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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Defining resilient pigs after a Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) challenge using activity and feeding data from accelerometers
Zande, L.E. Van Der; Dunkelberger, J.R. ; Rodenburg, Bas ; Mathur, P.K. ; Cairns, W.J. ; Keyes, M.C. ; Eggert, J.M. ; Little, E.A. ; Dee, S.A. ; Knol, E.F. - \ 2019
In: Precision Livestock Farming 2019. - Teagasc (Precision Livestock Farming 2019 - Papers Presented at the 9th European Conference on Precision Livestock Farming, ECPLF 2019 ) - ISBN 9781841706542 - p. 471 - 475.
Accelerometers - Behaviour - Pig - PRRS - Resilience - RMSE

Porcine reproductive and respiratory syndrome (PRRS) is an infectious viral disease in pigs. PRRS causes reproductive failure in sows and respiratory infections in growing pigs. To improve pig health and minimise economic losses, resilient pigs are preferred within the herd. Resilient pigs still become infected, yet are able to recover following infection, showing less variation in activity and feeding. In this study, 232 commercial crossbred pigs were equipped with individual accelerometer ear tags to monitor the number of active, feeding, and hyperactive events per individual per hour. At eight weeks of age, pigs were inoculated with PRRS virus 1-7-4. Data from accelerometers were collected 23 days prior to challenge and 42 days post-infection (dpi). Expected levels of activity, feeding, and hyperactivity were estimated by regressing behavioural traits on observed datapoints prior to challenge. This regression line was extended to 42 dpi. Then, deviations from the regression line were quantified as Root Mean Square Error (RMSE) for each individual during the following time periods: pre-challenge, 0-13 dpi, and 13-42 dpi. All traits decreased and RMSE increased post-challenge. These results are consistant with clinical signs of PRRS, including lethargy and loss of appetite. In addition, association of these traits with survival was also investigated. RMSE prior to PRRS-infection was not predictive of survival after infection. However, RMSE of feeding and activity during the peak challenge period (0-13 dpi) was predictive of survival, where pigs with less deviation in behaviour were more resilient to the PRRS challenge.

Legitimate and reliable determination of the age-related intestinal microbiome in young piglets; rectal swabs and fecal samples provide comparable insights
Choudhury, R. ; Middelkoop, A. ; Bolhuis, J.E. ; Kleerebezem, M. - \ 2019
Frontiers in Microbiology 10 (2019)AUG. - ISSN 1664-302X
Early life - Feces - Gut microbiota - Pig - Rectal swab

A prerequisite for reliable microbiota analysis is having an effective and consistent sampling method. Fecal sampling, commonly used to study the intestinal microbiome, might not be suitable in all situations, especially considering the potential difficulties in obtaining fresh feces from young animals. Indeed, this study shows that the success rate of collecting fecal samples from young piglets (<2 weeks of age) was very low. Therefore, we evaluated rectal swabs as an alternative sample type (to feces) for studying porcine microbiome development and performed a comparative analysis of microbiome composition obtained from fresh fecal samples and rectal swabs in 15 healthy piglets at seven (6 piglets) and 20 (9 piglets) days of age. Three samples (fresh feces, rectal swab before and after defecation) were collected from individual piglets and microbiome composition was assessed by 16S rRNA gene sequencing. The results demonstrated that rectal swabs and fecal samples provide similar microbiome composition profiles, with samples clustering predominantly by individual animal rather than sample type. Furthermore, regardless of the sample type, the biological interpretation with respect to microbiota colonization patterns associated with different ages (7 and 20 days) was found to be comparable. Independent of sample type, we observed age-related changes like increasing microbiota diversity and alterations in relative abundances of the phyla Firmicutes, Bacteroidetes, and Fusobacteria, which was also reflected in consistent family-and genus-level microbiota changes. This study establishes that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early life, when fecal sampling is challenging.

Mild maternal hyperglycemia in INSC93S transgenic pigs causes impaired glucose tolerance and metabolic alterations in neonatal offspring
Renner, Simone ; Martins, Ana Sofia ; Streckel, Elisabeth ; Braun-Reichhart, Christina ; Backman, Mattias ; Prehn, Cornelia ; Klymiuk, Nikolai ; Bähr, Andrea ; Blutke, Andreas ; Landbrecht-Schessl, Christina ; Wünsch, Annegret ; Kessler, Barbara ; Kurome, Mayuko ; Hinrichs, Arne ; Koopmans, Sietse Jan ; Krebs, Stefan ; Kemter, Elisabeth ; Rathkolb, Birgit ; Nagashima, Hiroshi ; Blum, Helmut ; Ritzmann, Mathias ; Wanke, Rüdiger ; Aigner, Bernhard ; Adamski, Jerzy ; Hrabě de Angelis, Martin ; Wolf, Eckhard - \ 2019
Disease Models & Mechanisms 12 (2019)8. - ISSN 1754-8411
Developmental programming - Maternal diabetes - Metabolomics - Pig - Transgenic

Alongside the obesity epidemic, the prevalence of maternal diabetes is rising worldwide, and adverse effects on fetal development and metabolic disturbances in the offspring's later life have been described. To clarify whether metabolic programming effects are due to mild maternal hyperglycemia without confounding obesity, we investigated wild-type offspring of INSC93S transgenic pigs, which are a novel genetically modified large-animal model expressing mutant insulin (INS) C93S in pancreatic β-cells. This mutation results in impaired glucose tolerance, mild fasting hyperglycemia and insulin resistance during late pregnancy. Compared with offspring from wild-type sows, piglets from hyperglycemic mothers showed impaired glucose tolerance and insulin resistance (homeostatic model assessment of insulin resistance: +3-fold in males; +4.4-fold in females) prior to colostrum uptake. Targeted metabolomics in the fasting and insulin-stimulated state revealed distinct alterations in the plasma metabolic profile of piglets from hyperglycemic mothers. They showed increased levels of acylcarnitines, gluconeogenic precursors such as alanine, phospholipids (in particular lyso-phosphatidylcholines) and α-aminoadipic acid, a potential biomarker for type 2 diabetes. These observations indicate that mild gestational hyperglycemia can cause impaired glucose tolerance, insulin resistance and associated metabolic alterations in neonatal offspring of a large-animal model born at a developmental maturation status comparable to human babies.

Genomic evaluation for a crossbreeding system implementing breed-of-origin for targeted markers
Sevillano, Claudia A. ; Bovenhuis, Henk ; Calus, Mario P.L. - \ 2019
Frontiers in Genetics Livestock Genomics 10 (2019)MAY. - ISSN 1664-8021
Crossbred - Finisher - Genomic prediction - Origin of alleles - Pig

The genome in crossbred animals is a mosaic of genomic regions inherited from the different parental breeds. We previously showed that effects of haplotypes strongly associated with crossbred performance are different depending upon from which parental breed they are inherited, however, the majority of the genomic regions are not or only weakly associated with crossbred performance. Therefore, our objective was to develop a model that distinguishes between selected single nucleotide polymorphisms (SNP) strongly associated with crossbred performance and all remaining SNP. For the selected SNP, breed-specific allele effects were fitted whereas for the remaining SNP it was assumed that effects are the same across breeds (SEL-BOA model). We used data from three purebred populations; S, LR, and LW, and the corresponding crossbred population. We selected SNP that explained together either 5 or 10% of the total crossbred genetic variance for average daily gain in each breed of origin. The model was compared to a model where all SNP-alleles were allowed to have different effects for crossbred performance depending upon the breed of origin (BOA model) and to a model where all SNP-alleles had the same effect for crossbred performance across breeds (G model). Across the models, the heritability for crossbred performance was very similar with values of 0.29-0.30. With the SEL-BOA models, in general, the purebred-crossbred genetic correlation (rpc) for the selected SNP was larger than for the non-selected SNP. For breed LR, the rpc for selected SNP and non-selected SNP estimated with the SEL-BOA 5% and SEL-BOA 10% were very different compared to the rpc estimated with the G or BOA model. For breeds S and LW, there was not a big discrepancy for the rpc estimated with the SEL-BOA models and with the G or BOA model. The BOA model calculates more accurate breeding values of purebred animals for crossbred performance than the G model when rpc differs (≈10%) between the G and the BOA model. Superiority of the SEL-BOA model compared to the BOA model was only observed for SEL-BOA 10% and when rpc for the selected and non-selected SNP differed both (≈20%) from the rpc estimated by the G or BOA model.

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Schokker, Dirkjan ; Hulsegge, Ina ; Woelders, Henri ; Rebel, Johanna M.J. - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Development - Gene expression - Gut - Pig - Plasticity

Background: Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcriptomic datasets. These datasets were acquired from different experimental in-house studies or from experiments described in literature of porcine jejunum mucosa. Gene expression was measured under different experimental interventions, such as nutritional intervention, at various time-points (age). Results: The studies included in the meta-analysis provided gene expression data for various time-points (piglet ages) for piglets that had received a treatment versus control piglets. In separate studies, treatments were administered to the sow (i.e. amoxicillin), or nutritional supplementation directly to the piglets with medium chain fatty acids (MCFAs), and oral administration of fructooligosaccharides (FOS) or a high dose of zinc-oxide, respectively. In the meta-analysis, genes were grouped into 16 clusters according to their temporal gene expression profiles for control piglets, i.e. the changes of gene expression level over time. Functional analysis showed that these temporal profile clusters had different dominant processes, such as immune related processes or barrier function. Transcriptomics data of treatment piglets was subsequently superimposed over the control temporal profiles. In this way we could investigate which temporal profile clusters (and which biological processes) were modulated by the treatments. Interestingly, not all 16 temporal profiles were modulated. Conclusions: We showed that it is possible to re-use (publicly available) transcriptomics data and produce temporal gene expression profiles for control piglets with overexpression of genes representing specific biological processes. Subsequently, by superimposing gene expression data from (nutritional) intervention studies we observed deviations from some of these reference profile(s) and thus the plasticity of the system. By employing this meta-analysis approach we highlighted the importance of birth and weaning and the underlying biological processes.

Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin
Sevillano, Claudia A. ; Napel, Jan ten; Guimarães, Simone E.F. ; Silva, Fabyano F. ; Calus, Mario P.L. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Breed-of-origin - Crossbred - Genomic prediction - Pig

Background: This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, and how these are related to estimated effects for purebred performance. Results: SNP-allele substitution effects were estimated for a commonly used SNP panel using a genomic best linear unbiased prediction model with breed-specific partial relationship matrices. Estimated breeding values for purebred and crossbred performance were converted to SNP-allele effects by breed-of-origin. Differences between purebred and crossbred, and between breeds-of-origin were evaluated by comparing percentage of variance explained by genomic regions for back fat thickness (BF), average daily gain (ADG), and residual feed intake (RFI). From ten regions explaining most additive genetic variance for crossbred performance, 1 to 5 regions also appeared in the top ten for purebred performance. The proportion of genetic variance explained by a genomic region and the estimated effect of a haplotype in such a region were different depending upon the breed-of-origin. To illustrate underlying mechanisms, we evaluated the estimated effects across breeds-of-origin for haplotypes associated to the melanocortin 4 receptor (MC4R) gene, and for the MC4Rsnp itself which is a missense mutation with a known effect on BF and ADG. Although estimated allele substitution effects of the MC4Rsnp mutation were very similar across breeds, explained genetic variance of haplotypes associated to the MC4R gene using a SNP panel that does not include the mutation, was considerably lower in one of the breeds where the allele frequency of the mutation was the lowest. Conclusions: Similar regions explaining similar additive genetic variance were observed across purebred and crossbred performance. Moreover, there was some overlap across breeds-of-origin between regions that explained relatively large proportions of genetic variance for crossbred performance; albeit that the actual proportion of variance deviated across breeds-of-origin. Results based on a missense mutation in MC4R confirmed that even if a causal locus has similar effects across breeds-of-origin, estimated effects and explained variance in its region using a commonly used SNP panel can strongly depend on the allele frequency of the underlying causal mutation.

Protein fermentation in the gut; implications for intestinal dysfunction in humans, pigs, and poultry
Gilbert, Myrthe S. ; IJssennagger, Noortje ; Kies, Arie K. ; Mil, Saskia W.C. van - \ 2018
American Journal of Physiology. Gastrointestinal and Liver Physiology 315 (2018)2. - ISSN 0193-1857 - p. G159 - G170.
Broiler - Gut health - Human - Intestinal disease - Metabolomics - Pig - Protein fermentation

The amount of dietary protein is associated with intestinal disease in different vertebrate species. In humans, this is exemplified by the association between high-protein intake and fermentation metabolite concentrations in patients with inflammatory bowel disease. In production animals, dietary protein intake is associated with postweaning diarrhea in piglets and with the occurrence of wet litter in poultry. The underlying mechanisms by which dietary protein contributes to intestinal problems remain largely unknown. Fermentation of undigested protein in the hindgut results in formation of fermentation products including short-chain fatty acids, branchedchain fatty acids, ammonia, phenolic and indolic compounds, biogenic amines, hydrogen sulfide, and nitric oxide. Here, we review the mechanisms by which these metabolites may cause intestinal disease. Studies addressing how different metabolites induce epithelial damage rely mainly on cell culture studies and occasionally on mice or rat models. Often, contrasting results were reported. The direct relevance of such studies for human, pig, and poultry gut health is therefore questionable and does not suffice for the development of interventions to improve gut health. We discuss a roadmap to improve our understanding of gut metabolites and microbial species associated with intestinal health in humans and production animals and to determine whether these metabolite/bacterial networks cause epithelial damage. The outcomes of these studies will dictate proof-of-principle studies to eliminate specific metabolites and or bacterial strains and will provide the basis for interventions aiming to improve gut health.

A bead-based suspension array for the detection of Salmonella antibodies in pig sera
Wal, Fimme J. van der; Achterberg, René P. ; Maassen, Catharina B.M. - \ 2018
BMC Veterinary Research 14 (2018)1. - ISSN 1746-6148
Bead-based suspension array - LPS - Pig - Salmonella - Serology - Swine - Triazine chemistry

Background: Slaughter pigs are monitored for the presence of the zoonotic pathogen Salmonella, using both serology and bacteriology. ELISAs used to investigate pig herds are based on the detection of antibodies against components of the Salmonella cell envelope. Nearly all Salmonella isolates in food-producing animals are serovars of Salmonella enterica subspecies enterica, distributed over various serogroups as determined by the composition of their lipopolysaccharide (LPS). ELISAs for Salmonella serology are usually based on serogroup B and C1 LPS, often combined with serogroup D or E LPS. Although C2 LPS may improve serology, use of C2 LPS in a broad ELISA was never achieved. Results: To enable detection of serum antibodies against Salmonella in pigs, a bead-based suspension array was developed with five LPS variants (B, 2× C1, C2, D1), each conjugated to a different bead set using triazine chemistry. Reactivity of the beads was confirmed with rabbit agglutination sera and with experimental pig sera. With a mixture of bead sets, 175 sera from slaughter pigs were investigated for the presence of antibodies against Salmonella. With a combination of ROC analysis (B and D LPS) and a prevalence estimation based on historic data (C LPS), individual cut-offs were defined for each LPS-conjugated bead set, and assay performance was evaluated. Results of the suspension array (BC1C1C2D) suggest that more pigs are seroconverted than indicated by a commercial BC1D1-ELISA, and that most of these extra seropositive samples give a signal on one of the beads with C LPS. These results show that expansion of a standard panel with more C LPS variants improves antibody detection. Conclusions: A suspension array for Salmonella serology in pigs was developed, that detects more seropositive sera than ELISA, which is achieved by expanding the panel of Salmonella LPS variants, including C2 LPS. The results demonstrate that bead-based suspension arrays allow for testing of pig sera, with the advantage of being able to set cut-offs per antigen. Ultimately, this type of assay can be applied in routine veterinary serology to test for antibodies against multiple Salmonella serovars (or other pathogens) in one single serum sample, using up-to-date antigen panels.

Indirect Genetic Effects for Growth in Pigs Affect Behaviour and Weight Around Weaning
Camerlink, Irene ; Ursinus, Winanda W. ; Bartels, Andrea C. ; Bijma, Piter ; Bolhuis, J.E. - \ 2018
Behavior Genetics 48 (2018)5. - ISSN 0001-8244 - p. 413 - 420.
Breeding - Enrichment - Genotype-by-environment - Indirect genetic effects - Pig - Weaning

Selection for indirect genetic effects (IGE), i.e. the genetic effect of an individual on a trait of another individual, is a promising avenue to increase trait values in plant and animal breeding. Studies in livestock suggest that selection for IGE for growth (IGEg) might increase animals’ capacity to tolerate stress. We assessed the effect of a stressful phase (weaning) on the behaviour and performance of pigs (n = 480) divergently selected for high or low IGEg. High IGEg pigs were significantly slower to explore the feed and gained less weight than low IGEg pigs in the days after weaning. In line with previous findings, high IGEg animals may have prioritized the formation of social ranks.

Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex
Verschuren, Lisanne M.G. ; Calus, Mario P.L. ; Jansman, Alfons J.M. ; Bergsma, Rob ; Knol, Egbert F. ; Gilbert, Hélène ; Zemb, Olivier - \ 2018
Journal of Animal Science 96 (2018)4. - ISSN 0021-8812 - p. 1405 - 1418.
Diet - Fecal microbiome - Feed efficiency - Pig - Sex
Dietary fiber content and composition affect microbial composition and activity in the gut, which in turn influence energetic contribution of fermentation products to the metabolic energy supply in pigs. This may affect feed efficiency (FE) in pigs. The present study investigated the relationship between the fecal microbial composition and FE in individual growing-finishing pigs. In addition, the effects of diet composition and sex on the fecal microbiome were studied. Fecal samples were collected of 154 grower-finisher pigs (3-way crossbreeds) the day before slaughter. Pigs were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Fecal microbiome was characterized by 16S ribosomal DNA sequencing, clustered by operational taxonomic unit (OTU), and results were subjected to a discriminant approach combined with principal component analysis to discriminate diets, sexes, and FE extreme groups (10 high and 10 low FE pigs for each diet by sex-combination). Pigs on different diets and males vs. females had a very distinct fecal microbiome, needing only 2 OTU for diet (P = 0.020) and 18 OTU for sex (P = 0.040) to separate the groups. The 2 most important OTU for diet, and the most important OTU for sex, were taxonomically classified as the same bacterium. In pigs fed the CS diet, there was no significant association between FE and fecal microbiota composition based on OTU (P > 0.05), but in pigs fed the WB diet differences in FE were associated with 17 OTU in males (P = 0.018) and to 7 OTU in females (P = 0.010), with 3 OTU in common for both sexes. In conclusion, our results showed a diet and sex-dependent relationship between FE and the fecal microbial composition at slaughter weight in grower-finisher pigs.
The ALFAM2 database on ammonia emission from field-applied manure : Description and illustrative analysis
Hafner, Sasha D. ; Pacholski, Andreas ; Bittman, Shabtai ; Burchill, William ; Bussink, Wim ; Chantigny, Martin ; Carozzi, Marco ; Génermont, Sophie ; Häni, Christoph ; Hansen, Martin N. ; Huijsmans, Jan ; Hunt, Derek ; Kupper, Thomas ; Lanigan, Gary ; Loubet, Benjamin ; Misselbrook, Tom ; Meisinger, John J. ; Neftel, Albrecht ; Nyord, Tavs ; Pedersen, Simon V. ; Sintermann, Jörg ; Thompson, Rodney B. ; Vermeulen, Bert ; Voylokov, Polina ; Williams, John R. ; Sommer, Sven G. - \ 2018
Agricultural and Forest Meteorology 258 (2018). - ISSN 0168-1923 - p. 66 - 79.
Ammonia - Cattle - Emission - Manure - Pig - Slurry
Ammonia (NH3) emission from animal manure contributes to air pollution and ecosystem degradation, and the loss of reactive nitrogen (N) from agricultural systems. Estimates of NH3 emission are necessary for national inventories and nutrient management, and NH3 emission from field-applied manure has been measured in many studies over the past few decades. In this work, we facilitate the use of these data by collecting and organizing them in the ALFAM2 database. In this paper we describe the development of the database and summarise its contents, quantify effects of application methods and other variables on emission using a data subset, and discuss challenges for data analysis and model development. The database contains measurements of emission, manure and soil properties, weather, application technique, and other variables for 1895 plots from 22 research institutes in 12 countries. Data on five manure types (cattle, pig, mink, poultry, mixed, as well as sludge and "other") applied to three types of crops (grass, small grains, maize, as well as stubble and bare soil) are included. Application methods represented in the database include broadcast, trailing hose, trailing shoe (narrow band application), and open slot injection. Cattle manure application to grassland was the most common combination, and analysis of this subset (with dry matter (DM) limited to <15%) was carried out using mixed- and fixed-effects models in order to quantify effects of management and environment on ammonia emission, and to highlight challenges for use of the database. Measured emission in this subset ranged from <1% to 130% of applied ammonia after 48 h. Results showed clear, albeit variable, reductions in NH3 emission due to trailing hose, trailing shoe, and open slot injection of slurry compared to broadcast application. There was evidence of positive effects of air temperature and wind speed on NH3 emission, and limited evidence of effects of slurry DM. However, random-effects coefficients for differences among research institutes were among the largest model coefficients, and showed a deviation from the mean response by more than 100% in some cases. The source of these institute differences could not be determined with certainty, but there is some evidence that they are related to differences in soils, or differences in application or measurement methods. The ALFAM2 database should be useful for development and evaluation of both emission factors and emission models, but users need to recognize the limitations caused by confounding variables, imbalance in the dataset, and dependence among observations from the same institute. Variation among measurements and in reported variables highlights the importance of international agreement on how NH3 emission should be measured, along with necessary types of supporting data and standard protocols for their measurement. Both are needed in order to produce more accurate and useful ammonia emission measurements. Expansion of the ALFAM2 database will continue, and readers are invited to contact the corresponding author for information on data submission. The latest version of the database is available at
Drinker position influences the cleanness of the lying area of pigs in a welfare-friendly housing facility
Ocepek, Marko ; Goold, Conor M. ; Busancic, Mirjana ; Aarnink, André J.A. - \ 2018
Applied Animal Behaviour Science 198 (2018). - ISSN 0168-1591 - p. 44 - 51.
Defecation - Drinker position - Lying - Pig - Urination

Understanding eliminative behaviour in pigs is a priority for designing pig facilities. Pigs prefer to lie in areas separated from where they eliminate (urinate, defecate). Welfare-friendly housing facilities include separate areas for lying (solid floors) and elimination (slatted floors). To prevent pen fouling, ways to reduce the amount of eliminative behaviour on the solid floor area are essential. This study investigated whether the position of the drinkers influences areas preferred for eliminative behaviour in growing-finishing pigs (n = 432; over two batches) assigned to one of three drinker treatments: two drinkers placed in the inner slatted area (IN group; n = 8 pens), two drinkers in the outer slatted area (OUT group; n = 8 pens), or a drinker in each of the inner and outer slatted areas (IN_OUT group; n = 8 pens). We predicted that the OUT group would have fewer elimination events on the inner solid area than the IN group. The number of eliminations in the IN_OUT group was predicted to be a compromise between the IN and OUT group patterns. In addition, we quantified the diurnal variation of lying and eliminative behaviour in different pen areas with respect to temperature, and the effect of pigs lying in eliminatory areas on eliminative behaviour. On the solid floor area, the OUT group urinated 32.5% less frequently and defecated 30.4% less frequently than the IN group. For urination preferences, the IN_OUT group was intermediate between IN and OUT groups on the inner solid floor, but not for defecation. No significant differences in lying preferences were found between drinker groups on the inner solid area. Elimination (urination and defecation) was most prevalent in the afternoon (15:00 and 14:00. h, respectively) and least prevalent during the night (03:00 and 00:02. h, respectively). A one SD increase in temperature (approximately 6. °C) was associated with a 42.3% decrease in lying observations on the inner solid area, while the percentage of elimination on the solid floor increased (urination: 75.8%; defecation: 139.5%). Our results showed that the placement of drinkers in the outer area compared to the inner area resulted in less pen fouling (fewer eliminations on the solid floor) and, thus, provided pigs with a cleaner solid area for lying. This study has identified a simple method of increasing the cleanliness of pigs' dedicated lying areas, which has important implications for improving the design of pig housing facilities and maximising pig welfare.

Digestibility and intestinal fermentability of canola meal from Brassica juncea and Brassica napus fed to ileal-cannulated grower pigs
Le, M.H.A. ; Buchet, A.D.G. ; Beltranena, E. ; Gerrits, W.J.J. ; Zijlstra, R.T. - \ 2017
Animal Feed Science and Technology 234 (2017). - ISSN 0377-8401 - p. 43 - 53.
Canola meal - Digestibility - Energy - Pig - Volatile fatty acid
Yellow-seeded Brassica (B.) juncea is a novel canola species. Therefore, its meal co-product requires feed quality evaluation and comparison to conventional, dark-seeded B. napus canola meal for pigs. The B. juncea canola meal contains less fibre than B. napus canola meal (190 vs. 260 g NDF/kg, as is), but also less lysine (20.3 vs. 22.1 g/kg). Nutrient digestibility and fermentibility of B. juncea and B. napus canola meal were assessed in a 2 × 2factorial arrangement. Six ileal-cannulated pigs (47 kg BW) were fed six diets in a 6 × 6 Latin square: basal diet (460 g wheat/kg and corn starch), 4 diets with 460 g wheat/kg and either B. juncea or B. napus canola meal at 250 or 500 g/kg replacing corn starch, sugar and canola oil, and an N-free diet based on corn starch. The B. juncea canola meal had greater (P < 0.05) CATTD of gross energy than B. napus canola meal (0.70 vs. 0.63) most likely due to its lower fibre content. Ileal total VFA concentration was lower (P < 0.001) in pigs fed B. juncea than B. napus canola meal diets (15.2 vs. 20.8 μmol/g of wet digesta). In pigs fed B. juncea canola meal instead of B. napus canola meal diets, the molar ratio was greater (P < 0.01) for digesta propionate and faecal acetate, but lower (P < 0.05) for digesta and faecal butyrate. Canola meal species did not affect the CAID of gross energy, CSID of amino acid and faecal VFA content. The digestible energy (DE) value was greater (P < 0.01; 12.1 vs. 10.9 MJ/kg, standardised to 100 g/kg moisture) for B. juncea than B. napus canola meal. Increasing dietary inclusion of canola meal up to 500 g/kg reduced (P < 0.01) diet digestibility of gross energy but not amino acids and decreased (P < 0.05) intestinal fermentability of B. napus but not B. juncea. In conclusion, B. juncea canola meal had greater fermentability and ATTD of gross energy than B. napus canola meal, but digestibility of amino acids did not differ. Increasing dietary inclusion of canola meal up to 500 g/kg reduced digestibility of gross energy but not digestibility of AA. Fermentability of B. napus canola meal but not B. juncea canola meal decreased in the pig intestine with increased dietary inclusion. Hence, yellow-seeded B. juncea canola meal had a greater DE value, similar amino acid digestibility as conventional dark-seed B. napus canola meal and may limit protein fermentation in the pig intestine.
The effects of starter microbiota and the early life feeding of medium chain triglycerides on the gastric transcriptome profile of 2- or 3-week-old cesarean delivered piglets
Trevisi, Paolo ; Priori, Davide ; Motta, Vincenzo ; Luise, Diana ; Jansman, Alfons J.M. ; Koopmans, Sietse Jan ; Bosi, Paolo - \ 2017
Journal of Animal Science and Biotechnology 8 (2017). - ISSN 1674-9782
Development - Microbiota - Pig - Stomach - Transcriptome

Background: The stomach is an underestimated key interface between the ingesta and the digestive system, affecting the digestion and playing an important role in several endocrine functions. The quality of starter microbiota and the early life feeding of medium chain triglycerides may affect porcine gastric maturation. Two trials (T1, T2) were carried out on 12 and 24 cesarean-delivered piglets (birth, d0), divided over two microbiota treatments, but slaughtered and sampled at two or three weeks of age, respectively. All piglets were fed orally: sow serum (T1) or pasteurized sow colostrum (T2) on d0; simple starter microbiota (Lactobacillus amylovorus, Clostridium glycolicum and Parabacteroides spp.) (d1-d3); complex microbiota inoculum (sow diluted feces, CA) or a placebo (simple association, SA) (d3-d4) and milk replacer ad libitum (d0-d4). The The T1 piglets and half of the T2 piglets were then fed a moist diet (CTRL); the remaining half of the T2 piglets were fed the CTRL diet fortified with medium chain triglycerides and 7% coconut oil (MCT). Total mRNA from the oxyntic mucosa was analyzed using Affymetrix

Genetic parameters for semen quality and quantity traits in five pig lines
Marques, D.B.D. ; Lopes, Marcos S. ; Broekhuijse, M.L.W.J. ; Guimarães, S.E.F. ; Kno, E.F. ; Bastiaansen, J.W.M. ; Silva, F. ; Lopes, Paulo S. - \ 2017
Journal of Animal Science 95 (2017)10. - ISSN 0021-8812 - p. 4251 - 4259.
Multiple-trait analysis - Pig - Selection - Semen - Variation analysis
We aimed to estimate genetic parameters for semen quality and quantity traits as well as for within-boar variation of these traits to evaluate their inclusion in breeding goals. Genetic parameters were estimated within line using a multiple-trait (4 × 4) repeatability animal model fitted for 5 pig lines, considering 4 semen traits: sperm motility (MOT), sperm progressive motility (PROMOT), log-transformed number of sperm cells per ejaculate (lnNcells), and total morphological abnormalities (ABN). The within-boar variation of these traits was analyzed based on a multiple-trait (2 × 2) approach for SD and average (AVG) and a single-trait analysis for CV. The average heritabilities across the 5 lines estimated by multiple-trait analysis were 0.18 ± 0.07 (MOT), 0.22 ± 0.08 (PROMOT), 0.16 ± 0.04 (lnNcells), and 0.20 ± 0.04 (ABN). The average genetic correlations were favorable between MOT and PROMOT (0.86 ± 0.10), between MOT and ABN (−0.66 ± 0.25), and between PROMOT and ABN (−0.65 ± 0.25). As determined by within-boar variation analysis, AVG exhibited the greatest heritabilities followed by SD and CV, respectively, for the traits MOT and ABN. For PROMOT, average SD heritability was lower than CV heritability, whereas for lnNcells, they were the same. The average genetic correlations between AVG and SD were favorable for MOT (−0.60 ± 0.13), PROMOT (−0.79 ± 0.14), and ABN (0.78 ± 0.17). The moderate heritabilities indicate the possibility of effective selection of boars based on semen traits. Average and SD are proposed as appropriate traits for selection regarding uniformity.
Molecular analysis of three Clostridium difficile strain genomes isolated from pig farm-related samples
Martín-Burriel, I. ; Andrés-Lasheras, S. ; Harders, F. ; Mainar-Jaime, R.C. ; Ranera, B. ; Zaragoza, P. ; Falceto, V. ; Bolea, Y. ; Kuijper, E.J. ; Bolea, R. ; Bossers, A. ; Chirino-Trejo, M. - \ 2017
Anaerobe 48 (2017). - ISSN 1075-9964 - p. 224 - 231.
Clostridium difficile - Environment - Genome sequencing - PCR-ribotype 078 - Pig - Rat

Clostridium difficile is an anaerobic spore-forming bacillus that usually causes gastrointestinal disorders in man and other animal species. Most of the strains isolated from animals are toxigenic being the virulent ribotype (RT) 078 predominant in several animal species. Although C. difficile is pathogenic to both humans and animals, there is no direct evidence of zoonosis. Deep genome sequencing provides sufficient resolution to analyse which strains found in animals might be related to human pathogens. So far, there are only a few fully sequenced genomes of C. difficile strains isolated from domestic and wild animals. Using Illumina technology, we have sequenced the genome of three isolates; a strain isolated from the vagina of a sow (5754), one from rat (Rattus spp) intestinal content (RC10) and a third one isolated from environmental rat faeces (RF17). Both, rat and rat faeces were sampled in fattening pig farms. Our study reveals a close genetic relationship of two of these isolates with the virulent strain M120 (RT078) isolated from a human patient. The analysis of the sequences has revealed the presence of antibiotic resistance genes, mobile elements, including the transposon linked with virulence Tn6164, and the similarity of virulence factors between these isolates and human strains. This is the first study focused on the sequencing of C. difficile genomes obtained from wild animals like rats, which can be considered as potential reservoirs for humans and other animal species. This study can help to understand the genome composition and epidemiology of this bacterium species.

Tail and ear damage of pigs kept under different sanitary conditions
Meer, Y. van der - \ 2017
Amino acid - Dietary protein - Ear biting - Performance - Pig - pig damaging behaviour - sanitary conditions - Tail biting
Tail and ear damage scores of pigs kept under different sanitary conditions.
The importance of hormonal circadian rhythms in daily feeding patterns : An illustration with simulated pigs
Boumans, Iris J.M.M. ; Boer, Imke J.M. de; Hofstede, Gert Jan ; Fleur, Susanne E. la; Bokkers, Eddy - \ 2017
Hormones and Behavior 93 (2017). - ISSN 0018-506X - p. 82 - 93.
Alternans pattern - Circadian rhythm - Cortisol - Decision-making - Energy balance - Feeding behaviour - Melatonin - Modelling - Motivation - Pig

The interaction between hormonal circadian rhythms and feeding behaviour is not well understood. This study aimed to deepen our understanding of mechanisms underlying circadian feeding behaviour in animals, using pigs, Sus scrofa, as a case study. Pigs show an alternans feeding pattern, that is, a small peak of feed intake at the beginning of the day and a larger peak at the end of the day. We simulated the feeding behaviour of pigs over a 24 h period. The simulation model contained mechanisms that regulate feeding behaviour of animals, including: processing of feed in the gastrointestinal tract, fluctuation in energy balance, circadian rhythms of melatonin and cortisol and motivational decision-making. From the interactions between these various processes, feeding patterns (e.g. feed intake, meal frequency, feeding rate) emerge. These feeding patterns, as well as patterns for the underlying mechanisms (e.g. energy expenditure), fitted empirical data well, indicating that our model contains relevant mechanisms. The circadian rhythms of cortisol and melatonin explained the alternans pattern of feeding in pigs. Additionally, the timing and amplitude of cortisol peaks affected the diurnal and nocturnal peaks in feed intake. Furthermore, our results suggest that circadian rhythms of other hormones, such as leptin and ghrelin, are less important in circadian regulation of feeding behaviour than previously thought. These results are relevant to animal species with a metabolic and endocrine system similar to that of pigs, such as humans. Moreover, the modelling approach to understand feeding behaviour can be applied to other animal species.

Exploration feeding and higher space allocation improve welfare of growing-finishing pigs
Vermeer, Herman M. ; Dirx-Kuijken, Nienke C.P.M.M. ; Bracke, Marc B.M. - \ 2017
Animals 7 (2017)5. - ISSN 2076-2615
Animal welfare - Environmental enrichment - Feeding method - Pig - Stocking density
Lack of environmental enrichment and high stocking densities in growing-finishing pigs can lead to adverse social behaviors directed to pen mates, resulting in skin lesions, lameness, and tail biting. The objective of the study was to improve animal welfare and prevent biting behavior in an experiment with a 2 × 2 × 2 factorial design on exploration feeding, stocking density, and sex. We kept 550 pigs in 69 pens from 63 days to 171 days of life. Pigs were supplemented with or without exploration feeding, kept in groups of seven (1.0 m2/pig) or nine animals (0.8 m2/pig) and separated per sex. Exploration feeding provided small amounts of feed periodically on the solid floor. Skin lesion scores were significantly lower in pens with exploration feeding (p = 0.028, p < 0.001, p < 0.001 for front, middle, and hind body), in pens with high compared to low space allowance (p = 0.005, p = 0.006, p < 0.001 for front, middle and hind body), and in pens with females compared to males (p < 0.001, p = 0.005, p < 0.001 for front, middle and hind body). Males with exploration feeding had fewer front skin lesions than females with exploration feeding (p = 0.022). Pigs with 1.0 m2 compared to 0.8 m2 per pig had a higher daily gain of 27 g per pig per day (p = 0.04) and males compared to females had a higher daily gain of 39 g per pig per day (p = 0.01). These results indicate that exploration feeding might contribute to the development of a more welfare-friendly pig husbandry with intact tails in the near future.
Performance of pigs kept under different sanitary conditions affected by protein intake and amino acid supplementation
Meer, Y. van der; Lammers, A. ; Jansman, A.J.M. ; Rijnen, M.M.J.A. ; Hendriks, W.H. ; Gerrits, W.J.J. - \ 2016
Journal of Animal Science 94 (2016)11. - ISSN 0021-8812 - p. 4704 - 4719.
Amino acid - Immune system - Performance - Pig - Protein - Sanitary conditions

There is growing evidence that requirements for particular AA increase when pigs are kept under low sanitary conditions. The extent towhich reduction in growth performance is related to these increased requirements is unclear. To evaluate this relationship, an experiment (2 × 2 × 2 factorial arrangement) was performed with 612 male pigs (9 per pen) kept under low sanitary conditions (LSC) or high sanitary conditions (HSC) and offered ad libitum access to either a normal CP concentration diet (NP; 17, 15, and 15% CP for the starter, grower, and finisher phase, respectively) or a low CP concentration diet (LP; 20% CP reduced relative to NP for each phase), each of which containing a basal AA profile (AA-B) or a supplemented AA profile (AA-S). The supplemented diet type contained 20% more Met, Thr, and Trp relative to Lys on an apparent ileal digestible basis compared with the basal diet type. Pigs were followed for a complete fattening period and slaughtered at a targeted pen weight of 110 kg. Haptoglobin concentrations in serum (0.92 g/L for LSC and 0.78 g/L for HSC) and IgG antibody titers against keyhole limpet hemocyanin (3.53 for LSC and 3.08 for HSC) collected in the starter, grower, and finisher phases and pleuritis scores at slaughter (0.51 for LSC and 0.20 for HSC) were greater for LSC pigs compared with HSC pigs (P ≤ 0.01), illustrating that sanitary conditions affected health conditions. The ADG and G:F were greater for HSC pigs compared with LSC pigs (P ≤ 0.01). The number of white blood cells (WBC) was higher in (AA-S)–fed pigs compared with (AA-B)–fed pigs when kept at LSC but not at HSC [SS (sanitary conditions) × AA interaction, P = 0.04]. Pigs fed NP had a lower number of WBC compared with pigs fed LP (P = 0.02). The number of platelets in pigs fed AA-S diets was higher compared with pigs fed AA-B diets (P ≤ 0.01). A 20% reduction in dietary supplementation of Met, Thr, and Trp relative to Lys decreased G:F more in LSC pigs than in HSC pigs (interaction, P = 0.03), illustrating that dietary requirements for these AA differ depending on sanitary conditions. This study, performed under practical conditions, shows that AA requirements are dependent on sanitary conditions. Furthermore, supplementation of diets with particular AA may improve performance, especially under poor hygienic conditions. Dietary protein concentration as well as Met, Thr, and Trp supplementation can modify immune status, which may influence resistance to sub-clinical and clinical diseases.

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