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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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
Domestication - Evolution - Gene flow - Neolithic

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Metatranscriptomics reveals mycoviral populations in the ovine rumen
Hitch, Thomas C.A. ; Edwards, Joan E. ; Gilbert, Rosalind A. - \ 2019
FEMS Microbiology Letters 366 (2019)13. - ISSN 0378-1097
fungi - mycobiome - mycovirus - RNA - rumen

The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.

A predictive strategy for mapping locations where future MOSSFA events are expected
Murk, A.J. ; Hollander, D.J. ; Chen, S. ; Hu, C. ; Liu, Y. ; Vonk, S.M. ; Schwing, Patrick T. ; Gilbert, S. ; Foekema, E.M. - \ 2019
In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 355 - 368.
A MOSSFA (marine oil snow sedimentation and flocculent accumulation) event was the reason that substantial amounts of the spilled oil were transported to the seafloor during the Deepwater Horizon (DWH) oil well blowout. The region-wide sinking and flocculent accumulation of marine oil snow on the sediment surface changed redox conditions, slowed down the biodegradation of the oil, and increased the spatial and temporal impacts on the benthic community and habitat suitability. Recent field research has confirmed that, in addition to the DWH MOSSFA event in the northern Gulf of Mexico (nGoM), another extensive MOSSFA event occurred in a biologically sensitive area in the southern Gulf of Mexico (sGoM) during the 1979 - 1980 Ixtoc I oil well blowout. Thus, MOSSFA events are not unexpected and have the potential to not only alter sediment chemical conditions but also to extend, expand, and intensify the ecological impact of an oil spill. Consequently this risk should be taken into consideration when preparing response...
Effect of marine snow on microbial oil degradation
Langenhoff, A.A.M. ; Rahsepar, Shokouh ; Eenennaam, J.S. van; Radović, Jagoš R. ; Oldenburg, Thomas B.P. ; Foekema, E.M. ; Murk, A.J. - \ 2019
In: Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 301 - 311.
In the aftermath of an oil spill, a possible response is the addition of chemical dispersants to prevent further spreading of the spilled oil on the ocean surface. The main objective is to enhance the formation of smaller oil droplets by reducing the interfacial tension between oil and water, thus dispersing the oil into the water column. The resulting solubilized oil with microdroplets along with the associated toxic compounds will be swiftly incorporated into the seawater. The formation of smaller oil droplets and the dispersant enhanced solubilized oil will increase its availability for bacteria and thus the biodegradability. Subsequently, the number and activity of oil-degrading bacteria increases, and more oil will be degraded in a shorter period of time (Kessler et al., Science 331:312–315, 2011). However, during the immediate release of the dispersed oil, volatile hydrocarbons including some of the more toxic compounds of benzene, toluene, ethylbenzene, and xylenes (BTEX) can inhibit the oil degradation (Sherry et al., Front Microbiol 5:131, 2014).
Depending on the oceanic conditions, the addition of chemical dispersants can result in excessive formation of marine snow. It has been shown that the application of dispersants during phytoplankton blooms can trigger the formation of marine snow to which the sticky dispersed oil can bind. In the presence of mineral particles, oiled snow complexes are being formed that become negatively buoyant and sink to the ocean floor. As a result, oiled marine snow accumulates on the ocean floor where biodegradation is inhibited due to oxygen depletion.
The abovementioned two mechanisms of inhibition of oil biodegradation upon application of oil spill dispersants will be discussed in this chapter.
Testing the Effect of MOSSFA (Marine Oil Snow Sedimentation and Flocculent Accumulation) Events in Benthic Microcosms
Foekema, E.M. ; Eenennaam, Justine van; Hollander, D.J. ; Langenhoff, A.A.M. ; Oldenburg, Thomas B.P. ; Radović, Jagoš R. ; Rohal, Melissa ; Romero, Isabel C. ; Schwing, Patrick T. ; Murk, A.J. - \ 2019
In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., - p. 288 - 299.
In multispecies experiments performed in microcosms with natural sediment, it was investigated how the presence of marine snow affects the fate and ecological impact of deposited oil residues. The response of different taxonomic groups like nematodes, foraminifera, crustaceans and molluscs onto the presence of marine snow with or without oil was compared with the impact of deposited oil residues without marine snow. Also the effect of the presence of marine snow on oil biodegradation and transfer for oil-derived compounds to selected biota was studied. Although not designed to mimic the specific deep sea conditions in the Gulf of Mexico, the outcome of the experiments gave new insights in how a MOSSFA event can affect the benthic community. In general the experments indicated that at field realistic oil-derived compound concentrations, the adverse impact of the marine snow on the sediment surface has a stronger impact on the benthic ecosystem than...
Living in cold blood: Arcobacter, Campylobacter, and Helicobacter in reptiles
Gilbert, Maarten J. ; Duim, Birgitta ; Zomer, Aldert L. ; Wagenaar, Jaap A. - \ 2019
Frontiers in Microbiology 10 (2019)MAY. - ISSN 1664-302X
Arcobacter - Biodiversity - Campylobacter - Ecology - Epsilonproteobacteria - Evolution - Helicobacter - Reptile

Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.

Late Quaternary lahars and lava dams: Fluvial responses of the Upper Tana River (Kenya)
Schoorl, J.M. ; Veldkamp, A. ; Claessens, L. ; Wijbrans, J.R. ; Olago, D.O. ; Lievens, C. - \ 2019
Geomorphology 341 (2019). - ISSN 0169-555X - p. 28 - 45.
40 39 Ar/ Ar geochronology - Basalt flows - Delta - Fluvial terrace - Lahar
Geomorphological and sedimentary records near the confluences of the Tana River and major tributaries draining the eastern slopes of Mt. Kenya and the Nyambeni Range, indicate impacts of Late Quaternary volcanic activity in their fluvial records. The main reconstructed event was triggered by a 366.9 ka basalt flow (40Ar/39Ar dated) which flowed along Kazita River from the Nyambeni Range blocking both Kazita River and Tana River near Kibuka Grand Falls, causing a temporary lake. Consequently, Tana River and Kazita River started to build volcanoclastic Gilbert type deltas. The preserved pro-delta sediments rich in trachytic pumice fragments display a mineralogical and age match with known Ithanguni trachytic tuffs, indicating delta build up right after a contemporary Ithanguni eruption. This trachytic eruption caused the deposition of lahars and fluvial volcaniclastic sediments in all river records draining the Eastern side of Mt. Kenya. The multiple lahars seem to be triggered by eruptions under glacial conditions (basalt age indicates MIS 10). The lava dammed lake was only short lived (estimated to have lasted only a few years to decades) and breached before a complete lake infill could occur. The current Kibuka Grand Falls can be viewed as the delayed incisional response of this lava dam breach, indicating that after >366.9 ka, Tana River is still responding and adjusting to this short-lived disruptive phase. The current Kazita River has re-incised adjacent to a MIS 4 basalt flow down into the crystalline Basement System rocks. The MIS 10 pre-volcanic sedimentary record indicates that more sediments were in the fluvial system during glacial conditions than during the interglacial conditions. An implication of our reconstruction is that the Late Quaternary fluvial record of Tana River is of only limited use to reconstruct uplift rates because reconstructed Quaternary incision rates are reflecting both volcanic disruptions as climate change trends of aridification and decreasing glaciation extents.
Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
Huang, Zheng Y.X. ; Xu, Chi ; Langevelde, Frank van; Ma, Yuying ; Langendoen, Tom ; Mundkur, Taej ; Si, Yali ; Tian, Huaiyu ; Kraus, Robert H.S. ; Gilbert, Marius ; Han, Guan Zhu ; Ji, Xiang ; Prins, Herbert H.T. ; Boer, Willem F. de - \ 2019
Journal of Animal Ecology 88 (2019)7. - ISSN 0021-8790 - p. 1044 - 1053.
avian influenza - community composition - dilution effect - diversity–disease relationship - phylogenetic distance - waterfowl

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long-distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related. Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental-scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity. Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence. Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.

A two-echelon inventory routing problem for perishable products
Rohmer, S.U.K. ; Claassen, G.D.H. ; Laporte, Gilbert - \ 2019
Computers and Operations Research 107 (2019). - ISSN 0305-0548 - p. 156 - 172.
Perishable products - Inventory-routing - Adaptive large neighbourhood search - Last-mile logistics - Two-echelon system
This paper presents a two-echelon inventory-routing problem for perishable products. Products are de- livered from a supplier to an intermediary depot, where storage may occur and from which they are delivered by smaller vehicles to the customer locations. Holding costs are incurred for storage at the de- pot. Customer availability is taken into account in the form of customer delivery patterns. The objective is to minimise the total transportation and holding costs. We formulate the problem as a mixed integer linear program and solve it by means of an adaptive large neighbourhood search metaheuristic in com- bination with the solution of a reduced formulation. Three variants of the heuristic are compared on a variety of randomly generated instances. Given the two-stage structure of the problem, computational results show the importance of taking the cost structure into account when choosing the most suitable solution approach.
Halophilic bacteria as a food source for the brine shrimp Artemia
Lopes-dos-Santos, R.M.A. ; Groot, Ruben ; Liying, Sui ; Bossier, Peter ; Stappen, Gilbert Van - \ 2019
Aquaculture 500 (2019). - ISSN 0044-8486 - p. 631 - 639.
Artemia - Cyst production - Gnotobiotic - Halophilic bacteria - Mono-diets

Artemia cysts are highly demanded by the aquaculture industry to be hatched into nauplii and used as live food for larvae of most farmed fish and shellfish species. In recent years, pond production of Artemia cysts has been proposed as an effective measure to reduce the high dependence of the industry on cysts harvested from wild populations. Nonetheless, the feeding management strategies of this type of intensive Artemia culture, focusing until now on costly phytoplankton boosting are still in need of optimization. The growth stimulation of the naturally occurring halophilic bacterial flora in the culture ponds, as a complementary food source for the Artemia nauplii, is currently being considered as a viable way to improve Artemia biomass and cyst production. Field studies conducted until now did not however, allow for patent conclusions about the actual dietary value of this bacterial biomass to the Artemia diet, hindering the widespread application of these practices. The purpose of this research was therefore to investigate the capacity of Artemia nauplii to survive and grow on diets consisting exclusively of mono-diets of live or dead biomass of six halophilic bacteria, belonging to genera commonly found in hypersaline environments where Artemia occur. To this end, a standard gnotobiotic Artemia culture system was used at a salinity relevant for a field situation (100 g l−1) and at seawater salinity (35 g l−1). The results showed that the addition of most tested halophilic bacteria, either as live or dead biomass, to the Artemia culture water, allowed for significantly superior nauplii survival than the corresponding negative control (starvation treatment). Furthermore, significantly higher individual length in comparison to the positive control (a standard marine bacterial diet used in Artemia gnotobiotic tests) was also observed, especially when feeding the nauplii with live halophilic bacteria biomass. The success at both salinities of the tested halophilic bacteria mono-diets when compared to both controls, clearly denoted that despite having a low nutritional value as far as fatty acids are concerned, they can be an intergral part of its diet during its first developmental stages. Although our findings need to be confirmed in field conditions, they are of importance for Artemia pond production as they confirm the potential of these microorganisms to be used as a viable dietary source, complementing the present focus on phytoplankton blooms to sustain Artemia populations.

Geomorfologische analyse van de Raamvallei
Maas, Gilbert ; Delft, Bas van; Mol, Gerben - \ 2018
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2918) - 79
Serious Games as planning support systems : Learning from playing maritime spatial planning challenge 2050
Jean, Steven ; Gilbert, Laura ; Medema, Wietske ; Keijser, Xander ; Mayer, Igor ; Inam, Azhar ; Adamowski, Jan - \ 2018
Water 10 (2018)12. - ISSN 2073-4441
Knowledge co-creation - Maritime spatial planning - Planning support systems - Serious games - Sustainability

The inherent complexity of planning at sea, called maritime spatial planning (MSP), requires a planning approach where science (data and evidence) and stakeholders (their engagement and involvement) are integrated throughout the planning process. An increasing number of innovative planning support systems (PSS) in terrestrial planning incorporate scientific models and data into multi-player digital game platforms with an element of role-play. However, maritime PSS are still early in their innovation curve, and the use and usefulness of existing tools still needs to be demonstrated. Therefore, the authors investigate the serious game, MSP Challenge 2050, for its potential use as an innovative maritime PSS and present the results of three case studies on participant learning in sessions of game events held in Newfoundland, Venice, and Copenhagen. This paper focusses on the added values of MSP Challenge 2050, specifically at the individual, group, and outcome levels, through the promotion of the knowledge co-creation cycle. During the three game events, data was collected through participant surveys. Additionally, participants of the Newfoundland event were audiovisually recorded to perform an interaction analysis. Results from survey answers and the interaction analysis provide evidence that MSP Challenge 2050 succeeds at the promotion of group and individual learning by translating complex information to players and creating a forum wherein participants can share their thoughts and perspectives all the while (co-) creating new types of knowledge. Overall, MSP Challenge and serious games in general represent promising tools that can be used to facilitate the MSP process.

Corrigendum: 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)9. - ISSN 0021-8812 - p. 4013 - 4013.
Post-weaning diarrhoea in piglets in practice is associated with protein fermentation, but specific protein fermentation metabolites contribute differently
Gilbert, M.S. ; Hee, B. van der; Gulersonmez, M. ; Stigter, E. ; Kies, Arie ; Gerrits, W.J.J. - \ 2018
Post-weaning diarrhoea in piglets in practice is associated with protein fermentation, but specific protein fermentation metabolites contribute differently
Gilbert, Myrthe - \ 2018
Nederlandse steden en hun ondergrond : testboek
Grond, Vincent ; Maas, Gilbert ; Timmermans, Wim ; Broks, Kees - \ 2018
Amersfoort : Stowa (Stowa rapport 2018-64) - 67
Quantifying the environmental and economic benefits of cooperation : A case study in temperature-controlled food logistics
Stellingwerf, Helena M. ; Laporte, Gilbert ; Cruijssen, Frans C.A.M. ; Kanellopoulos, Argyris ; Bloemhof, Jacqueline M. - \ 2018
Transportation Research. Part D, Transport and Environment 65 (2018). - ISSN 1361-9209 - p. 178 - 193.
CO emissions - Fresh food - Inventory - Logistics - Route optimization

Inefficient road transportation causes unnecessary costs and polluting emissions. This problem is even more severe in refrigerated transportation, in which temperature control is used to guarantee the quality of the products. Organizing logistics cooperatively can help decrease both the environmental and the economic impacts. In Joint Route Planning (JRP) cooperation, suppliers and customers jointly optimize routing decisions so that cost and emissions are minimized. Vendor Managed Inventory (VMI) cooperation extends JRP cooperation by optimizing routing and inventory planning decisions simultaneously. However, in addition to their economic advantages, VMI and JRP may also yield environmental benefits. To test this assertion, we perform a case study on cooperation between a number of supermarket chains in the Netherlands. The data of this case study are analyzed to quantify both the economic and environmental benefits of implementing cooperation via JRP and VMI, using vehicle routing and an inventory routing models. We found that JRP cooperation can substantially reduce cost and emissions compared with uncooperative routing. In addition, VMI cooperation can further reduce cost and emissions, but minimizing cost and minimizing emissions no longer result in the same solution and there is a trade-off to be made.

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.

Homologous recombination between genetically divergent campylobacter fetus lineages supports host-associated speciation
Gilbert, Maarten J. ; Duim, Birgitta ; Graaf-van Bloois, Linda van der; Wagenaar, Jaap A. ; Zomer, Aldert L. - \ 2018
Genome Biology and Evolution 10 (2018)3. - ISSN 1759-6653 - p. 716 - 722.
Campylobacter fetus - Homologous recombination - Host association - Reptile - Speciation - Whole genome sequencing

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1-5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

Campylobacter blaseri sp. Nov., isolated from common seals (Phoca vitulina)
Gilbert, Maarten J. ; Zomer, Aldert L. ; Timmerman, Arjen J. ; Spaninks, Mirlin P. ; Rubio-García, Ana ; Rossen, John W. ; Duim, Birgitta ; Wagenaar, Jaap A. - \ 2018
International Journal of Systematic and Evolutionary Microbiology 68 (2018)5. - ISSN 1466-5026 - p. 1787 - 1794.
Average nucleotide identity - Campylobacter - Common seal - Core genome phylogeny - Microbiome - Novel species
During a study to assess the faecal microbiome of common seals (Phoca vitulina) in a Dutch seal rehabilitation centre, 16S rRNA gene sequences of an unknown Campylobacter taxon were identified. Campylobacter isolates, which differed from the established Campylobacter taxa, were cultured and their taxonomic position was determined by a polyphasic study based on ten isolates. The isolates were characterized by 16S rRNA and atpA gene sequence analyses and by conventional phenotypic testing. Based on the whole genome sequences, the average nucleotide identity and core genome phylogeny were determined. The isolates formed a separate phylogenetic clade, divergent from all other Campylobacter taxa and most closely related to Campylobacter corcagiensis, Campylobacter geochelonis and Campylobacter ureolyticus. The isolates can be distinguished phenotypically from all other Campylobacter taxa based on their lack of motility, growth at 25 °C and growth on MacConkey agar. This study shows that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter blaseri sp. nov. is proposed. The type strain for this novel species is 17S00004-5T (=LMG 30333T=CCUG 71276T).
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.
Ranavirus genotypes in Netherlands and their potential association with virulence in water frogs (Pelophylax spp.) article
Saucedo, Bernardo ; Hughes, Joseph ; Spitzen-Van Der Sluijs, Annemarieke ; Kruithof, Natasja ; Schills, Marc ; Rijks, Jolianne M. ; Jacinto-Maldonado, Mónica ; Suarez, Nicolás ; Haenen, Olga L.M. ; Voorbergen-Laarman, Michal ; Broek, Jan Van Den; Gilbert, Maarten ; Gröne, Andrea ; Beurden, Steven J. Van; Verheije, M.H. - \ 2018
Emerging Microbes and Infections 7 (2018)1. - ISSN 2222-1751
Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (Pelophylax spp.) in Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011-2016 revealed three CMTV groups present in distinct geographical areas in Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance.
Short communication : Supplementation of fructo-oligosaccharides does not improve insulin sensitivity in heavy veal calves fed different sources of carbohydrates
Pantophlet, Andre J. ; Gilbert, M.S. ; Gerrits, W.J.J. ; Vonk, R.J. - \ 2017
Journal of Dairy Science 100 (2017)11. - ISSN 0022-0302 - p. 9442 - 9446.
Fructo-oligosaccharides - Insulin sensitivity - Milk replacer - Veal calf

Heavy veal calves (4-6 mo old) often develop problems with insulin sensitivity. This could lead to metabolic disorders and impaired animal growth performance. Studies in various animal species have shown that the supplementation of short-chain fructo-oligosaccharides (scFOS) can improve insulin sensitivity. We therefore studied the effects of scFOS supplementation on insulin sensitivity in heavy veal calves. Forty male Holstein-Friesian calves (BW = 190 ± 2.9 kg; age = 162 ± 1.4 d at the start of the trial) were fed either a control milk replacer (MR) diet or a diet in which one-third of the lactose was replaced by glucose, fructose, or glycerol for 10 wk prior to the start of the trial. At the start of the trial, calves were subjected to a frequently sampled intravenous glucose tolerance test to assess whole-body insulin sensitivity (muscle and hepatic insulin sensitivity). Calves within each dietary treatment group were ranked based on their insulin sensitivity value. Half of the calves received scFOS (12 mg/kg of BW) with the MR for 6 wk (supplementation was equally distributed over the insulin sensitivity range). Subsequently, a second frequently sampled intravenous glucose tolerance test was conducted to assess the effect of scFOS. In addition, fasting plasma levels of glucose, insulin, triglycerides, and cholesterol were determined to calculate the quantitative insulin sensitivity check index and triglyceride:high-density lipoprotein cholesterol ratio (fasting indicators of insulin sensitivity). Whole-body insulin sensitivity was low at the start of the trial and remained low in all groups [1.0 ± 0.1 and 0.8 ± 0.1 (mU/L)-1 · min-1 on average, respectively]. Supplementation of scFOS did not improve insulin sensitivity in any of the treatment groups. The quantitative insulin sensitivity check index and the triglyceride:high-density lipoprotein cholesterol ratio also did not differ between scFOS and non-scFOS calves and averaged 0.326 ± 0.003 and 0.088 ± 0.004, respectively, at the end of the trial. We conclude that scFOS supplementation does not improve insulin sensitivity in heavy veal calves regardless of the carbohydrate composition of the MR. This is in contrast to other animals (e.g., dogs and horses), where scFOS supplementation did improve insulin sensitivity. The absence of an effect of scFOS might be related to the dosage or to metabolic differences between ruminants and nonruminants. Increasing evidence indicates that dietary interventions in veal calves have little or no effect on insulin sensitivity, possibly because of low levels of insulin sensitivity.

Feed efficiency and the faecal microbiome at slaughter weight in pigs
Verschuren, L.M.G. ; Calus, M.P.L. ; Jansman, A.J.M. ; Bergsma, R. ; Knol, E.F. ; Gilbert, H. ; Zemb, O. - \ 2017
- 1 p.
Feed efficiency (FE) is an important trait in the pig industry, as feed costs are responsible for the major part of production costs. Availability in the market and cost of feed ingredients dictate changes in feed composition. As a result, fibre level and composition can vary between pig diets. Microbiota in the gastrointestinal tract play an important role in fibre digestion, because they produce enzymes that break down fibre structures and deliver volatile fatty acids to the pig. These volatile fatty acids can be used as metabolic energy source. As such, microbial fermentation could influence FE in pigs. The aim of this study was to investigate the association between FE and faecal microbiome in commercial grower-finisher pigs. Three-way crossbreed grower-finisher pigs (154) were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley (WB). Faecal samples were collected on the day before slaughter (mean bodyweight 122 kg) and sequenced for the V3V4 16S ribosomal DNA regions. Sequences were clustered according to operational taxonomic units (OTU) for each individual, forming a table of OTU abundancy. A partial least square regression was applied to the dataset, together with a discriminant analysis using principal components of FE extreme groups (10 high and 10 low FE animals for each diet x sex-combination). Pigs on different diets and males vs. females had a very distinct microbiome, needing only two OTUs for diet (P=0.018) and 18 OTUs for sex (P=0.002) to separate the groups. Faecal microbiome was not related to FE groups fed the CS diet, but there were sex specific OTUs related to FE in the male and female pigs in the groups fed the WB diet. In conclusion, our results show a diet and sex dependent relationship between the faecal microbial composition and FE in grower-finisher pigs at slaughter weight. This study is part of the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement no 633531.
Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host
Gilbert, Maarten J. ; Duim, Birgitta ; Timmerman, Arjen J. ; Zomer, Aldert L. ; Wagenaar, Jaap A. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322 - 8 p.

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.

Only 7% of the variation in feed efficiency in veal calves can be predicted from variation in feeding motivation, digestion, metabolism, immunology, and behavioral traits in early life
Gilbert, M.S. ; Borne, J.J.G.C. van den; Reenen, C.G. van; Gerrits, W.J.J. - \ 2017
Journal of Dairy Science 100 (2017)10. - ISSN 0022-0302 - p. 8087 - 8101.
Feed efficiency - Glycerol - Growth performance - Lactose - Veal calf

High interindividual variation in growth performance is commonly observed in veal calf production and appears to depend on milk replacer (MR) composition. Our first objective was to examine whether variation in growth performance in healthy veal calves can be predicted from early life characterization of these calves. Our second objective was to determine whether these predictions differ between calves that are fed a high- or low-lactose MR in later life. A total of 180 male Holstein-Friesian calves arrived at the facilities at 17 ± 3.4 d of age, and blood samples were collected before the first feeding. Subsequently, calves were characterized in the following 9 wk (period 1) using targeted challenges related to traits within each of 5 categories: feeding motivation, digestion, postabsorptive metabolism, behavior and stress, and immunology. In period 2 (wk 10-26), 130 calves were equally divided over 2 MR treatments: a control MR that contained lactose as the only carbohydrate source and a low-lactose MR in which 51% of the lactose was isocalorically replaced by glucose, fructose, and glycerol (2:1:2 ratio). Relations between early life characteristics and growth performance in later life were assessed in 117 clinically healthy calves. Average daily gain (ADG) in period 2 tended to be greater for control calves (1,292 ± 111 g/d) than for calves receiving the low-lactose MR (1,267 ± 103 g/d). Observations in period 1 were clustered per category using principal component analysis, and the resulting principal components were used to predict performance in period 2 using multiple regression procedures. Variation in observations in period 1 predicted 17% of variation in ADG in period 2. However, this was mainly related to variation in solid feed refusals. When ADG was adjusted to equal solid feed intake, only 7% of the variation in standardized ADG in period 2, in fact reflecting feed efficiency, could be explained by early life measurements. This indicates that >90% of the variation in feed efficiency in later life could not be explained by early life characterization of the calves. It is speculated that variation in health status explains a substantial portion of variation in feed efficiency in later life. Significant relations between fasting plasma glucose concentrations, fecal pH, drinking speed, and plasma natural antibodies in early life (i.e., not exposed to the lactose replacer) and feed efficiency in later life depended on MR composition. These measurements are therefore potential tools for screening calves in early life on their ability to cope with MR varying in lactose content.

Campylobacter pinnipediorum sp. Nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov
Gilbert, Maarten J. ; Miller, William G. ; St. Leger, Judy ; Chapman, Mary H. ; Timmerman, Arjen J. ; Duim, Birgitta ; Foster, Geoffrey ; Wagenaar, Jaap A. - \ 2017
International Journal of Systematic and Evolutionary Microbiology 67 (2017)6. - ISSN 1466-5026 - p. 1961 - 1968.
Average nucleotide identity - Campylobacter - Novel species - Pinnipeds - Urease - Whole genome sequencing

During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established taxa of the genus Campylobacter, were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobactermucosalis. Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).

Connecting Earth observation to high-throughput biodiversity data
Bush, Alex ; Sollmann, Rahel ; Wilting, Andreas ; Bohmann, Kristine ; Cole, Beth ; Balzter, Heiko ; Martius, Christopher ; Zlinszky, András ; Calvignac-Spencer, Sébastien ; Cobbold, Christina A. ; Dawson, Terence P. ; Emerson, Brent C. ; Ferrier, Simon ; Gilbert, M.T.P. ; Herold, Martin - \ 2017
Nature Ecology & Evolution 1 (2017)7. - ISSN 2397-334X - 9 p.
Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track
biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation,
indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even
unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, highthroughput
DNA sequencing and modern ecological modelling to extract much more of the information available in Earth
observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts
on biodiversity and its functions and services.
Measuring temporal liking simultaneously to Temporal Dominance of Sensations in several intakes. An application to Gouda cheeses in 6 Europeans countries
Thomas, A. ; Chambault, M. ; Dreyfuss, L. ; Gilbert, C.C. ; Hegyi, A. ; Henneberg, S. ; Knippertz, A. ; Kostyra, E. ; Kremer, S. ; Silva, A.P. ; Schlich, P. - \ 2017
Food Research International 99 (2017)1. - ISSN 0963-9969 - p. 426 - 434.
Gouda cheese - Liking - Temporal Dominance of Sensations (TDS) - Temporal Drivers of Liking (TDL)
The idea of having untrained consumers performing Temporal Dominance of Sensations (TDS) and dynamic liking in the same session was recently introduced (Thomas, van der Stelt, Prokop, Lawlor, & Schlich, 2016). In the present study, a variation of the data acquisition protocol was done, aiming to record TDS and liking simultaneously on the same screen in a single session during multiple product intakes. This method, called Simultaneous Temporal Drivers of Liking (S-TDL), was used to describe samples of Gouda cheese in an international experiment.To test this idea, consumers from six European countries (n = 667) assessed 4 Gouda cheeses with different ages and fat contents during one sensory evaluation session. Ten sensory attributes and a 9-point hedonic scale were presented simultaneously on the computer screen. While performing TDS, consumers could reassess their liking score as often as they wanted. This new type of sensory data was coded by individual average liking scores while a given attribute was perceived as dominant (Liking While Dominant; LWD).Although significant differences in preference were observed among countries, there were global preferences for a longer dominance of melting, fatty and tender textures. The cheese flavour attribute was the best positive TDL, whereas bitter was a strong negative TDL. A cluster analysis of the 667 consumers identified three significant liking clusters, each with different most and least preferred samples. For the TDL computation by cluster, significant specific TDL were observed. These results showed the importance of overall liking segmentation before TDL analysis to determine which attributes should have a longer dominance duration in order to please specific consumer targets.
Green compressed fluid technologies for downstream processing of Scenedesmus obliquus in a biorefinery approach
Gilbert-López, Bienvenida ; Mendiola, José A. ; Broek, Lambertus A.M. van den; Houweling-Tan, Bwee ; Sijtsma, Lolke ; Cifuentes, Alejandro ; Herrero, Miguel ; Ibáñez, Elena - \ 2017
Algal Research 24 (2017). - ISSN 2211-9264 - p. 111 - 121.
Algae - Biorefinery - Carotenoid - Lipid - Pressurized liquid extraction - Supercritical fluid extraction

The fractionation of algae biomass in several high-value compounds that can be used as ingredients in other applications sets the basis of the algae biorefinery approach. The present study aimed at the extraction and fractionation of bioactive compounds from the microalga Scenedesmus obliquus, by means of applying a sequential process without the manipulation of the biomass in the extraction cell. This integrated platform of compressed fluid extraction technologies of low-environmental impact was designed in order to produce increases of solvent polarity using non-toxic solvents. The process involved the following steps:(1) supercritical fluid extraction (SFE) using supercritical carbon dioxide (ScCO2); (2) gas expanded liquids (GXL) using 75% ethanol and 25% ScCO2 (v/v) and; (3) pressurized liquid extraction (PLE) using water. Extraction conditions were optimized using response surface methodology (RSM) and kinetic studies. Extraction yield, antioxidant activity as well as contents of total phenols, carotenoids, proteins and sugars were the studied response variables. High performance liquid chromatography coupled to evaporative light-scattering detector (HPLC-ELSD) analyses of the fractions revealed that triacylglycerols were mainly extracted by SFE. Lutein and β-carotene were the main pigments identified in the extracts by HPLC coupled to diode array and mass spectrometry detectors (HPLC-DAD-MS/MS), which were preferentially extracted in the GXL step. Polar compounds such as proteins and sugars remained predominantly in the residue. Therefore, the green downstream platform developed in this study for valorization of the microalgae biomass, is able to produce different fractions with potential application in the food, pharmaceutical and cosmetic industries.

Comparative Genomics of Campylobacter fetus from Reptilesand Mammals Reveals Divergent Evolution in Host-Associated Lineages
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Zomer, Aldert ; Graaf-Van Bloois, Linda Van Der; Fitzgerald, C. ; Forbes, Ken J. ; Méric, Guillaume ; Sheppard, S. ; Wagenaar, J.A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 2006 - 2019.
Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies.
Safe food and feed through an integrated toolbox for mycotoxin management: the MyToolBox approach
Krska, R. ; Nijs, M. De; Mcnerney, O. ; Pichler, M. ; Gilbert, J. ; Edwards, S. ; Suman, M. ; Magan, N. ; Rossi, V. ; Fels, Ine van der; Bagi, F. ; Poschmaier, B. ; Sulyok, M. ; Berthiller, F. ; Egmond, H.P. Van - \ 2016
World Mycotoxin Journal 9 (2016)4. - ISSN 1875-0710 - p. 487 - 495.
There is a pressing need to mobilise the wealth of knowledge from the international mycotoxin research conductedover the past 25-30 years, and to perform cutting-edge research where knowledge gaps still exist. This knowledgeneeds to be integrated into affordable and practical tools for farmers and food processors along the chain inorder to reduce the risk of mycotoxin contamination of crops, feed and food. This is the mission of MyToolBox – a four-year project which has received funding from the European Commission. It mobilises a multi-actorpartnership (academia, farmers, technology small and medium sized enterprises, food industry and policystakeholders) to develop novel interventions aimed at achieving a significant reduction in crop losses due tomycotoxin contamination. Besides a field-to-fork approach, MyToolBox also considers safe use options ofcontaminated batches, such as the efficient production of biofuels. Compared to previous efforts of mycotoxin reduction strategies, the distinguishing feature of MyToolBox is to provide the recommended measures to theend users along the food and feed chain in a web-based MyToolBox platform (e-toolbox). The project focuseson small grain cereals, maize, peanuts and dried figs, applicable to agricultural conditions in the EU and China. Crop losses using existing practices are being compared with crop losses after novel pre-harvest interventionsincluding investigation of genetic resistance to fungal infection, cultural control (e.g. minimum tillage or cropdebris treatment), the use of novel biopesticides suitable for organic farming, competitive biocontrol treatment and development of novel modelling approaches to predict mycotoxin contamination. Research into post-harvestmeasures includes real-time monitoring during storage, innovative sorting of crops using vision-technology, novelmilling technology and studying the effects of baking on mycotoxins at an industrial scale.
Predicting variation in feed efficiency in veal calves by early life characterization
Gilbert, M.S. ; Borne, J.J.G.C. van den; Reenen, C.G. van; Gerrits, W.J.J. - \ 2016
In: Energy and protein metabolism and nutrition. - Wageningen Academic Publishers (EAAP publication 137) - ISBN 9789086862863 - p. 75 - 76.
Predicting variation in feed efficiency in veal calves by early life characterization
Gilbert, Myrthe - \ 2016
Comparative genomics of campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Kik, Marja ; Zomer, Aldert L. ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)9. - ISSN 1759-6653 - p. 3022 - 3029.
Campylobacter Iguaniorum - Comparative Genomics - Evolution - Phylogeny - Recombination - Reptile

Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, andC. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorumstrain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated froma green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-Associated C. fetus subsp.Testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regionswere identified inC. iguaniorum.One of these regions is>50 kb withdeviantG+Ccontent, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-Associated C. fetus subsp.Testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

Herstel en ontwikkeling van laagdynamische, aquatische systemen in het rivierengebied
Arts, Gertie ; Verdonschot, Ralf ; Maas, Gilbert ; Massop, Harry ; Ottburg, Fabrice ; Weeda, Eddy - \ 2016
Driebergen : Vereniging van Bos- en Natuurterreineigenaren, VBNE (Alterra-rapport 2729) - 128
aquatische ecosystemen - aquatisch milieu - ecologisch herstel - rivierengebied - nederland - aquatic ecosystems - aquatic environment - ecological restoration - netherlands
Na een inleiding (Hoofdstuk 1) beschrijft het rapport achtereenvolgens de macro-evertebraten (Hoofdstuk 2); de vissen, amfibieën en reptielen (Hoofdstuk 3); en de waterplanten van het rivierengebied (Hoofdstuk 4). Hoofdstuk 5 beschrijft de uitgevoerde GIS analyse en presenteert de resultaten en de kansenkaarten. Alle gegenereerde kaarten zijn opgenomen in twee bijlagerapporten. Hoofdstuk 6 geeft een discussie van het uitgevoerde onderzoek ten aanzien van de methode, de beschikbare gegevens en de analyse en plaatst de resultaten in het licht van uitgevoerde herstelmaatregelen in het rivierengebied. Hoofdstuk 7 vat de voornaamste conclusies samen. Hoofdstuk 8 geeft een overzicht van de gebruikte literatuur.
Insulin sensitivity in calves decreases substantially during the first 3 months of life and is unaffected by weaning or fructo-oligosaccharide supplementation
Pantophlet, A.J. ; Gilbert, M.S. ; Borne, J.J.G.C. van den; Gerrits, W.J.J. ; Priebe, M.G. ; Vonk, R.J. - \ 2016
Journal of Dairy Science 99 (2016)9. - ISSN 0022-0302 - p. 7602 - 7611.
Veal calves at the age of 4 to 6 mo often experience problems with glucose homeostasis, as indicated by postprandial hyperglycemia, hyperinsulinemia, and insulin resistance. It is not clear to what extent the ontogenetic development of calves or the feeding strategy [e.g., prolonged milk replacer (MR) feeding] contribute to this pathology. The objective of this study was therefore to analyze effects of MR feeding, weaning, and supplementation of short-chain fructo-oligosaccharides (FOS) on the development of glucose homeostasis and insulin sensitivity in calves during the first 3 mo of life. Thirty male Holstein-Friesian calves (18 ± 0.7 d of age) were assigned to 1 of 3 dietary treatments: the control (CON) group received MR only, the FOS group received MR with the addition of short-chain FOS, and the solid feed (SF) group was progressively weaned to SF. The CON and FOS calves received an amount of MR, which gradually increased (from 400 to 1,400 g/d) during the 71-d trial period. For the SF calves, the amount of MR increased from 400 to 850 g/d at d 30, and then gradually decreased, until completely weaned to only SF at d 63. The change in whole body insulin sensitivity was assessed by intravenous glucose tolerance tests. Milk tolerance tests were performed twice to assess changes in postprandial blood glucose, insulin, and nonesterified fatty acid responses. Whole-body insulin sensitivity was high at the start (16.7 ± 1.6 × 10−4 [μU/mL]−1), but decreased with age to 4.2 ± 0.6 × 10−4 [μU/mL]−1 at the end of the trial. The decrease in insulin sensitivity was most pronounced (∼70%) between d 8 and 29 of the trial. Dietary treatments did not affect the decrease in insulin sensitivity. For CON and FOS calves, the postprandial insulin response was 3-fold higher at the end of the trial than at the start, whereas the glucose response remained similar. The SF calves, however, showed pronounced hyperglycemia and hyperinsulinemia at the end of the trial, although weaning did not affect insulin sensitivity. We conclude that whole body insulin sensitivity decreases by 75% in calves during the first 3 mo of life. Weaning or supplementation of short-chain FOS does not affect this age-related decline in insulin sensitivity. Glucose homeostasis is not affected by supplementation of short-chain FOS in young calves, whereas postprandial responses of glucose and insulin to a MR meal strongly increase after weaning.
Redirection of auxin flow in Arabidopsis thaliana roots after infection by root-knot nematodes
Kyndt, Tina ; Goverse, Aska ; Haegeman, Annelies ; Warmerdam, Sonja ; Wanjau, Cecilia ; Jahani, Mona ; Engler, Gilbert ; Almeida Engler, Janice De; Gheysen, Godelieve - \ 2016
Journal of Experimental Botany 67 (2016)15. - ISSN 0022-0957 - p. 4559 - 4570.
Plant-parasitic root-knot nematodes induce the formation of giant cells within the plant root, and it has been recognized that auxin accumulates in these feeding sites. Here, we studied the role of the auxin transport system governed by AUX1/LAX3 influx proteins and different PIN efflux proteins during feeding site development in Arabidopsis thaliana roots. Data generated via promoter–reporter line and protein localization analyses evoke a model in which auxin is being imported at the basipetal side of the feeding site by the concerted action of the influx proteins AUX1 and LAX3, and the efflux protein PIN3. Mutants in auxin influx proteins AUX1 and LAX3 bear significantly fewer and smaller galls, revealing that auxin import into the feeding sites is needed for their development and expansion. The feeding site development in auxin export (PIN) mutants was only slightly hampered. Expression of some PINs appears to be suppressed in galls, probably to prevent auxin drainage. Nevertheless, a functional PIN4 gene seems to be a prerequisite for proper nematode development and gall expansion, most likely by removing excessive auxin to stabilize the hormone level in the feeding site. Our data also indicate a role of local auxin peaks in nematode attraction towards the root
The effect of replacing lactose by starch on protein and fat digestion in milk-fed veal calves
Pluschke, A.M. ; Gilbert, M.S. ; Williams, B.A. ; Borne, J.J.G.C. van den; Schols, H.A. ; Gerrits, W.J.J. - \ 2016
Animal 10 (2016)8. - ISSN 1751-7311 - p. 1296 - 1302.
lipase - milk-fed calf - starch - trypsin - α-amylase

Replacing dairy components from milk replacer (MR) with vegetable products has been previously associated with decreased protein and fat digestibility in milk-fed calves resulting in lower live weight gain. In this experiment, the major carbohydrate source in MR, lactose, was partly replaced with gelatinized corn starch (GCS) to determine the effect on protein and fat digestibility in milk-fed calves. In total, 16 male Holstein-Friesian calves received either MR with lactose as the carbohydrate source (control) or 18% GCS at the expense of lactose. In the adaptation period, calves were exposed to an increasing dose of GCS for 14 weeks. The indigestible marker cobalt ethylenediaminetetraacetic acid was incorporated into the MR for calculating apparent nutrient digestibility, whereas a pulse dose of chromium (Cr) chloride was fed with the last MR meal 4 h before slaughter as an indicator of passage rates. The calves were anesthetized and exsanguinated at 30 weeks of age. The small intestine was divided in three; small intestine 1 and 2 (SI1 and SI2, respectively) and the terminal ileum (last ~100 cm of small intestine) and samples of digesta were collected. Small intestinal digesta was analysed for α-amylase, lipase and trypsin activity. Digestibility of protein was determined for SI1, SI2, ileum and total tract, whereas digestibility of fat was determined for SI1, SI2 and total tract. Apparent protein digestibility in the small intestine did not differ between treatments but was higher in control calves at total tract level. Apparent crude fat digestibility tended to be increased in SI1 and SI2 for GCS calves, but no difference was found at total tract level. Activity of α-amylase in SI2 and lipase in both SI1 and SI2 was higher in GCS calves. Activity of trypsin tended to be higher in control calves and was higher in SI1 compared with SI2. A lower recovery of Cr in SI2 and a higher recovery of Cr in the large intestine suggest an increased rate of passage for GCS calves. Including 18% of GCS in a milk replacer at the expense of lactose increased passage rate and decreased apparent total tract protein digestibility. In the small intestine, protein digestion did not decrease when feeding GCS and fat digestion even tended to increase. Overall, effects on digestion might be levelled when partially replacing lactose with GCS, because starch digestion is lower than that of lactose but fat digestion may be slightly increased when feeding GCS.

Lactose in milk replacer can partly be replaced by glucose, fructose, or glycerol without affecting insulin sensitivity in veal calves
Pantophlet, A.J. ; Gilbert, M.S. ; Borne, J.J.G.C. van den; Gerrits, W.J.J. ; Roelofsen, H. ; Priebe, M.G. ; Vonk, R.J. - \ 2016
Journal of Dairy Science 99 (2016)4. - ISSN 0022-0302 - p. 3072 - 3080.
Fructose - Glucose homeostasis - Glycerol - Insulin sensitivity - Veal calves

Calf milk replacer (MR) contains 40 to 50% lactose. Lactose strongly fluctuates in price and alternatives are desired. Also, problems with glucose homeostasis and insulin sensitivity (i.e., high incidence of hyperglycemia and hyperinsulinemia) have been described for heavy veal calves (body weight >100 kg). Replacement of lactose by other dietary substrates can be economically attractive, and may also positively (or negatively) affect the risk of developing problems with glucose metabolism. An experiment was designed to study the effects of replacing one third of the dietary lactose by glucose, fructose, or glycerol on glucose homeostasis and insulin sensitivity in veal calves. Forty male Holstein-Friesian (body weight = 114 ± 2.4 kg; age = 97 ± 1.4 d) calves were fed an MR containing 462 g of lactose/kg (CON), or an MR in which 150 g of lactose/kg of MR was replaced by glucose (GLU), fructose (FRU), or glycerol (GLY). During the first 10 d of the trial, all calves received CON. The CON group remained on this diet and the other groups received their experimental diets for a period of 8 wk. Measurements were conducted during the first (baseline) and last week of the trial. A frequently sampled intravenous glucose tolerance test was performed to assess insulin sensitivity and 24 h of urine was collected to measure glucose excretion. During the last week of the trial, a bolus of 1.5 g of [U-13C] substrates was added to their respective meals and plasma glucose, insulin, and 13C-glucose responses were measured. Insulin sensitivity was low at the start of the trial and remained low [1.2 ± 0.1 and 1.0 ± 0.1 (mU/L)-1 × min-1], and no treatment effect was noted. Glucose excretion was low at the start of the trial (3.4 ± 1.0 g/d), but increased (P <0.01) in CON and GLU calves (26.9 ± 3.9 and 43.0 ± 10.6 g/d) but not in FRU and GLY calves. Postprandial glucose was higher in GLU, lower in FRU, and similar in GLY compared with CON calves. Postprandial insulin was lower in FRU and GLY and similar in GLU compared with CON calves. Postprandial 13C-glucose increased substantially in FRU and GLY calves, indicating that calves are able to partially convert these substrates to glucose. We concluded that replacing one third of lactose in MR by glucose, fructose, or glycerol in MR differentially influences postprandial glucose homeostasis but does not affect insulin sensitivity in veal calves.

Effects of replacing lactose from milk replacer by glucose, fructose, or glycerol on energy partitioning in veal calves
Gilbert, M.S. ; Pantophlet, A.J. ; Borne, J.J.G.C. van den; Hendriks, W.H. ; Schols, H.A. ; Gerrits, W.J.J. - \ 2016
Journal of Dairy Science 99 (2016)2. - ISSN 0022-0302 - p. 1121 - 1132.
Energy retention - Fructose - Glucose - Glycerol - Veal calf

Calf milk replacers contain 40 to 50% lactose. Fluctuating dairy prices are a major economic incentive to replace lactose from milk replacers by alternative energy sources. Our objective was, therefore, to determine the effects of replacement of lactose with glucose, fructose, or glycerol on energy and protein metabolism in veal calves. Forty male Holstein-Friesian calves (114 ± 2.4 kg) were fed milk replacer containing 46% lactose (CON) or 31% lactose and 15% of glucose (GLUC), fructose (FRUC), or glycerol (GLYC). Solid feed was provided at 10 g of dry matter (DM)/kg of metabolic body weight (BW0.75) per day. After an adaptation of 48 d, individual calves were harnessed, placed in metabolic cages, and housed in pairs in respiration chambers. Apparent total-tract disappearance of DM, energy, and N and complete energy and N balances were measured. The GLUC, FRUC, and GLYC calves received a single dose of 1.5 g of [U-13C]glucose, [U-13C]fructose, or [U-13C]glycerol, respectively, with their milk replacer at 0630 h and exhaled 13CO2 and 13C excretion with feces was measured. Apparent total-tract disappearance was decreased by 2.2% for DM, 3.2% for energy, and 4.2% for N in FRUC compared with CON calves. Energy and N retention did not differ between treatments, and averaged 299 ± 16 kJ/kg of BW0.75 per day and 0.79 ± 0.04 g/kg of BW0.75 per day, respectively, although FRUC calves retained numerically less N (13%) than other calves. Recovery of 13C isotopes as 13CO2 did not differ between treatments and averaged 72 ± 1.6%. The time at which the maximum rate of 13CO2 production was reached was more than 3 h delayed for FRUC calves, which may be explained by a conversion of fructose into other substrates before being oxidized. Recovery of 13C in feces was greater for FRUC calves (7.7 ± 0.59%) than for GLUC (1.0 ± 0.27%) and GLYC calves (0.5 ± 0.04%), indicating incomplete absorption of fructose from the small intestine resulting in fructose excretion or fermentation. In conclusion, energy and N retention was not affected when replacing >30% of the lactose with glucose, fructose, or glycerol. Increased fecal losses of DM, energy, and N were found in FRUC calves compared with CON, GLUC, and GLYC calves. Postabsorptive losses occurred with the urine for glucose and glycerol, which caused a lower respiratory quotient for GLUC calves during the night. Fructose was oxidized more slowly than glucose and glycerol, probably as a result of conversion into other substrates before oxidation.

Whole Genome PCR Scanning (WGPS) of C. burnetii strains from ruminants
Sidi-Boumedine, Karim ; Adam, Gilbert ; Angen, Oysten ; Aspán, A. ; Bossers, A. ; Roest, H.I.J. ; Prigent, Myriam ; Thiéry, R. ; Rousset, Elodie - \ 2015
Microbes and Infection 17 (2015)11-12. - ISSN 1286-4579 - p. 772 - 775.
Coxiella burnetii is the causative agent of Q fever, a zoonosis that spreads from ruminants to humans via the inhalation of aerosols contaminated by livestock's birth products. This study aimed to compare the genomes of strains isolated from ruminants by “Whole Genome PCR Scanning (WGPS)” in order to identify genomic differences. C. burnetii isolated from different ruminant hosts were compared to the Nine Mile reference strain using WGPS. The identified genomic regions of differences (RDs) were confirmed by sequencing. A set of 219 primers for amplification of 10 kbp segments covering the entire genome was obtained. The analyses revealed the presence of: i) conserved genomic regions, ii) genomic polymorphism including insertions and deletions and iii) amplification failures in some cases as well. WGPS, a descriptive approach, allowed the identification and localization of divergent genetic loci from various strains of C. burnetii which consisted of deletions, insertions and maybe genomic rearrangements. It also substantiates the role played by the IS1111 element in the genomic plasticity of C. burnetii. We believe that this approach could be combined with new sequencing technologies, as a selective/directed sequencing approach, particularly when repeated sequences are present in the analysed genomes
Campylobacter iguaniorum sp. nov., isolated from reptiles
Gilbert, Maarten J. ; Kik, Marja ; Miller, William G. ; Duim, Birgitta ; Wagenaar, Jaap A. - \ 2015
International Journal of Systematic and Evolutionary Microbiology 65 (2015)3. - ISSN 1466-5026 - p. 975 - 982.

During sampling of reptiles for members of the class Epsilonproteobacteria, strains representing a member of the genus Campylobacter not belonging to any of the established taxa were isolated from lizards and chelonians. Initial amplified fragment length polymorphism, PCR and 16S rRNA sequence analysis showed that these strains were most closely related to Campylobacter fetus and Campylobacter hyointestinalis. A polyphasic study was undertaken to determine the taxonomic position of five strains. The strains were characterized by 16S rRNA and atpA sequence analysis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and conventional phenotypic testing. Whole-genome sequences were determined for strains 1485ET and 2463D, and the average nucleotide and amino acid identities were determined for these strains. The strains formed a robust phylogenetic clade, divergent from all other species of the genus Campylobacter. In contrast to most currently known members of the genus Campylobacter, the strains showed growth at ambient temperatures, which might be an adaptation to their reptilian hosts. The results of this study clearly show that these strains isolated from reptiles represent a novel species within the genus Campylobacter, for which the name Campylobacter iguaniorum sp. nov. is proposed. The type strain is 1485ET (=LMG 28143T=CCUG 66346T).

Replacing lactose from calf milk replacers : effects on digestion and post-absorptive metabolism
Gilbert, M.S. - \ 2015
Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Walter Gerrits; Henk Schols. - Wageningen : Wageningen University - ISBN 9789462576032 - 171
vleeskalveren - lactose - kunstmelk - polysacchariden - glucose - fructose - glycerol - zetmeelvertering - metabolisme - fermentatie - kalvervoeding - diervoeding - voedingsfysiologie - veal calves - lactose - filled milk - polysaccharides - glucose - fructose - glycerol - starch digestion - metabolism - fermentation - calf feeding - animal nutrition - nutrition physiology

Summary PhD thesis Myrthe S. Gilbert

Replacing lactose from calf milk replacers – Effects on digestion and post-absorptive metabolism

Veal calves are fed milk replacer (MR) and solid feed. The largest part of the energy provided to veal calves originates from the MR. Calf MR contains 40 to 50% lactose, originating from whey, a by-product from cheese production. High and strongly fluctuating dairy prices are a major economic incentive to replace lactose from the calf MR by alternative energy sources. The objective of this thesis was to study the effects of replacing lactose from calf MR on nutrient digestion and fermentation and post-absorptive metabolism.

In Chapter 2 and 3, four starch products (SP) were evaluated for replacing lactose. The four SP differed in size and branching, and consequently required different ratios of starch-degrading enzymes for their complete hydrolysis to glucose. Gelatinized starch required α-amylase and (iso)maltase; maltodextrin required (iso)maltase and α-amylase; maltodextrin with α-1,6-branching required isomaltase, maltase and α-amylase and maltose required maltase. In Chapter 2, adaptation to these SP was assessed during 14 weeks, using a within-animal titration study. Forty male Holstein-Friesian calves (n = 8 per treatment) were assigned to either a lactose control MR or one of four titration strategies, each testing the stepwise exchange of lactose for one of the SP. For control calves, fecal dry matter (DM) content and fecal pH did not change over time. The response in fecal DM content and fecal pH in time did not differ between SP treatments and decreased linearly with 0.57% and 0.32 per week, respectively, where one week corresponded to an increase in SP inclusion of 3%. This indicates that the capacity for starch digestion was already exceeded at low inclusion levels, resulting in SP fermentation. All SP required maltase to achieve complete hydrolysis to glucose and it was, therefore, suggested that maltase is the rate-limiting enzyme in starch digestion in milk-fed calves.

Following the titration, a fixed inclusion level of 18% of the SP in the MR was applied. Effects on starch-degrading enzyme activity, nutrient disappearance, SP fermentation and jugular glucose appearance were measured (Chapter 3). Lactase activity in the brush border was high in the proximal small intestine of all calves, resulting in a high apparent ileal disappearance of lactose (≥ 99% of intake). Maltase and isomaltase activities in the brush border were not increased for any of the SP treatments. Luminal α-amylase activity was lower in the proximal small intestine but greater in the distal small intestine of SP-fed calves compared to control calves. This amylase activity in the distal small intestine of SP-fed calves might have been of microbial origin. Apparent SP disappearance did not differ between SP treatments. The difference between apparent ileal (62%) and total tract (99%) SP disappearance indicated substantial SP fermentation in the large intestine (37% of intake). In addition, total tract SP fermentation was quantified using fecal 13C excretion which originated from the naturally 13C-enriched corn SP. Total tract SP fermentation averaged 89% of intake, regardless of SP treatment. MR leaking into the reticulorumen was measured as the recovery of Cr in the reticulorumen at slaughter after feeding MR pulse-dosed with Cr 4h prior to slaughter. MR leaking into the reticulorumen averaged 11% for SP-fed calves. By difference, this leaves 41% of the SP intake fermented in the small intestine. This coincided with increased fecal nitrogen (N) and DM losses for SP-fed calves. However, apparent total tract crude fat disappearance tended to increase when replacing lactose with SP. The substantial SP fermentation indicates that only 10% of the SP intake was enzymatically hydrolyzed and absorbed as glucose. This was in agreement with the marginal increase in 13C enrichment in peripheral plasma glucose after feeding naturally 13C-enriched gelatinized starch and maltose, compared to a clear increase after feeding naturally 13C-enriched lactose to control calves. It was concluded that fermentation, rather than enzymatic digestion, is the main reason for small intestinal starch disappearance in milk-fed calves. The expected decrease in growth performance with such extensive SP fermentation is partially compensated by the greater crude fat digestion and possibly by a reduced urinary glucose excretion when replacing lactose with SP.

Glucose, fructose and glycerol do not require enzymatic hydrolysis and can be absorbed directly from the small intestine. However, these lactose replacers might differentially affect glucose and insulin metabolism and with that energy partitioning. The effects of partly replacing lactose with glucose, fructose or glycerol on energy and N partitioning and glucose homeostasis and insulin sensitivity were, therefore, studied in Chapter 4 and 5. Forty male Holstein-Friesian calves either received a lactose control MR or a MR in which one third of the lactose was replaced with glucose, fructose or glycerol (n = 10 per treatment). Energy and N retention were not affected by MR composition. Fructose absorption from the small intestine was incomplete resulting in fructose fermentation. This resulted in fecal losses of DM, energy and N and the lowest numerical energy and N retention for fructose-fed calves. Postprandial plasma concentrations of glucose exceeded the renal threshold for glucose in glucose-fed calves and control calves, which resulted in urinary glucose excretion. Glycerol was likely excreted with the urine of glycerol-fed calves. Oxidation of glucose, fructose and glycerol was quantified by feeding a single dose of [U-13C]glucose, [U-13C]fructose or [U-13C]glycerol with the MR and subsequently measuring 13CO2 production. Oxidation of lactose replacers did not differ between lactose replacers and averaged 72% of intake. However, the time at which the maximum rate of oxidation was reached was delayed for fructose-fed compared to glucose-fed and glycerol-fed calves, indicating that fructose was converted into other substrates before being oxidized. Conversion of fructose and glycerol into glucose was confirmed by an increase in 13C enrichment of peripheral plasma glucose after feeding [U-13C]fructose and [U-13C]glycerol, respectively. Insulin sensitivity did not differ between MR treatments, but was already low at the start of the experiment at 15 weeks of age and remained low throughout the experiment. It was concluded that glucose and glycerol can replace one third of the lactose from the calf MR, but that inclusion of fructose should be lower to prevent incomplete absorption from the small intestine.

In literature and the studies in this thesis, high inter-individual variation in growth performance was found in veal calves. The experiment described in Chapter 6 was, therefore, designed to assess the predictability of later life growth performance by charactering calves in early life. In addition, it was examined whether the ability of calves to cope with MR in which lactose is partially replaced by alternative energy sources can be predicted. From 2 to 11 weeks of age, male Holstein-Friesian calves were fed a lactose control MR and solid feed according to a practical feeding scheme and were characterized individually using targeted challenges related to feeding motivation, digestion, post-absorptive metabolism, immunology, behavior and stress. Based on the results in Chapter 4, a combination of glucose, fructose and glycerol in a 2:1:2 ratio was used to replace half of the lactose from the MR (GFG). From 11 to 27 weeks of age, calves received a lactose control MR or the GFG MR (n = 65 per treatment). Growth performance from 11 to 27 weeks of age tended to be lower for GFG-fed than for control calves (-25 g/d). Measurements in early life explained 12% of the variation in growth performance in later life. However, this was mainly related to variation in solid feed refusals. When growth performance was adjusted to equal solid feed intake, only 4% of the variation in standardized growth performance in later life, reflecting feed efficiency, could be explained by early life measurements. This indicates that > 95% of the variation in feed efficiency in later life could not be explained by early life characterization. It is hypothesized that variation in health status explains substantial variation in feed efficiency in veal calves. Significant relations between fasting plasma glucose concentrations, fecal dry matter and fecal pH in early life and feed efficiency in later life depended on MR composition. These measurements are, therefore, potential tools for screening calves in early life on their ability to cope with a MR in which half of the lactose is replaced by glucose, fructose and glycerol (in a 2:1:2 ratio).

The studies reported in this thesis demonstrate that glycerol, glucose and a combination of glucose, fructose and glycerol in a 2:1:2 ratio are promising lactose replacers. The effects of replacing lactose by other carbohydrate or energy sources described in this thesis are required to evaluate the potential of lactose replacers for inclusion in calf milk replacers and provide input for feed evaluation for calves and ruminants.

Fermentation in the small intestine contributes substantially to intestinal starch disappearance in calves
Gilbert, M.S. ; Pantophlet, A.J. ; Berends, H. ; Pluschke, A.M. ; Borne, J.J.G.C. van den; Hendriks, W.H. ; Schols, H.A. ; Gerrits, W.J.J. - \ 2015
The Journal of Nutrition 145 (2015)6. - ISSN 0022-3166 - p. 1147 - 1155.
Background: The proportion of starch disappearing from the small intestinal lumen is generally lower in ruminants than in monogastric animals, and there are indications that the starch digestion capacity in ruminants is limited. Objectives: Milk-fed calves were used to study the rate-limiting enzyme in starch hydrolysis and to quantify starch fermentation in ruminants. Methods: Forty male Holstein-Friesian calves were fed milk replacer containing either lactose (control) or 1 of 4 corn starch products. The following starch products differed in the enzyme ratios required for their complete hydrolysis to glucose: gelatinized starch [a-amylase and (iso)maltase], maltodextrin [(iso)maltase and a-amylase], maltodextrin with a-1,6-branching (isomaltase, maltase, and a-amylase), and maltose (maltase). In the adaptation period, calves were stepwise exposed to an increasing dose of the starch product for 14 wk to allow maximal adaptation of all enzyme systems involved. In the experimental period, apparent total tract and ileal starch product disappearance, total tract starch product fermentation, and a-amylase, maltase, and isomaltase activities were determined at 18% inclusion of the starch product. Results: Maltase and isomaltase activities in the brush border did not increase for any of the starch product treatments. Luminal a-amylase activity was lower in the proximal (3.9 ± 3.2 and 2.7 ± 1.7 U/mg Co for control and starch product calves, respectively) but greater in the distal small intestine of starch-fed calves than in control calves (0.0 ± 0.0 and 6.4 ± 1.5 U/mg Co for control and starch product calves, respectively; means ± SEs for control and means ± pooled SEMs for starch product treatments). Apparent ileal (61.6% ± 6.3%) and total tract (99.1% ± 0.4%) starch product disappearance did not differ between starch product treatments, suggesting that maltase activity limits starch digestion in ruminants. Total tract starch product fermentation averaged 414 ± 43 g/d, corresponding to 89% of intake, of which half was fermented before the terminal ileum, regardless of starch product treatment. Conclusion: Fermentation, rather than enzymatic digestion, is the main reason for small intestinal starch disappearance in milk-fed calves.
Effects of solid feed level and roughage-to-concentrate ratio on ruminal drinking and passage kinetics of milk replacer, concentrates, and roughage in veal calves
Berends, H. ; Borne, J.J.G.C. van den; Stockhofe-Zurwieden, N. ; Gilbert, M.S. ; Zandstra, T. ; Pellikaan, W.F. ; Reenen, C.G. van; Bokkers, E.A.M. ; Gerrits, W.J.J. - \ 2015
Journal of Dairy Science 98 (2015)8. - ISSN 0022-0302 - p. 5621 - 5629.
Effects of solid feed (SF) level and roughage-to-concentrate (R:C) ratio on ruminal drinking and passage kinetics of milk replacer, concentrate, and roughage were studied in veal calves. In total, 80 male Holstein-Friesian calves (45 ± 0.2 kg of body weight) were divided over 16 pens (5 calves per pen). Pens were randomly assigned to either a low (LSF) or a high (HSF) SF level and to 1 of 2 R:C ratios: 20:80 or 50:50 on a dry matter (DM) basis. Roughage was composed of 50% corn silage and 50% chopped wheat straw on a DM basis. At 27 wk of age, measurements were conducted in 32 calves. During the measurement period, SF intake was 1.2 kg of DM/d for LSF and 3.0 kg of DM/d for HSF, and milk replacer intake averaged 2.3 kg of DM/d for LSF and 1.3 kg of DM/d for HSF. To estimate passage kinetics of milk replacer, concentrate, and straw, indigestible markers (CoEDTA, hexatriacontane C36, Cr-neutral detergent fiber) were supplied with the feed as a single dose 4, 24, and 48 h before assessment of their quantitative recovery in the rumen, abomasum, small intestine, and large intestine. Rumen Co recovery averaged 20% of the last milk replacer meal. Recoveries of Co remained largely unaffected by SF level and R:C ratio. The R:C ratio did not affect rumen recovery of C36 or Cr. Rumen fractional passage rate of concentrate was estimated from recovery of C36 in the rumen and increased from 3.3%/h for LSF to 4.9%/h for HSF. Rumen fractional passage rate of straw was estimated from Cr recovery in the rumen and increased from 1.3%/h for LSF to 1.7%/h for HSF. An increase in SF level was accompanied by an increase in fresh and dry rumen contents. In HSF calves, pH decreased and VFA concentrations increased with increasing concentrate proportion, indicating increased fermentation. The ratio between Cr and C36 was similar in the small and large intestine, indicating that passage of concentrate and straw is mainly determined by rumen and abomasum emptying. In conclusion, increasing SF level introduces large variation in passage kinetics of dietary components, predominantly in the rumen compartment. The SF level, rather than the R:C ratio, influences rumen recovery of concentrate and roughage. Our data provide insight in passage kinetics of milk (Co representing the milk replacer) and SF (Cr and C36 representing roughage and concentrate, respectively) and may contribute to the development of feed evaluation models for calves fed milk and SF.
Downstream processing of Isochrysis galbana: a step towards microalgal biorefinery
Gilbert-López, B. ; Mendiola, J.A. ; Fontecha, J. ; Broek, L.A.M. van den; Sijtsma, L. ; Cifuentes, A. ; Herrero, M. ; Ibáñez, E. - \ 2015
Green Chemistry 17 (2015)9. - ISSN 1463-9262 - p. 4599 - 4609.
An algae-based biorefinery relies on the efficient use of algae biomass through its fractionation of several valuable/bioactive compounds that can be used in industry. If this biorefinery includes green platforms as downstream processing technologies able to fulfill the requirements of green chemistry, it will end-up with sustainable processes. In the present study, a downstream processing platform has been developed to extract bioactive compounds from the microalga Isochrysis galbana using various pressurized green solvents. Extractions were performed in four sequential steps using (1) supercritical CO2 (ScCO2), (2) ScCO2/ethanol (Gas Expanded Liquid, GXL), (3) pure ethanol, and (4) pure water as solvents, respectively. The residue of the extraction step was used as the raw material for the next extraction. Optimization of the ScCO2 extraction was performed by factorial design in order to maximize carotenoid extraction. During the second step, different percentages of ethanol were evaluated (15%, 45% and 75%) in order to maximize the extraction yield of fucoxanthin, the main carotenoid present in this alga; the extraction of polar lipids was also an aim. The third and fourth steps were performed with the objective of recovering fractions with high antioxidant activity, eventually rich in carbohydrates and proteins. The green downstream platform developed in this study produced different extracts with potential for application in the food, pharmaceutical and cosmetic industries. Therefore, a good approach for complete revalorization of the microalgae biomass is proposed, by using processes complying with the green chemistry principles.
Effects of solid feed level and roughage-to-concentrate ratio on ruminal drinking and passage kinetics of milk, concentrates, and roughage in veal calves
Berends, H. ; Borne, J.J.G.C. van den; Stockhofe, N. ; Gilbert, M.S. ; Zandstra, T. ; Pellikaan, W.F. ; Reenen, K. van; Bokkers, E.A.M. ; Gerrits, W.J.J. - \ 2015
In: Book of abstracts of 2015 Joint Annual Meeting of ADSA-ASAS. - - p. 869 - 869.
Effects of solid feed (SF) level and roughage-to-concentrate (R:C) ratio on ruminal drinking and passage kinetics of milk, concentrate, and roughage in veal calves were studied. Eighty calves (2 wk of age, 45 kg bodyweight) were divided over 16 pens. Pens were randomly assigned to a low (LSF) or a high (HSF) SF level, and to one of 2 R:C ratios; 20:80 or 50:50 on a DM basis. Roughage was composed of 50% corn silage and 50% chopped straw on a DM basis. During the measurement period at 27 wk of age, SF intake was 1.2 kg DM/d for LSF and 3.0 kg DM/d for HSF, and milk (replacer) intake averaged 2.3 kg DM/d for LSF and 1.3 kg DM/d for HSF. To estimate passage kinetics of milk, concentrate, and straw, indigestible markers (respectively CoEDTA, hexatriacontane C36, Cr-NDF) were supplied with the feed as a single dose at respectively 4, 24, and 48 h before slaughter. At slaughter, marker recovery was quantified in the rumen, abomasum, small intestine, and large intestine. Rumen Co recovery averaged 20% of the last milk meal. Recoveries of milk remained largely unaffected by SF level and R:C ratio. Ruminal recovery of C36 and Cr was unaffected by R:C ratio. Rumen fractional passage rate of concentrate was estimated from recovery of C36 in the rumen and increased (P <0.001) from 3.3%/h for LSF to 4.9%/h for HSF. Rumen fractional passage rate of straw was estimated from Cr recovery in the rumen and increased (P <0.01) from 1.3%/h for LSF to 1.7%/h for HSF. A greater SF level increased (P <0.001) fresh and dry rumen contents. In HSF calves, pH decreased (from 6.9 to 6.0; P <0.01) and VFA concentrations increased (P <0.05) with a lower R:C ratio, indicating increased fermentation. The Cr:C36 ratio was similar in the small and large intestine, indicating that passage of concentrate and straw was mainly determined by rumen and abomasum emptying. In conclusion, SF level rather than R:C ratio influences rumen passage of concentrate and roughage. Our data provide insight in passage kinetics of milk and SF and may contribute to the development of feed evaluation models for veal calves
Alterra en de kunst van het kronkelen
Kleis, R. ; Makaske, A. ; Maas, H.A. - \ 2015
Resource: weekblad voor Wageningen UR 10 (2015)1. - ISSN 1874-3625 - p. 9 - 9.
waterlopen - herstelbeheer - geomorfologie - natuurlandschap - ecologisch herstel - waterstroming - waterbeheer - streams - restoration management - geomorphology - natural landscape - ecological restoration - water flow - water management
Een groot deel van onze beken heeft op dit moment een verre van natuurlijk verloop. Om wateroverlast tegen te gaan zijn in de vorige eeuw veel van oudsher kronkelige beken rechtgetrokken. Rechte beken voeren het water sneller af. Maar tegenwoordig is dat niet meer gewenst. Die snelle afvoer leidt tot verdroging en rechtgetrokken beken bieden weinig kansen voor een diversiteit in flora en fauna. Met beekherstel probeert men dat tij te keren. Bart Makaske en Gilbert Maas van Alterra schreven een boek over hoe je beken het beste laat kronkelen.
Organogel formation via supramolecular assembly of oleic acid and sodium oleate
Nikiforidis, C.V. ; Gilbert, E.P. ; Scholten, E. - \ 2015
RSC Advances : An international journal to further the chemical sciences 5 (2015)59. - ISSN 2046-2069 - p. 47466 - 47475.
system - solvent - liquid - amphiphiles - particles - micelles - lecithin - bilayers - laurate - water
To create materials with novel functionalities, the formation of gels within hydrophobic media has become popular. This is often accomplished through the assembly of low molecular weight organogelators into a variety of complex phases through intermolecular interactions. In the case of edible materials, the assembly of saturated fatty acids to form fat crystal networks is often used for structuring. Here, the first example of structuring with unsaturated fatty acids is reported, namely mixtures of oleic acid and sodium oleate, to structure edible lipid phases. Small-angle scattering demonstrates that the resultant structures, which vary with oleic acid and sodium oleate molar ratio, comprise either inverse micellar or lamellar phases, combined with the formation of crystalline space-filling networks. Network formation was found for filler concentrations above 10 wt%. Rheological measurements show that gel strength depends on the ratio of oleic acid to sodium oleate, and is greater when only oleic acid is used. The addition of up to 1.5 wt% of water enhanced the strength of the organogels, probably through supplementary hydrogen bonding but, for concentrations greater than 2.0 wt%, the assembly was inhibited leading to collapse of the gel.
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