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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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.

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