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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Afrikaanse varkenspest
Loeffen, W.L.A. - \ 2018
Wageningen : Wageningen University & Research - 1 p.
animal welfare - wild animals - wild pigs - animal production - pigs - animal health - african swine fever
Insecten als voer en voedsel
Veldkamp, T. - \ 2018
Wageningen : Wageningen UR Livestock Research - 2 p.
animal welfare - animal production - poultry - pigs - fish - animal nutrition
Boars with balls
Backus, Ge - \ 2018
animal welfare - animal production - pigs - animal behaviour - animal ethics - animal health - castration
Nieuwe eisen voor varkensstallen
Vermeer, Herman - \ 2018
animal welfare - animal production - pigs - animal housing - animal health
De dilemma’s van niet-gecoupeerde staarten
Duteweerd, Theo - \ 2017
Wageningen : Livestock Stories blog, Wageningen University & Research
animal welfare - animal production - pigs - animal health - animal behaviour - legislation - policy
8 gamechangers voor een duurzame productie van gezond en veilig voedsel
Vogelezang, J.V.M. ; Angelino, Steven ; Dubbeldam, Ria - \ 2017
Topsector Agri & Food - 13 p.
animal welfare - animal production - cattle - pigs - poultry - animal ethics - animal housing
Stressvrij omgaan met varkens
Ruis, Markus - \ 2017
animal welfare - animal production - pigs - animal behaviour - animal health - housing - animal housing
Groepskraamhok goed voor de big: Resultaten promotie-onderzoek leiden tot vervolgonderzoek door bedrijfsleven en WUR
Nieuwamerongen, Sofie van; Peet-Schwering, Carola van der - \ 2017
animal welfare - animal health - pigs - piglets - animal production - animal housing

Het groepskraamhok bevordert de bigontwikkeling. Dat concludeert promovendus Sofie van Nieuwamerongen in haar proefschrift. Voor het bedrijfsleven zijn de resultaten van haar promotieonderzoek aanleiding om samen met Wageningen University & Research vervolgonderzoek te doen.

Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Kamminga, Tjerko - \ 2017
Wageningen University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Peter Schaap; J.J.E. Bijlsma. - Wageningen : Wageningen University - ISBN 9789463436519 - 152
interdisciplinary research - molecular biology - mycoplasma hyopneumoniae - vaccines - systems biology - systems analysis - pigs - pneumonia - animals - interdisciplinair onderzoek - moleculaire biologie - vaccins - systeembiologie - systeemanalyse - varkens - longontsteking - dieren

Mycoplasma hyopneumoniae (M. hyopneumoniae) is a bacterial pathogen that has evolved from a gram-positive ancestor and specifically colonizes the lower respiratory tract of pigs where it causes enzootic pneumonia and plays a major role in the development of respiratory disease in pigs. Whole-cell inactivated vaccines are available that lower the severity of disease and are widely applied in pig industry to prevent clinical signs and improve pig herd health. However, production of these vaccines is challenging because it is not known which bacterial components are needed for protection and complex cultivation media are needed because growth requirements are not completely understood. The aim of this thesis was to understand growth and survival strategies of M. hyopneumoniae during infection, to integrate this knowledge with metabolic modeling under conditions used for vaccine production and apply this knowledge to improve the current production process for M. hyopneumoniae vaccines.

Chapter 1 provides a general introduction into the disease, treatment and prevention methods with a focus on vaccines. I then introduce the characteristics of the M. hyopneumoniae genome, transcriptome and review the current knowledge on infectious mechanisms and the response of the pig to infection and vaccination. Finally, I discuss the challenges related to vaccine production and introduce systems biology tools that will be applied in the thesis. In chapter 2 we define a strategy for risk-based process development of bacterial vaccines which provided the framework for future studies performed during this thesis. We propose to integrate the academic workflow for rational strain design with the industry standard for process design. Systems biology tools, especially genome-scale metabolic models, play an essential role in this strategy because application of these tools reduces process risks and increases process understanding. Therefore, in line with this strategy, we created a manually curated genome-scale metabolic model of M. hyopneumoniae which we applied to dynamically model the cultivation step in the vaccine production process (chapter 3). We found that only 16% of cellular energy in a standard fermentation was used for growth and 84% was used for non-growth associated maintenance. By model-driven experimentation we were able to increase the fraction of cellular energy used for growth by addition of pyruvate to the production medium, and showed in dedicated fermentor experiments that the improved process reached a 2.3 times higher biomass yield. Although the metabolic model helped to increase process yield, it did not allow prediction of a defined cultivation medium without components from porcine origin. Therefore, to better understand the dependency of M. hyopneumoniae on host derived components, we performed a functional comparison of 80 mycoplasma genomes and used multivariate and machine-learning algorithms to relate functional capability to the specific host and niche of mycoplasma species (chapter 4). This analysis allowed us to identify protein domains possibly needed for growth and survival in the pig lung. In addition, we found that protein domains expected to be essential for bacterial growth were not persistently present in mycoplasma genomes suggesting that alternative domain configurations exist that bypass their essentiality. To better understand whether the proteins we identified as possibly important for survival in pigs actually play a role during M. hyopneumoniae infection, we sequenced the bacterial mRNA during infection in chapter 5 and compared the in vivo transcriptome to that of broth grown mycoplasma. We found 22 up-regulated and 30 down-regulated genes during infection (FDR<0.01 and fold change >2LOG2) and identified differentially expressed ncRNAs. In chapter 6 we build upon our mycoplasma basis to further analyse the role of ncRNAs in bacterial genomes. We identified an exponential relationship between the AT content of genomes and the number of ncRNAs and propose that this relation is the result of spurious transcription, which is more likely to occur in AT rich genomes. This hypothesis is further substantiated by showing that spurious transcription demands minimal cellular energy and that overexpression of cis-binding ncRNAs in M. pneumoniae did not influence the level of proteins translated from their overlapping mRNAs. Finally, in chapter 7 I discuss four system strategies, identified in this thesis and derived from recent literature, and discuss how these strategies could be integrated in the metabolic model of M. hyopneumoniae. Lastly, I provide an outlook on the next steps needed for improvement of the production process for M. hyopneumoniae vaccines.

In conclusion, this work provided novel insight in the metabolic capability of M. hyopneumoniae based on the proteome domain content, captured in a genome-scale metabolic model and studied under in vitro and in vivo conditions. Biomass yield of the cultivation step for vaccine production was increased and the basis was laid to further improve the production process for M. hyopneumoniae vaccines using model-based experimentation.

Stadsvarkens als schakel in de circulaire economie
Vijn, M.P. - \ 2017
Ekoland 37 (2017)10. - ISSN 0926-9142 - p. 24 - 25.
varkens - varkenshouderij - stadslandbouw - cradle to cradle - wetgeving - reststromen - voedselveiligheid - varkensvlees - pigs - pig farming - urban agriculture - legislation - residual streams - food safety - pigmeat
Aan welke regelgeving moet je voldoen om varkens in de stad te houden en te voeden met reststromen? Wageningen University & Research heeft hier onderzoek naar gedaan voor de Stichting Stadsvarkens in Ede. Deze stichting heeft als doelstelling het realiseren van een lokale circulaire economie door de inzet van (stads)varkens en de educatie hierover.
Monitoring verduurzaming veehouderij 1.0 : een eerste proeve van een Monitorings-systematiek voor de 15 ambities van de Uitvoeringsagenda Duurzame Veehouderij, met initiële resultaten voor drie diersectoren en een aantal keteninitiatieven
Bos, A.P. ; Puente-Rodríguez, Daniel ; Reijs, Joan W. ; Peet, G.F.V. van der; Groot Koerkamp, Peter W.G. - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1045) - 113
dierenwelzijn - dierlijke productie - melkvee - varkens - pluimvee - huisvesting, dieren - diergezondheid - diergedrag - animal welfare - animal production - dairy cattle - pigs - poultry - animal housing - animal health - animal behaviour
In 2013, the governance network UDV formulated fifteen ambitions towards a sustainable livestock production. In this way, the UDV’s stakeholders defined the long-term goals of an integrated and sustainable livestock production. To what extent have these 15 ambitions been achieved? And, how substantial is the contribution of supra-legal initiatives to this process? In this report, we present the first elaboration of a monitoring system that enables the visualization of the progress made. Moreover, it also enables comparing the different livestock production systems and creates the basis for a comparison between conventional animal production and supra-legal initiatives. In this concept-report the system is applied initially to the three larger livestock production sectors in the Netherlands (i.e., dairy, pigs, and poultry) and –as far as enough data is available– to four supra-legal initiatives. The system is currently under construction. Particularly because it involves interpretation and a number of value-laden choices that –notwithstanding their current support by arguments and references to the literature– should become shared and supported by (at least) the UDV stakeholders in the near future.
Evaluatie Actieplan Stalbranden 2012-2016
Bokma-Bakker, Martien ; Bokma, Sjoerd ; Ellen, Hilko ; Hagen, René ; Ruijven, Charlotte van - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1035) - 80
dierenwelzijn - dierlijke productie - diergezondheid - pluimvee - varkens - melkvee - schapen - geiten - paarden - stallen - brand - voorkomen van branden - veiligheid - animal welfare - animal production - animal health - poultry - pigs - dairy cattle - sheep - goats - horses - stalls - fire - fire prevention - safety
Elearning Cursus mens-dier interactie in de varkenshouderij
Ruis, M.A.W. - \ 2017
Wageningen : Wageningen Livestock Research - 2 p.
dierenwelzijn - dierlijke productie - varkens - diergedrag - diergezondheid - huisvesting, dieren - varkenshouderij - gedrag - behandeling - animal welfare - animal production - pigs - animal behaviour - animal health - animal housing - pig farming - behaviour - treatment
Hoe ervaart een varken de omgeving? En waarom is het van belang om hierbij stil te staan? Deze cursus richt zich op het belang van een goede mens-dier relatie, waarbij onder andere gekeken wordt naar de manier waarop een varken de wereld ervaart. Dit geeft inzicht in de manier van omgang, met als gevolg minder stress voor dier én mens. Het doel is een win-win situatie; het bevorderen van dierge - zondheid en dierenwelzijn dat onder andere zorgt voor meer werkplezier en meer benutting van het productie potentieel van het varken.
Systeemomschrijving “Plateau 2.0”
Hoofs, Anita - \ 2017
Wageningen : Wageningen Livestock Research - 5
dierenwelzijn - varkens - huisvesting, dieren - diergezondheid - diergedrag - animal welfare - pigs - animal housing - animal health - animal behaviour
En varkenshok met plateau is een hok waarin varkens vrij beschikken over twee verblijfsniveaus, één op de begane grond en één op het plateau. Varkens kunnen gemakkelijk het plateau op - en aflopen via een trap. Bij toepassing van een plateau, dat voldoet aan de systeemomschrijving, mag het beschikbare vloeroppervlak van het plateau als beschikbaar vloeroppervlak meegerekend worden.
Simulating pigs : Understanding their motivations, behaviour, welfare and productivity
Boumans, Iris - \ 2017
Wageningen University. Promotor(en): Imke de Boer, co-promotor(en): Eddy Bokkers; Gert Jan Hofstede. - Wageningen : Wageningen University - ISBN 9789463432122 - 200
pigs - pig farming - sustainability - motivation - animal behaviour - behaviour disorders - animal welfare - simulation models - animal production - varkens - varkenshouderij - duurzaamheid (sustainability) - motivatie - diergedrag - gedragsstoornissen - dierenwelzijn - simulatiemodellen - dierlijke productie

The transition towards sustainable pig production systems is receiving increasing attention nowadays. Pig behaviour plays a central role in sustainability, as it is an important indicator for pig welfare and can also affect other sustainability issues. Understanding behaviour and related welfare consequences requires to understand motivations underlying behaviour. The two aims of this thesis were: 1) to assess the use of agent-based modelling for understanding pig behaviour and underlying motivation, and 2) to apply agent-based modelling for increasing our understanding of pig behaviour, and related animal welfare and productivity performance.

We first explored the use of agent-based modelling with tail biting behaviour in pigs as a case study. An agent-based model was developed to understand the causation of tail biting behaviour. Subsequently, we developed a mechanistic and dynamic simulation model to gain more understanding of feeding behaviour and internal (physiological) factors. The model integrates knowledge from physiology and ethology, and combines growth with a behavioural decision model based on motivation. This model included motivations underlying feeding behaviour and various feeding patterns of an individually housed growing pig. To deepen our understanding of mechanisms underlying feeding patterns of pigs within 24 hours, hormonal circadian rhythms were included in the model in a follow-up study. The circadian rhythms of cortisol and melatonin explained the alternans pattern, a small peak of feed intake at the beginning of the day and a larger peak at the end of the day, of feeding in pigs. Next, an agent-based model of feeding and social interaction in commercially group-housed pigs was developed to deepen our understanding of the complex interaction between internal physiological factors and external social factors. Social factors (e.g. competition level and social facilitation) and behavioural strategies (e.g. avoidance and approach) affected social interactions among pigs and feeding behaviour. The causation of variation among pigs was further explored in this model. Pig characteristics were important in various feeding, social interaction and growth patterns in pigs.

In general, agent-based modelling proved to be a useful method to understand animal behaviour and underlying motivations. It contributed to further understanding of tail biting, feeding and social behaviour in pigs. Furthermore, agent-based modelling showed to be a novel method to find and assess behaviours as welfare indicators, and to contribute to understanding trade-offs and synergies between sustainability issues, such as animal welfare and productivity.

Stalboekje Varkens 2016: handboek voor natuurlijke diergezondheidzorg met kruiden en andere natuurproducten : Natuurlijk gezond met kruiden en andere natuurproducten
Groot, Maria ; Asseldonk, Tedje van - \ 2017
IJmuiden : RIKILT Wageningen UR (RIKILT-uitgave 2016.701) - 168
varkens - veehouderij - biologische landbouw - geneeskrachtige kruiden - diervoeding - diergezondheid - dierenwelzijn - dierlijke productie - pigs - livestock farming - organic farming - herbal drugs - animal nutrition - animal health - animal welfare - animal production
Signaalindicatoren bij handhaving van "Open Normen" voor dierenwelzijn : pilot klimaat in varkensstallen
Vermeer, Herman ; Hopster, Hans - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1017) - 44
dierenwelzijn - dierlijke productie - varkens - huisvesting, dieren - diergedrag - diergezondheid - wetgeving - toezicht - animal welfare - animal production - pigs - animal housing - animal behaviour - animal health - legislation - surveillance
Varkens bijten elkaar door eiwittekort
Meer, Yvonne van der - \ 2017
animal welfare - animal production - animal behaviour - pigs - animal health

Varkens met een lage gezondheidsstatus die weinig ruw eiwit in hun voer krijgen, bijten elkaar meer. Dit probleem kan deels worden opgelost door extra aminozuren aan het voer toe te voegen, blijkt uit een studie van Wageningse dierwetenschappers.

Nutrition of pigs kept under low and high sanitary conditions : effects on animo acid and energy metabolism and damaging behaviour
Meer, Yvonne van der - \ 2017
Wageningen University. Promotor(en): Walter Gerrits, co-promotor(en): Alfons Jansman; Aart Lammers. - Wageningen : Wageningen University - ISBN 9789463431972 - 181
pigs - feeds - pig feeding - animal nutrition - amino acid metabolism - animal health - energy metabolism - abnormal behaviour - behaviour disorders - immune system - nutrition physiology - varkens - voer - varkensvoeding - diervoeding - aminozuurmetabolisme - diergezondheid - energiemetabolisme - abnormaal gedrag - gedragsstoornissen - immuunsysteem - voedingsfysiologie

It is economically and environmentally important to match the nutrient supply to the nutrient requirements in pig production. Until now, the effects of different sanitary conditions on energy and nutrient requirements are not implemented in recommendations for nutrient composition of pig diets. The current nutrient requirement data are based on studies with pigs in experimental settings, which can be regarded as rather optimal. Changes in nutrient requirements caused by differences in sanitary conditions are poorly documented. As in the pig production sector farm conditions are variable it is of major importance to determine the effects of low sanitary conditions (LSC) on requirements for amino acids and energy in growing pigs. Pigs under LSC have an increased risk of clinical and subclinical infections, resulting in a chronic stimulation of their immune system. Immune system stimulation is known to influence energy and amino acid metabolism. However, most studies in pigs evaluating the relationship between immune system stimulation and nutrient requirements often use specific experimental challenge models. Whereas such models have the obvious advantage of reproducibility and allow mechanistic insight in the effects of stimulating specific parts of the immune system, these models often induce clinical illness, rather than subclinical infections. Results obtained with such models may therefore be difficult to translate to practical situations. Therefore the objective of the present thesis was to study the effect of low and high sanitary conditions (HSC) on amino acids and energy metabolism in pigs. Also interactions between the immune system, nutrient metabolism and damaging behaviour of pigs were considered in this thesis.

The experiment described in Chapter 2 was designed to study the effect of different dietary crude protein levels and extra amino acid supplementation on the growth performance of pigs kept under different sanitary conditions. In a 2×2×2 factorial arrangement, 68 groups of 9 pigs were allocated to either LSC or HSC, and were offered ad libitum access to two different diets, a normal crude protein concentration diet or a low crude protein concentration diet, each having either a basal dietary amino acid profile or supplemented dietary amino acid profile containing 20% more methionine, threonine, and tryptophan compared with the basal profile. The pigs were followed from 10 weeks of age until slaughter. Haptoglobin concentrations in serum and IgG antibody titers against keyhole limpet heamocyanin, collected in the starter, grower, and finisher phases, and pleuritis scores at slaughter were greater for LSC pigs compared with HSC pigs, illustrating that sanitary conditions affected health conditions. The average daily gain and gain to feed ratio were greater for HSC pigs compared with LSC pigs. A 20% increase in dietary supplementation of methionine, threonine, and tryptophan relative to lysine increased gain to feed ratio more in LSC than in HSC pigs. The results therefore illustrated that dietary requirements for methionine. threonine, and tryptophan were greater for LSC compared with HSC pigs.

In Chapter 3 the damaging behaviour of 576 pigs from the experiment in Chapter 2 was evaluated. At 15, 18, and 24 weeks of age, prevalence of tail and ear damage, and of tail and ear wounds was scored. At 20 and 23 weeks of age, frequencies of biting behaviour and aggression were scored by behaviour sampling. The prevalence of ear damage during the finisher phase and the frequency of ear biting were increased in LSC compared with HSC pigs. The frequency of ear biting was increased in low protein fed pigs compared with normal protein fed pigs. The supplemented AA profile reduced ear biting only in LSC pigs. The prevalence of tail wounds was lower for pigs in LSC than for pigs in HSC in the grower phase. Regardless of dietary amino acid profile or sanitary status, pigs fed low protein diets showed more ear biting, tail biting, belly nosing, other oral manipulation directed at pen mates, and aggression than pigs fed normal protein diets, with no effect on ear or tail damage. In conclusion, both LSC and a reduction of dietary protein increased the occurrence of damaging behaviours in pigs and therefore may negatively impact pig welfare.

The experiment of Chapter 4 was designed to quantify the difference in energy requirements for maintenance, and in incremental efficiencies for deposition of dietary energy and protein in the body of clinically healthy pigs kept under LSC or HSC, fed a basal diet either or not supplemented with additional methionine, threonine and tryptophan.

In a 2 × 2 factorial arrangement, 24 groups of 6 pigs each were allocated to either a LSC or HSC, and were offered two different diets having either a basal or a dietary amino acid profile supplemented with methionine, threonine, and tryptophan. For each group of pigs, complete energy and nitrogen balances were determined during two consecutive weeks, during which feed was available ad libitum or at 70% of ad libitum. Fasting heat production was determined over a 25 h period of fasting after a period of restricted feeding. Low sanitary conditions increased fasting heat production from 696 to 750 kJ/(kg BW0.6 . d), regardless of the dietary amino acid supplementation. The incremental efficiency of ingested nitrogen for retention in the body was reduced in LSC pigs from 73 to 53%, but incremental efficiencies of digestible energy intake for fat deposition in the body were unaffected by the experimental treatments. These findings showed that the effects of continuous immune stimulation by introducing LSC, was affecting energy and nutrient efficiencies of pigs both at maintenance level and at a feeding level close to ad libitum intake.

In Chapter 5 diurnal patterns for heat production, respiratory quotient, and carbohydrate and fat oxidation of the pigs studied in the experiment of Chapter 4 were evaluated to get more insight in the mechanisms behind the effects found in Chapter 4. The LSC pigs had reduced activity compared with HSC and a higher resting metabolic rate during the period of restricted feeding, especially during the light parts of the day. Therefore the diurnal energy expenditure pattern of LSC and HSC pigs can be considered as different. Fat and carbohydrate oxidation patterns were not different for LSC and HSC pigs, indicating that protein and fat deposition during the day was similar for LSC and HSC pigs.

Overall, the results of this thesis indicate that both energy and AA requirements are greater in LSC pigs compared with HSC pigs. It is questionable, however, whether it is nutrient and cost effective and biologically possible to satisfy these increased nutrient requirements in LSC pigs, as the incremental efficiency of N for retained protein is low, and ADFI is reduced for LSC pigs compared with HSC pigs. The present thesis demonstrates that care should be taken in reducing dietary protein concentrations to improve protein efficiency in pigs, as it incurs a risk to increased damaging behaviours, particularly when pigs are kept under LSC.

Interactions and functionalities of the gut revealed by computational approaches
Benis, Nirupama - \ 2017
Wageningen University. Promotor(en): Mari Smits; Vitor Martins dos Santos, co-promotor(en): Dirkjan Schokker; Maria Suarez Diez. - Wageningen : Wageningen University - ISBN 9789463434546 - 247
pigs - mice - digestive tract - digestive system - intestinal microorganisms - intestinal mucosa - computational science - immune system - feeds - animal nutrition - nutrition physiology - animal health - varkens - muizen - spijsverteringskanaal - spijsverteringsstelsel - darmmicro-organismen - darmslijmvlies - immuunsysteem - voer - diervoeding - voedingsfysiologie - diergezondheid

The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations.

The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response.

Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.

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