue will address a number of selected aspects pertaining to gut microbiota research.

    Enterotypes in the landscape of gut microbial community composition
    Costea, Paul I. ; Hildebrand, Falk ; Manimozhiyan, Arumugam ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O'Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2017
    Nature Microbiology 3 (2017)1. - ISSN 2058-5276 - p. 8 - 16.
    Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
    Hoe de implementatiekloof te dichten? Een analyse voor perspectieven in het overstromingsbeleid
    Coninx, I. - \ 2017
    KU Leuven. Promotor(en): Marleen, prof. dr. Brans. - Leuven : KU Leuven - 316
    Als overheidsbeleid de gestelde doelen niet haalt, dan is er sprake van een implementatiekloof (Laurian & Crawford, 2016). Ook het Vlaams overstromingsbeleid lijkt een implementatiekloof te kennen, want ondanks een palet aan preventieve, effectgerichte en curatieve overstromingsmaatregelen wordt de schade door overstromingen jaarlijks nog op zo een 50 miljoen euro geschat (Brouwers et al., 2015). Implementatie is in feite gedrag (O'Toole Jr, 2000; Robichau & Lynn Jr, 2009) en gedrag wordt ingegeven door houdingen (Ajzen, 1991; Fishbein & Ajzen, 1975). Daarom wil dit onderzoek nagaan of houdingen van betrokken beleidsactoren een rol spelen bij de implementatie van overstromingsmaatregelen (hoofdstuk 2). Beleidsactoren van 26 organisaties of groepen geven het Vlaams overstromingsbeleid een echt multiactor-, multisector- en multilevelkarakter (hoofdstuk 1). Het onderzoek beantwoordt enkele vragen over houdingen, zoals of ze een rol spelen bij de uitvoering, welke verschillende houdingen er zijn, hoe die houdingen bepaald worden en wat de dominante evaluatiecriteria zijn. Op basis van die inzichten worden mechanismen ontwikkeld om de implementatiekloof te dichten. Vervolgens worden perspectieven voor het Vlaams overstromingsbeleid beschreven. De analyse vond plaats voor 15 overstromingsmaatregelen bij 347 actoren en in 3 casegebieden in Vlaanderen. Dit gebeurde via verschillende dataverzameling- en data-analysemethoden om triangulatie op vele fronten te waarborgen (hoofdstuk 3).De analyse toont dat houdingen een rol spelen, want veel beleidsactoren staan nog negatief tegenover bepaalde overstromingsmaatregelen met een ruimtelijke impact (hoofdstuk 4). Diverse ‘evaluatiecriteria’ – criteria, gebruikt om houding te bepalen tijdens de evaluatieve afweging – bepalen die houdingen. Ten eerste worden houdingen gevormd door belangen en hebben mensen een positieve houding ten aanzien van maatregelen die hun baten opleveren (Gintis, 2000; Henrich et al., 2001; Jager, Janssen, De Vries, De Greef, & Vlek, 2000; Persky, 1995). Ten tweede worden houdingen bepaald door waarden, wat richtinggevende principes zijn van wat volgens de mens wenselijk en juist is (Kempton, Boster, & Hartley, 1995). Men heeft positieve houding ten aanzien van maatregelen die in lijn liggen met zijn waarden. Ten derde worden houdingen gevormd door denkkaders en percepties (Bartlett, 1932; Benford & Snow, 2000; Berger & Luckmann, 1966). Dat zijn cognitieve voorstellingen die gebruikt worden om betekenis te geven aan informatie (Buijs, 2009b; Minsky, 1975). Percepties spelen altijd een rol bij houdingbepaling, zo blijkt ook uit de analyse (hoofdstuk 5).De combinatie van evaluatiecriteria vormt een verhaallijn, die toe te kennen is aan elk van de actoren. Elke overstromingsmaatregel kent verschillende verhaallijnen. Hoe meer verhaallijnen, hoe meer divers de evaluatiecriteria die elke actor gebruikt. In dit onderzoek is vooral nagegaan waar spanning optreedt tussen de verhaallijnen en welke evaluatiecriteria aan de basis liggen van de negatieve houdingen (hoofdstuk 5). In het Vlaams overstromingsbeleid verklaren vooral percepties en waarden de implementatiekloof. Zelfs over het huidige beleidsparadigma ‘ruimte voor water’ bestaan er twee verschillende percepties: ‘ruimte maken’ en ‘ruimte vinden’ voor water. Die twee percepties weerspiegelen de bereidheid van mensen om het huidige ruimtegebruik aan te passen. Die percepties en andere fundamentele verschillen houden de uitvoering van het overstromingsbeleid in de tang. Het valt op dat binnen één actorgroep veel verschillende verhaallijnen te vinden zijn. Dat leidt tot vragen of het systeem van sectorale vertegenwoordiging in de CIW en de bekkenraden wel goed genoeg kan werken.Er is ook gekeken welk type evaluatiecriteria de actoren vooral gebruiken om houding te bepalen. De meeste actoren laten zich leiden door hun waarden. Alleen de sector ‘landbouw’ en actoren van het Vlaamse/nationale niveau gebruiken vooral belangengerichte evaluatiecriteria (hoofdstuk 6).Wetende dat houdingen een rol spelen bij de implementatiekloof, rest de vraag welke mechanismen kunnen helpen om de implementatiekloof te dichten? Allereerst is het raadzaam om de actoren die een rol spelen bij de uitvoering, al te betrekken bij het interactieve beleidsontwikkelingsproces. Door interactie en cocreatie worden nieuwe inzichten ontwikkeld, kennis uitgewisseld en belangen, waarden en percepties gedeeld (Ter Haar, Aarts, & Verhoeven, 2016). Als bestaande verhaallijnen beter op elkaar afgestemd geraken of mensen verschuiven naar één dominante verhaallijn, dan helpt dat om de implementatiekloof te voorkomen (Hajer, 2005). Bij de uitvoering van de maatregelen helpen interactieve beleidsinstrumenten om gezamenlijke actie tot stand te brengen. Dat is iets dat niet snel gebeurd wanneer beleidsinstrumenten zoals gezag of geld worden ingezet. (Tabel 1: mechanismen om implementatiekloof te dichten) Er wordt vastgesteld dat nog maar weinig van die mechanismen ingebouwd werden in het overstromingsbeleid, aangezien een betekenisvolle proportie actoren zich nog bevindt in de verhaallijn die overeenkomt met het ‘oude paradigma’ van ‘strijden tegen water’. Om de verschillen tussen de evaluatiecriteria te kennen, is het aan te raden om de verhaallijnen te verkennen via interviews en analyse van documenten (= mapping van verhaallijnen) (Kolkman, Veen, & Geurts, 2007).Wetenschap kan een rol spelen bij het dichten van de implementatiekloof, vooral als die verklaard wordt door percepties (Leeuwis & Aarts, 2016; Van Bommel, Röling, Aarts, & Turnhout, 2009), op voorwaarde dat de betrokken actoren de wetenschappelijke kennis beschouwen als gelegitimeerd, geloofwaardig en begrijpelijk (Cash et al., 2003). Anders zal de kennis in twijfel getrokken of zelfs misbruikt worden om specifieke verhaallijnen te ontkrachten. Bovendien zijn er ook andere typen van kennis dan louter wetenschappelijke. ‘Boundary organisations’ kunnen wetenschappelijke kennis inbrengen en zo de implementatiekloof dichten (Guston, 2001). Men moet er wel bewust van zijn dat machtsrelaties het succes van de genoemde mechanismen kunnen beïnvloeden (Van Bommel et al., 2009).Op basis van deze mechanismen zijn vervolgens perspectieven voor de verdere ontwikkeling van het overstromingsbeleid geformuleerd. Het eerste perspectief richt zich op het versterken van bestaande overstromingsmaatregelen via beperkte interventies zoals participatieve monitoring en bespreken en communiceren van (wetenschappelijk) bevindingen. Het tweede perspectief omvat meer ingrijpende interventies, zoals de formele introductie van meerlaagse veiligheid in het beleid, de versterking van de dialoog tussen verhaallijnen in de bekkenorganen en maatregelen om te komen tot een passende verantwoordelijkheidsverdeling tussen overheid en burger, zoals een meerjarig pilotprogramma. De resultaten van dat pilotprogramma kunnen dan geformaliseerd worden in beleidsdocumenten.De algemene conclusie is dat houdingen van betrokken actoren één van de verklaringen kunnen zijn voor een implementatiekloof. Het onderzoek laat zien dat die houdingen kunnen verschillen, maar ook dat houdingen veranderlijk zijn. Daarom is actieve sturing op die houdingverandering een absolute must voor het beleid om zo de implementatiekloof te dichten en zelfs te voorkomen.
    SUN-LB306: Potentially Modifiable Determinants of Malnutrition in Older Adults: A Systematic Review
    O’Keeffe, M. ; Kelly, M. ; O’Herlihy, E. ; O’Toole, P. ; Kearney, P. ; Timmons, S. ; Stanton, C. ; Rolland, Y. ; Sulmont Rosse, C. ; Maitre, I. ; Boeing, H. ; Stelmach, M. ; Nagel, G. ; Wolters, M. ; Hebestreit, A. ; Groot, C.P.G.M. De; Teh, R. ; Agnes Peyron, M. ; Dardevet, D. ; Papet, I. ; Streicher, M. ; Torbahn, G. ; Kiesswetter, E. ; Visser, M. ; Volkert, D. ; O’Connor, E. - \ 2017
    Clinical Nutrition 36 (2017)Supplement 1. - ISSN 0261-5614 - p. S167 - S167.
    Towards standards for human fecal sample processing in metagenomic studies
    Costea, Paul I. ; Zeller, Georg ; Sunagawa, Shinichi ; Pelletier, Eric ; Alberti, Adriana ; Levenez, Florence ; Tramontano, Melanie ; Driessen, Marja ; Hercog, Rajna ; Jung, Ferris Elias ; Kultima, Jens Roat ; Hayward, Matthew R. ; Coelho, Luis Pedro ; Allen-Vercoe, Emma ; Bertrand, Laurie ; Blaut, Michael ; Brown, Jillian R.M. ; Carton, Thomas ; Cools-Portier, Stéphanie ; Daigneault, Michelle ; Derrien, Muriel ; Druesne, Anne ; Vos, Willem M. De; Finlay, B.B. ; Flint, Harry J. ; Guarner, Francisco ; Hattori, Masahira ; Heilig, Hans ; Luna, Ruth Ann ; Hylckama Vlieg, Johan Van; Junick, Jana ; Klymiuk, Ingeborg ; Langella, Philippe ; Chatelier, Emmanuelle Le; Mai, Volker ; Manichanh, Chaysavanh ; Martin, Jennifer C. ; Mery, Clémentine ; Morita, Hidetoshi ; O'Toole, Paul W. ; Orvain, Céline ; Patil, Kiran Raosaheb ; Penders, John ; Persson, Søren ; Pons, Nicolas ; Popova, Milena ; Salonen, Anne ; Saulnier, Delphine ; Scott, Karen P. ; Singh, Bhagirath ; Slezak, Kathleen ; Veiga, Patrick ; Versalovic, James ; Zhao, Liping ; Zoetendal, Erwin G. ; Ehrlich, S.D. ; Dore, Joel ; Bork, Peer - \ 2017
    Nature Biotechnology 35 (2017)11. - ISSN 1087-0156 - p. 1069 - 1076.
    Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
    Towards the review of the European Union Water Framework management of chemical contamination in European surface water resources
    Brack, Werner ; Dulio, Valeria ; Ågerstrand, Marlene ; Allan, Ian ; Altenburger, Rolf ; Brinkmann, Markus ; Bunke, Dirk ; Burgess, Robert M. ; Cousins, Ian ; Escher, Beate I. ; Hernández, Félix J. ; Hewitt, L.M. ; Hilscherová, Klára ; Hollender, Juliane ; Hollert, Henner ; Kase, Robert ; Klauer, Bernd ; Lindim, Claudia ; Herráez, David López ; Miège, Cécil ; Munthe, John ; O'Toole, Simon ; Posthuma, Leo ; Rüdel, Heinz ; Schäfer, Ralf B. ; Sengl, Manfred ; Smedes, Foppe ; Meent, Dik van de; Brink, Paul J. van den; Gils, Jos van; Wezel, Annemarie P. van; Vethaak, A.D. ; Vermeirssen, Etienne ; Ohe, Peter C. von der; Vrana, Branislav - \ 2017
    Science of the Total Environment 576 (2017). - ISSN 0048-9697 - p. 720 - 737.
    Chemical legislation - Effect-based tools - Passive sampling - Prioritization of contaminants - Solution-oriented management - Water Framework Directive review

    Water is a vital resource for natural ecosystems and human life, and assuring a high quality of water and protecting it from chemical contamination is a major societal goal in the European Union. The Water Framework Directive (WFD) and its daughter directives are the major body of legislation for the protection and sustainable use of European freshwater resources. The practical implementation of the WFD with regard to chemical pollution has faced some challenges. In support of the upcoming WFD review in 2019 the research project SOLUTIONS and the European monitoring network NORMAN has analyzed these challenges, evaluated the state-of-the-art of the science and suggested possible solutions. We give 10 recommendations to improve monitoring and to strengthen comprehensive prioritization, to foster consistent assessment and to support solution-oriented management of surface waters. The integration of effect-based tools, the application of passive sampling for bioaccumulative chemicals and an integrated strategy for prioritization of contaminants, accounting for knowledge gaps, are seen as important approaches to advance monitoring. Including all relevant chemical contaminants in more holistic “chemical status” assessment, using effect-based trigger values to address priority mixtures of chemicals, to better consider historical burdens accumulated in sediments and to use models to fill data gaps are recommended for a consistent assessment of contamination. Solution-oriented management should apply a tiered approach in investigative monitoring to identify toxicity drivers, strengthen consistent legislative frameworks and apply solutions-oriented approaches that explore risk reduction scenarios before and along with risk assessment.

    Field applications of pure biochar in the North Sea region and across Europe
    Ruysschaert, Greet ; Nelissen, Victoria ; Postma, Romke ; Bruun, Esben ; O'Toole, Adam ; Hammond, Jim ; Rödger, Jan Markus ; Hylander, Lars ; Kihlberg, Tor ; Zwart, Kor ; Hauggaard-Nielsen, Henrik ; Shackley, Simon - \ 2016
    In: Biochar in European Soils and Agriculture: Science and Practice / Shackley, Simon, Ruysschaert, Greet, Zwart, Kor, Glaser, Bruno, Taylor and Francis Inc. - ISBN 9780415711661 - p. 99 - 135.
    As demonstrated by several scientific studies there is no doubt that biochar in general is very recalcitrant compared to other organic matter additions and soil organic matter fractions and also that it is possible to sequester carbon at a climate change relevant time scale (~100 years or more) by soil application of biochar. However, the carbon stability of biochar in soil is strongly correlated with the degree of thermal alteration of the original feedstock (the lower the temperature, the larger the labile fraction) and in depth understanding of the technology used and its effect on the biochar quality is necessary in order to produce the most beneficial biochars for soil application. Beside carbon sequestration in soil biochar may improve the GHG balance by reducing N2O and CH4 soil emissions, although contrasting results are found in the literature. The mechanisms behind these reductions remain unclear and more research is required in order to investigate the various hypotheses in more detail, and to unravel the complex interaction between biochar, crop and soil, especially under field conditions. In conclusion, our current knowledge is largely based on short-term lab studies and pot experiments, which have provided detailed insight in certain processes and aspects of biochar application to soils, but suffer from large uncertainties when scaled-up to the farmers field level. In order to produce more realistic scenarios of the potential impact of biochar on C sequestration and soil GHG emissions there is a need to bring biochar research up to the field-scale, and to perform longer-term studies.
    Studying the Mammalian Intestinal Microbiome Using Animal Models
    Hugenholtz, F. ; Zhang, J. ; O'Toole, P.W. ; Smidt, H. - \ 2016
    In: Manual of Environmental Microbiology / Yates, Marylyn V., Nakatsu, Cindy H., Miller, Robert V., Pillai, Suresh D., Washington DC : ASM Press - ISBN 9781555816025 - p. 4.4.2 - 1-4.4.2-10.
    The gastrointestinal (GI) tract of humans and animals is colonized by microorganisms immediately after birth. The composition of the GI tract microbiota undergoes remarkable alterations during early age, reaches a relative stable status in adulthood, and is driven by external factors such as habitual diet, location along the intestine, antibiotic therapy and maternal microbiota, and intrinsic factors such as host species and genotype. Whereas usually faecal samples are used for assessing the impact on the microbiota in human intervention studies, in vitro and animal models provide an easier way to collect many (invasive) samples, have multiple comparisons and regulating the genotype background. Animal models, and in particular mammalian models, provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract, including studies that aim to see the impact of the host system as well. The main animals used to study the mammalian GI tract are rodents (mainly mice and rats) and pigs. Rodent and pig models, including gnotobiotic and humanized rodents and pigs and minipigs, have been extensively employed in gut microbiota studies, and especially the piglet model has been suggested as an appropriate model for human infant studies. With pig models, several intestinal sampling techniques can be applied in kinetic microbiota studies, including small intestinal segment perfusion and cannulation. In many cases, to test a certain treatment, a tiered approach consisting of complementary methods is employed, comprising in vitro, in vivo animal models, eventually leading towards human intervention studies.
    Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
    Sun, Z. ; Harris, H.M.B. ; McCann, A. ; Guo, C. ; Argimón, S. ; Zhang, W. ; Yang, X. ; Jeffery, I.B. ; Cooney, J.C. ; Kagawa, T.F. ; Liu, W. ; Song, Y. ; Salvetti, E. ; Wrobel, A. ; Rasinkangas, P. ; Parkhill, J. ; Rea, M.C. ; O'Sullivan, O. ; Ritari, J. ; Douillard, F.P. ; Paul Ross, R. ; Yang, R. ; Briner, A.E. ; Felis, G.E. ; Vos, W.M. de; Barrangou, R. ; Klaenhammer, T.R. ; Caufield, P.W. ; Cui, Y. ; Zhang, H. ; O'Toole, P.W. - \ 2015
    Nature Communications 6 (2015). - ISSN 2041-1723 - 13 p.
    Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species
    The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota
    Scanlan, P.D. ; Stensvold, C.R. ; Rajilic-Stojanovic, M. ; Heilig, H.G. ; Vos, W.M. de; O'Toole, P.W. ; Cotter, P.D. - \ 2014
    FEMS microbiology ecology 90 (2014)1. - ISSN 0168-6496 - p. 326 - 330.
    genetic diversity - cysteine proteases - subtypes - bacterial - insights - animals - fungi - cells
    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10 years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine.
    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
    Diet-microbiota-health interactions in older persons - the ELDERMET study and probing causality in the NuAge project
    O'Toole, P.W. ; Vos, W.M. de; Brigidi, P. - \ 2013
    In: 20th International Congress of Nutrition (ICN), Granada, Spain, 15 - 20 September, 2013. - Granada, Spain : Karger - p. 41 - 41.
    Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
    Claesson, M.J. ; O'Sullivan, O. ; Wang, Q. ; Nikkilä, J. ; Marchesi, J.R. ; Smidt, H. ; Vos, W.M. de; Ross, R.P. ; O'Toole, P.W. - \ 2009
    PLoS ONE 4 (2009)8. - ISSN 1932-6203 - 15 p.
    BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. METHODS AND FINDINGS: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400-1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. CONCLUSIONS: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genus-level with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult
    Interactive policy-making in the Netherlands
    Oosterveld, H.J.W. ; (Grondmij) Pullen, H. - \ 1998
    In: Par- ticipation and the Quality of Environmental Decision Making / Coenen, F.H.J.M., Huitema, D., O'Toole, L.J.,
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