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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    Anaerobic Fungi : Past, Present, and Future
    Hess, Matthias ; Paul, Shyam S. ; Puniya, Anil K. ; Giezen, Mark van der; Shaw, Claire ; Edwards, Joan E. ; Fliegerová, Kateřina - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    anaerobic digestion - carbohydrate-active enzymes - food security - herbivores - methanogenesis - Neocallimastigomycota - rumen - sustainable agriculture

    Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

    Transfer of pyrrolizidine alkaloids from ragwort, common groundsel and viper’s bugloss to milk from dairy cows
    Mulder, Patrick P.J. ; Klijnstra, Mirjam D. ; Goselink, Roselinde M.A. ; Vuuren, Ad M. van; Cone, John W. ; Stoopen, Geert ; Hoogenboom, Ron L.A.P. - \ 2020
    Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 37 (2020)11. - ISSN 1944-0049 - p. 1906 - 1921.
    dairy cows - feed - Pyrrolizidine alkaloids - rumen - transfer

    To investigate the transfer of pyrrolizidine alkaloids (PAs) from feed to milk, rumen-cannulated dairy cows were intra-ruminally fed with 200 g/day of dried plant material of either ragwort (mixture of Jacobaea vulgaris and Senecio inaequidens), common groundsel (Senecio vulgaris) or viper’s bugloss (Echium vulgare) for a period of 4 days. PA levels in the plant materials were 3767, 2792 and 1674 µg g−1 respectively. Feed intake, milk yield and several blood parameters indicative for liver function were not influenced by the treatment. When fed ragwort, increased levels of PAs were detected in the milk, in particular jacoline and an unidentified cyclic diester, possibly a hydroxylated metabolite from retrorsine. The latter was the most important PA in milk from cows fed common groundsel. For viper’s bugloss, echimidine was the most abundant identified PA but in addition several hydroxylated PA metabolites were detected. For ragwort, the overall PA transfer was estimated at 0.05% and 1.4% for jacoline (N-oxide). Transfer rates were similar for viper’s bugloss (0.05%) but lower for common groundsel (0.01%). Only a small portion of the administered PAs was quantified in milk, urine and faeces, with an overall balance of 4.5%, 2.9% and 5.8%, for ragwort, common groundsel and viper’s bugloss, respectively. Samples taken from the rumen indicated that the N-oxides were converted into the free bases, which was confirmed by in vitro studies with the same plant species incubated with ruminal fluid. These results confirm that the transfer of PAs to milk is relatively low but may be of concern for human health regarding the genotoxic and carcinogenic properties of these compounds. The transfer rate depends on the type of PAs present in the weeds. The incomplete balance of input vs output stresses the need to further investigate the metabolism and the potential transfer of metabolites into edible products.

    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.

    CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
    Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, J.E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
    Aberystwyth University
    rumen - microbiome - metataxonomics - metagenomics
    Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome
    Aspects of rumen adaptation in dairy cattle : morphological, functional, and gene expression changes of the rumen papillae and changes of the rumen microbiota during the transition period
    Dieho, Kasper - \ 2017
    Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Jan Dijkstra; Andre Bannink; J.Th. Schonewille. - Wageningen : Wageningen University - ISBN 9789463430258 - 248
    dairy cattle - rumen - rumen microorganisms - morphology - gene expression - animal nutrition - dry period - lactation - melkvee - pens - pensmicro-organismen - morfologie - genexpressie - diervoeding - gustperiode - lactatie

    In dairy cattle the nutrient requirements change rapidly around calving. During the dry period nutrients are required for maintenance, recovery from the previous lactation, and fetal growth. After calving, milk production commences and the energy requirements can increase by a factor 3 to ~184 MJ net energy for lactation during the first weeks of lactation, compared with the dry period, whereas feed intake doubles to ~24 kg dry matter (DM)/d compared with the dry period. In addition, high quality lactation rations are fed, usually containing a sizable portion of concentrate, thereby increasing fermentable organic matter (FOM) intake to ~14 kg/d. As a result, daily volatile fatty acid (VFA) production by the rumen microbiota increases from ~60 mol/d during the dry period to ~132 mol/d during early lactation. To maintain rumen pH at levels favorable for microbial fermentation, and prevent a negative impact on production and health, clearance of the produced VFA is essential. This mainly occurs through absorption over the rumen wall. The increase in capacity of the rumen for absorption of VFA is associated with morphological and functional changes of the rumen papillae which cover the rumen wall. However, current knowledge of these changes as they occur around calving is scarce (Chapter 1). Increasing our understanding of the adaptation of the rumen can provide new insights to optimize dairy cattle nutrition and thereby health, welfare, and production.

    The objective of this thesis was to study the adaptation of the rumen to ration changes during the dry period and early lactation. Changes in rumen papillae morphology, fractional absorption rate of VFA (kaVFA), and changes in the composition of the rumen microbiota were the primary targets for study. In addition, the expression of genes and proteins associated with absorption and metabolism of VFA by the rumen epithelium were studied to better understand the relationship between functional changes and morphological changes of the papillae. Uniquely, all these aspects were studied in parallel in the same dairy cows during the dry period and early lactation using a repeated measurement setup. Two experiments were conducted. In the lactation experiment, the effect of transition from the dry period to the subsequent lactation, and the effect of early lactation concentrate build-up strategy on the adaptation of the rumen were studied. In the dry period experiment, the effect of feeding supplemental concentrate during the late dry period in order to ‘prepare’ the rumen for the lactation was studied. Treatments of both experiments were aimed at creating a difference in FOM intake (kg/d) and thereby VFA production (mol/d), as VFA production was hypothesized to affect rumen papillae development and thereby the capacity for VFA absorption.

    During the lactation experiment, intake of FOM did not change during the dry period (5.7 kg/d), but increased during the subsequent lactation to 15.0 kg/d at 80 d postpartum (pp). In addition, the rapid increase in concentrate allowance resulted in a temporarily 22% greater FOM intake compared with a gradual increase at 16 d pp (Chapter 2). The total production rate of VFA, measured using an isotope dilution technique (Chapter 3), was affected by these changes in FOM intake and increased 2.3 fold to 123 mol/d after calving, compared with the dry period (53 mol/d). The temporarily greater FOM intake with the rapid increase in concentrate allowance at 16 d pp coincided with a 54% greater propionate production (34 mol/d) compared with a gradual increase in concentrate allowance, whereas acetate (66 mol/d) and butyrate (10 mol/d) production were not affected. Papillae surface area (Chapter 2) decreased by 19% between 50 d antepartum (ap) and 3 d pp to 28.0 mm2, but increased during early lactation to 63.0 mm2. Papillae surface area increased faster with the rapid increase in concentrate allowance and surface area was 38, 34 and 22% larger at 16, 30, and 44 d postpartum respectively, than with a gradual rate of increase of concentrate allowance. Histology (Chapter 2) revealed that rumen papillae and epithelium thickness decreased slightly after calving, but were not affected by the concentrate treatment. Feeding concentrate during the dry period did not affect daily FOM intake (6.0 kg/d) but did increase VFA concentration in the rumen fluid by 21 mM to 121 mM, and increased papillae surface by 29% (Chapter 4). However, the increased papillae surface area in the dry period was not maintained to the subsequent lactation period. After calving, papillae surface area increased by 50% to 58.0 mm2 at 45 d pp. The postpartum development of the rumen papillae was not affected by the treatment during the dry period. These results indicate that rumen papillae respond to changes in FOM and VFA production intake during the dry period and early lactation, and that the magnitude of this response depends on the rate of change in FOM intake.

    During both experiments, kaVFA was measured using a buffer incubation technique in an empty washed rumen. During the lactation experiment (Chapter 3), in accordance with the developments in papillae surface area, the kaVFA decreased during the dry period from 0.48/h at 50 d ap to 0.34/h at 3 d pp. During the subsequent lactation, it increased rapidly to 0.56/h at 16 d pp and further to 0.72/h at 80 d pp. However, the greater papillae surface area due to the rapid increase in concentrate did not coincide with a greater kaVFA. During the dry period experiment (Chapter 4), kaVFA increased after calving by 50% to 0.48/h at 45 d pp, but the increase in papillae surface area due to supplemental concentrate during the dry period did not affect the kaVFA during the dry period (0.36/h) or the subsequent lactation. These results indicate that papillae surface area is not the limiting factor for kaVFA.

    Changes in the expression of genes were studied at the mRNA level in papillae tissue from both experiments (Chapter 5). The expression of apoptosis related genes was not affected by sampling day or its interaction with treatment for both experiments, suggesting papillae proliferation during the transition period was mainly the result of an increased mitosis rate. The limited changes in the expression of genes associated with rumen epithelial transport and metabolism of VFA in dairy cows during the transition period do not suggest that these capacities of the epithelium increased per unit of surface area. Thus the major response to the increase in daily VFA production after calving was tissue proliferation. In addition, papillae from the lactation experiment were used to study expression at the protein level using immunoblotting. Results showed that expression of several proteins changed during early lactation indicating modulation of intracellular pH regulation and sodium homeostasis, and VFA metabolism. Only for one gene, a significant but weak correlation between the examined mRNA and protein expression levels was observed, indicating that care must be taken when interpreting results obtained at either level.

    Ration changes associated with the transition from the dry period to lactation affected the rumen microbiota during the lactation experiment (Chapter 6). The rapid increase in concentrate allowance postpartum temporarily decreased bacterial community richness by as much as 30% compared with a gradual increase in concentrate. This transient depression in bacterial community richness with a rapid, but not a gradual, rate of increase of concentrate allowance pp indicates that the rate of change in ration composition and feed intake has a greater effect than the change in ration composition and feed intake level as such. The relative abundances of most major bacterial taxa were affected by the transition to lactation, but few were affected by the rate of increase of the concentrate allowance. The relative abundances of rumen protozoal taxa changed after calving, and were affected by the concentrate treatment. However, differences between treatments groups disappeared again when concentrate intake became similar. The archaeal community was likewise affected by both the transition to lactation and the treatment. The observed changes in rumen microbiota composition, including changes in bacterial community richness, did not appear to affect the fractional degradation rate of NDF, starch, CP, and OM measured in situ using a nylon bag technique.

    The results in the present thesis show that morphologically and functionally the rumen papillae can adapt rapidly to the changes in FOM intake and daily VFA production associated with the transition from the dry period into the subsequent lactation. However, the contrast in response of rumen papillae surface area development and the fractional absorption rate of VFA to the concentrate treatments indicates that papillae surface area is not the limiting factor for VFA absorption. This proposition is further supported by the limited histological changes of the rumen epithelium and limited changes in gene expression. Considering that the capacity for absorption and metabolism of VFA per unit of papillae surface area remains similar, an extra-epithelial factor, likely visceral blood flow, limits VFA absorption. The capacity of the rumen to adapt after calving and the limited beneficial effect of supplementing concentrate during the dry period indicate that dry period feeding strategies can best be optimized for the prevention of periparturient diseases.

    Rumen by-pass copper = Koper voorbij de Pens
    Goselink, R.M.A. - \ 2015
    Wageningen : Wageningen UR Livestock Research (Livestock Research rapport 905) - 22
    herkauwers - koper - verteringsabsorptie - pens - pensfermentatie - spijsvertering - voedingsfysiologie - diervoeding - ruminants - copper - digestive absorption - rumen - rumen fermentation - digestion - nutrition physiology - animal nutrition
    De absorptie van koper (Cu) bij herkauwers is relatief laag vanwege de interacties tussen Cu en andere bestanddelen van het rantsoen, waardoor onoplosbare complexen gevormd worden die niet worden geabsorbeerd in de dunne darm. Dit kan mogelijk verbeterd worden door pensbestendige Cu bronnen aan te bieden, waardoor de Cu uitscheiding via de mest naar het milieu verminderd kan worden. Het doel van dit project was het evalueren van het effect van pensbestendige Cu bronnen op de Cu absorptie bij herkauwers. Dit is onderzocht met behulp van een in vitro model waarbij verschillende Cu bronnen zijn geïncubeerd om de fermentatie- en verteringsprocessen in het maagdarmkanaal te simuleren. Daarna is een proef uitgevoerd met 18 vleeskalveren waarbij twee pensbestendige Cu bronnen zijn vergeleken met kopersulfaat als controle. Het verschil in Cu absorptie tussen pensbestendige Cu bronnen en kopersulfaat was echter onvoldoende om in deze beperkte proefopzet aangetoond te kunnen worden.
    Animal board Invited Review: Genetic possibilities to reduce enteric methane emissions from ruminants
    Pickering, N.K. ; Oddy, V.H. ; Basarab, J. ; Cammack, K. ; Hayes, B. ; Hegarty, R. ; Lassen, J. ; McEwan, J. ; Miller, S. ; Pinares-Patino, C. ; Haas, Y. de - \ 2015
    Animal 9 (2015)9. - ISSN 1751-7311 - p. 1431 - 1440.
    special topics-mitigation - nitrous-oxide emissions - dairy-cows - genomic selection - sheep - rumen - fermentation - accuracy - cattle - livestock
    Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for the environment and for policy making. Potentially, the most sustainable way of reducing enteric CH4 emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. There is potential for adopting genetic selection and in the future genomic selection, for reduced CH4 emissions from ruminants. From this review it has been observed that both CH4 emissions and production (g/day) are a heritable and repeatable trait. CH4 emissions are strongly related to feed intake both in the short term (minutes to several hours) and over the medium term (days). When measured over the medium term, CH4 yield (MY, g CH4/kg dry matter intake) is a heritable and repeatable trait albeit with less genetic variation than for CH4 emissions. CH4 emissions of individual animals are moderately repeatable across diets, and across feeding levels, when measured in respiration chambers. Repeatability is lower when short term measurements are used, possibly due to variation in time and amount of feed ingested prior to the measurement. However, while repeated measurements add value; it is preferable the measures be separated by at least 3 to 14 days. This temporal separation of measurements needs to be investigated further. Given the above issue can be resolved, short term (over minutes to hours) measurements of CH4 emissions show promise, especially on systems where animals are fed ad libitum and frequency of meals is high. However, we believe that for short-term measurements to be useful for genetic evaluation, a number (between 3 and 20) of measurements will be required over an extended period of time (weeks to months). There are opportunities for using short-term measurements in standardised feeding situations such as breath 'sniffers' attached to milking parlours or total mixed ration feeding bins, to measure CH4. Genomic selection has the potential to reduce both CH4 emissions and MY, but measurements on thousands of individuals will be required. This includes the need for combined resources across countries in an international effort, emphasising the need to acknowledge the impact of animal and production systems on measurement of the CH4 trait during design of experiments.
    Estimation of the in situ degradation of the washout fraction of starch by using a modified in situ protocol and in vitro measurements
    Jonge, L.H. de; Laar, H. van; Dijkstra, J. - \ 2015
    Animal 9 (2015)9. - ISSN 1751-7311 - p. 1465 - 1472.
    dairy-cows - digestion - rumen - gas - degradability - barley - vivo - digestibility - feedstuff - cultivars
    The in situ degradation of the washout fraction of starch in six feed ingredients (i.e. barley, faba beans, maize, oats, peas and wheat) was studied by using a modified in situ protocol and in vitro measurements. In comparison with the washing machine method, the modified protocol comprises a milder rinsing method to reduce particulate loss during rinsing. The modified method markedly reduced the average washout fraction of starch in these products from 0.333 to 0.042 g/g. Applying the modified rinsing method, the fractional degradation rate (k d ) of starch in barley, oats and wheat decreased from on average 0.327 to 0.144 h-1 whereas for faba beans, peas and maize no differences in k d were observed compared with the traditional washing machine rinsing. For barley, maize and wheat, the difference in non-fermented starch in the residue between both rinsing methods during the first 4 h of incubation increased, which indicates secondary particle loss. The average effective degradation of starch decreased from 0.761 to 0.572 g/g when using the new rinsing method and to 0.494 g/g when applying a correction for particulate matter loss during incubation. The in vitro k d of starch in the non-washout fraction did not differ from that in the total product. The calculated ratio between the k d of starch in the washout and non-washout fraction was on average 1.59 and varied between 0.96 for oats and 2.39 for maize. The fractional rate of gas production was significantly different between the total product and the non-washout fraction. For all products, except oats, this rate of gas production was larger for the total product compared with the non-washout fraction whereas for oats the opposite was observed. The rate of increase in gas production was, especially for grains, strongly correlated with the in vitro k d of starch. The results of the present study do not support the assumption used in several feed evaluation systems that the degradation of the washout fraction of starch in the rumen is much faster than that of the non-washout fraction.
    A new approach to estimate the in situ fractional degradation rate of organic matter and nitrogen in wheat yeast concentrates
    Jonge, L.H. de; Laar, H. van; Hendriks, W.H. ; Dijkstra, J. - \ 2015
    Animal 9 (2015)3. - ISSN 1751-7311 - p. 437 - 444.
    rumen - degradability - feedstuff - protein
    In the classic in situ method, small particles are removed during rinsing and hence their fractional degradation rate cannot be determined. A new approach was developed to estimate the fractional degradation rate of nutrients in small particles. This approach was based on an alternative rinsing method to reduce the particulate matter loss during rinsing and on quantifying the particulate matter loss that occurs during incubation in the rumen itself. To quantify particulate matter loss during incubation, loss of small particles during the in situ incubation was studied using undegradable silica with different particle sizes. Particulate matter loss during incubation was limited to particles smaller than ~40 µm with a mean fractional particulate matter loss rate of 0.035 h-1 (first experiment) and 0.073 h-1 (second experiment) and an undegradable fraction of 0.001 and 0.050, respectively. In the second experiment, the fractional particulate matter loss rate after rinsing in a water bath at 50 strokes per minute (s.p.m.) (0.215 h-1) and the undegradable fraction at 20 s.p.m. (0.461) were significantly larger than that upon incubation in the rumen, whereas the fractional particulate matter loss rate (0.140 and 0.087 h-1, respectively) and the undegradable fraction (0.330 and 0.075, respectively) after rinsing at 30 and 40 s.p.m. did not differ with that upon rumen incubation. This new approach was applied to estimate the in situ fractional degradation rate of insoluble organic matter (OM) and insoluble nitrogen (N) in three different wheat yeast concentrates (WYC). These WYC were characterised by a high fraction of small particles and estimating their fractional degradation rate was not possible using the traditional washing machine rinsing method. The new rinsing method increased the mean non-washout fraction of OM and N in these products from 0.113 and 0.084 (washing machine method) to 0.670 and 0.782, respectively. The mean effective degradation (ED) without correction for particulate matter loss of OM and of N was 0.714 and 0.601, respectively, and significant differences were observed between the WYC products. Applying the correction for particulate matter loss reduced the mean ED of OM to 0.676 (30 s.p.m.) and 0.477 (40 s.p.m.), and reduced the mean ED of N to 0.475 (30 s.p.m.) and 0.328 (40 s.p.m.). These marked reductions in fractional degradation rate upon correction for small particulate matter loss emphasised the pronounced effect of correction for undegraded particulate matter loss on the fractional disappearance rates of OM and N in WYC products.
    Estimating enteric methane emissions from Chilean beef fattening systems using a mechanistic model
    Arias, R.A. ; Catrileo, A. ; Larraín, R. ; Vera, R. ; Velásquez, A. ; Toneatti, M. ; France, J. ; Dijkstra, J. ; Kebreab, E. - \ 2015
    The Journal of Agricultural Science 153 (2015)1. - ISSN 0021-8596 - p. 114 - 123.
    dairy-cows - feedlot cattle - rumen - supplementation - fermentation - performance - management - monensin - strategies - prediction
    A mechanistic model (COWPOLL) was used to estimate enteric methane (CH4) emissions from beef production systems in Chile. The results expressed as a proportion of gross energy intake (GEI) were compared with enteric fermentation data reported in the last Chilean greenhouse gases inventory, which utilized an earlier the Intergovernmental Panel on Climate Change Tier 2 approach. The simulation analysis was based on information from feedstuffs, dry matter intake (DMI), body weight (BW) and average daily gain (ADG) of steers raised and finished at two research facilities located in Central and Southern Chile, as well as three simulated scenarios for grass-based finishing systems in Southern Chile. Data for feedlot production systems in the central region were assessed by considering steers fed a forage : concentrate ratio of 23 : 77 using maize silage and wheat straw as roughage sources during the stages of backgrounding and fattening. Average DMI were 7·3±0·62 and 9·2±0·55 kg/day per steer for backgrounding and fattening, respectively, whereas ADG were 1·1±0·22 and 1·3±0·37 kg/day for backgrounding and fattening. For the Southern Chilean fattening production systems, the forage : concentrate ratio was 56 : 44 with ryegrass pasture as the sole forage source. In this case, average DMI was 9·97±0·51 and ADG was 1·1±0·24 kg/day per steer. Two of the grass-based scenarios used the same initial BW information as that used for the Central and Southern Chilean systems, but feedlot diets were replaced by ryegrass pasture. The third grass-based scenario used an initial BW of 390 kg. In all the grass-based scenarios an ADG of 0·90 kg/day, with maximum DMI estimated as a proportion of BW (0·01 of NDF, kg/kg BW), was assumed. The results of the simulation analysis showed that emission factors (Ym; fraction of GEI) ranged from 0·062 to 0·079 of GEI. Smaller values were associated with finishing systems that included a lower proportion of forage in the diet due to higher propionate production, which serves as a sink for hydrogen in the rumen. Cattle finished in feedlot systems had an average of 0·062 of GEI lost as CH4, whereas grass-based cattle had losses of 0·079 of GEI. Enteric CH4 emissions for the systems using grass-based and concentrate diets were 261 and 159 g/kg weight gain, respectively. The Chilean CH4 inventory employs a fixed Ym of 0·060 to estimate enteric fermentation for all cattle. This value is lower than the average Ym obtained in the current simulation analysis (0·071 of GEI), which results in underestimation of enteric CH4 emissions from beef cattle. However, these results need to be checked against field measurements of CH4 emissions. Implementation of mechanistic models in the preparation of national greenhouse gas inventories is feasible if appropriate information is provided, allowing dietary characteristics and regional particularities to be taken into consideration.
    Relatie eigenschappen maïscelwanden en fermentatiekarakteristieken in de pens van herkauwers
    Cone, J.W. - \ 2014
    Wageningen : Animal Nutrition Group (ANU rapport Oktober 2014) - 52
    maïs - celwanden - fermentatie - pens - herkauwers - diervoeding - penssap - ruwvoer (forage) - rundveehouderij - melkveehouderij - dierenwelzijn - maize - cell walls - fermentation - rumen - ruminants - animal nutrition - rumen fluid - forage - cattle husbandry - dairy farming - animal welfare
    Dit rapport beschrijft onderzoek naar de relatie tussen de eigenschappen van maïscelwanden en fermentatiekarakteristieken van deze celwanden in de pens van herkauwers. Het betreft hier zowel chemische onderzoek als anatomisch en histologisch onderzoek en in-vitro-onderzoek naar de afbreekbaarheid van maïscelwanden in pensvloeistof. Het doel is om inzicht te krijgen in de achtergrond van verschillen in celwandstructuur en samenstelling tussen verschillende monsters, ook op moleculair niveau.
    Methods to determine the relative value of genetic traits in dairy cows to reduce greenhouse gas emissions along the chain
    Middelaar, C.E. van; Berentsen, P.B.M. ; Dijkstra, J. ; Arendonk, J.A.M. van; Boer, I.J.M. de - \ 2014
    Journal of Dairy Science 97 (2014)8. - ISSN 0022-0302 - p. 5191 - 5205.
    enteric methane emissions - life-cycle assessment - land-use change - economic values - milk-production - grazing behavior - farm-level - model - cattle - rumen
    Current decisions on breeding in dairy farming are mainly based on economic values of heritable traits, as earning an income is a primary objective of farmers. Recent literature, however, shows that breeding also has potential to reduce greenhouse gas (GHG) emissions. The objective of this paper was to compare 2 methods to determine GHG values of genetic traits. Method 1 calculates GHG values using the current strategy (i.e., maximizing labor income), whereas method 2 is based on minimizing GHG per kilogram of milk and shows what can be achieved if the breeding results are fully directed at minimizing GHG emissions. A whole-farm optimization model was used to determine results before and after 1 genetic standard deviation improvement (i.e., unit change) of milk yield and longevity. The objective function of the model differed between method 1 and 2. Method 1 maximizes labor income; method 2 minimizes GHG emissions per kilogram of milk while maintaining labor income and total milk production at least at the level before the change in trait. Results show that the full potential of the traits to reduce GHG emissions given the boundaries that were set for income and milk production (453 and 441 kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively) is about twice as high as the reduction based on maximizing labor income (247 and 210 kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively). The GHG value of milk yield is higher than that of longevity, especially when the focus is on maximizing labor income. Based on a sensitivity analysis, it was shown that including emissions from land use change and using different methods for handling the interaction between milk and meat production can change results, generally in favor of milk yield. Results can be used by breeding organizations that want to include GHG values in their breeding goal. To verify GHG values, the effect of prices and emissions factors should be considered, as well as the potential effect of variation between farm types.
    Evaluation of the SF6 tracer technique for estimating methane emission rates with reference to dairy cows using a mechanistic model
    Berends, H. ; Gerrits, W.J.J. ; France, J. ; Ellis, J.L. ; Zijderveld, S.M. van; Dijkstra, J. - \ 2014
    Journal of Theoretical Biology 353 (2014). - ISSN 0022-5193 - p. 1 - 8.
    sulfur-hexafluoride tracer - chamber techniques - eructated gas - cattle - rumen - sheep - methanogenesis - performance - ruminants - digestion
    A dynamic, mechanistic model of the sulfur hexafluoride (SF6) tracer technique, used for estimating methane (CH4) emission rates from ruminants, was constructed to evaluate the accuracy of the technique. The model consists of six state variables and six zero-pools representing the quantities of SF6 and CH4 in rumen and hindgut fluid, in rumen and hindgut headspace, and in blood and collection canister. The model simulates flows of CH4 and SF6 through the body, subsequent eructation and exhalation and accumulation in a collection canister. The model predicts CH4 emission by multiplying the SF6 release rate of a permeation device in the rumen by the ratio of CH4:SF6 in collected air. This prediction is compared with the actual CH4 production rate, assumed to be continuous and used as a driving variable in the model. A sensitivity analysis was conducted to evaluate the effect of changes in several parameters. The predicted CH4 emission appeared sensitive to parameters affected by the difference in CH4:SF6 ratio in exhaled and eructed air respectively, viz., hindgut fractional passage rate and hindgut CH4 production. This is caused by the difference in solubility of CH4 and SF6 and by hindgut CH4 production. In addition, the predicted CH4 emission rate appeared sensitive to factors that affect proportions of exhaled and eructed air sampled, i.e., eructation time fraction, exhalation time fraction, and distance from sampling point to mouth/nostrils. Changes in rumen fractional passage rate, eructation rate, SF6 release rate, background values and air sampling rate did not noticeably affect the predicted CH4 emission. Simulations with 13CH4 as an alternative tracer show that the differences and sensitivity to parameters greatly disappear. The model is considered a useful tool to evaluate critical points in the SF6 technique. Data from in vivo experiments are needed to further evaluate model simulations.
    Assessing environmental consequences of using co-products in animal feed
    Zanten, H.H.E. van; Mollenhorst, H. ; Vries, J.W. de; Middelaar, C.E. van; Kernebeek, H.R.J. van; Boer, I.J.M. de - \ 2014
    The International Journal of Life Cycle Assessment 19 (2014)1. - ISSN 0948-3349 - p. 79 - 88.
    bio-energy - digestion - impact - rumen - perspective - absorption - manure - tract - model
    The livestock sector has a major impact on the environment. This environmental impact may be reduced by feeding agricultural co-products (e.g. beet tails) to livestock, as this transforms inedible products for humans into edible products, e.g. pork or beef. Nevertheless, co-products have different applications such as bioenergy production. Based on a framework we developed, we assessed environmental consequences of using co-products in diets of livestock, including the alternative application of that co-product. We performed a consequential life cycle assessment, regarding greenhouse gas emissions (including emissions related to land use change) and land use, for two case studies. Case 1 includes increasing the use of wheat middlings in diets of dairy cattle at the expense of using it in diets of pigs. The decreased use of wheat middlings in diets of pigs was substituted with barley, the marginal product. Case 2 includes increasing the use of beet tails in diets of dairy cattle at the expense of using it to produce bioenergy. During the production of biogas, electricity, heat and digestate (that is used as organic fertilizer) were produced. The decrease of electricity and heat was substituted with fossil fuel, and digestate was substituted with artificial fertilizer. Using wheat middlings in diets of dairy cattle instead of using it in diets of pigs resulted in a reduction of 329 kg CO2 eq per ton wheat middlings and a decrease of 169 m(2) land. Using beet tails in diets of dairy cattle instead of using it as a substrate for anaerobic digestion resulted in a decrease of 239 kg CO2 eq per ton beet tails and a decrease of 154 m(2) land. Emissions regarding land use change contributed significantly in both cases but had a high uncertainty factor, +/- 170 ton CO2 ha(-1). Excluding emissions from land use change resulted in a decrease of 9 kg CO2 eq for case 1 'wheat middlings' and an increase of 50 kg CO2 eq for case 2 'beet tails'. Assessing the use of co-products in the livestock sector is of importance because shifting its application can reduce the environmental impact of the livestock sector. A correct assessment of the environmental consequences of using co-products in animal feed should also include potential changes in impacts outside the livestock sector, such as the impact in the bioenergy sector.
    Effect of supplementing coconut or krabok oil, rich in medium-chain fatty acids on ruminal fermentation, protozoa and archaeal population of bulls
    Panyakaew, P. ; Boon, N. ; Goel, G. ; Yuangklang, C. ; Schonewille, J.T. ; Hendriks, W.H. ; Fievez, V. - \ 2013
    Animal 7 (2013)12. - ISSN 1751-7311 - p. 1950 - 1958.
    different hypervariable regions - gradient gel-electrophoresis - myristic acid - in-vitro - methane suppression - ciliate protozoa - energy-balance - lauric acid - dairy-cows - rumen
    Medium-chain fatty acids (MCFA), for example, capric acid (C10:0), myristic (C14:0) and lauric (C12:0) acid, have been suggested to decrease rumen archaeal abundance and protozoal numbers. This study aimed to compare the effect of MCFA, either supplied through krabok (KO) or coconut (CO) oil, on rumen fermentation, protozoal counts and archaeal abundance, as well as their diversity and functional organization. KO contains similar amounts of C12:0 as CO (420 and 458 g/kg FA, respectively), but has a higher proportion of C14:0 (464 v. 205 g/kg FA, respectively). Treatments contained 35 g supplemental fat per kg DM: a control diet with tallow (T); a diet with supplemental CO; and a diet with supplemental KO. A 4th treatment consisted of a diet with similar amounts of MCFA (i.e. C10:0+C12:0+C14:0) from CO and KO. To ensure isolipidic diets, extra tallow was supplied in the latter treatment (KO+T). Eight fistulated bulls (two bulls per treatment), fed a total mixed ration predominantly based on cassava chips, rice straw, tomato pomace, rice bran and soybean meal (1.5% of BW), were used. Both KO and CO increased the rumen volatile fatty acids, in particular propionate and decreased acetate proportions. Protozoal numbers were reduced through the supplementation of an MCFA source (CO, KO and KO+T), with the strongest reduction by KO. Quantitative real-time polymerase chain reaction assays based on archaeal primers showed a decrease in abundance of Archaea when supplementing with KO and KO+T compared with T and CO. The denaturing gradient gel electrophoresis profiles of the rumen archaeal population did not result in a grouping of treatments. Richness indices were calculated from the number of DGGE bands, whereas community organization was assessed from the Pareto–Lorenz eveness curves on the basis of DGGE band intensities. KO supplementation (KO and KO+T treatments) increased richness and evenness within the archaeal community. Further research including methane measurements and productive animals should elucidate whether KO could be used as a dietary methane mitigation strategy.
    Diet factors and subclinical laminitis score in lactating cows of smallholder dairy farms in Thailand
    Pilachai, R. ; Schonewille, J.T. ; Thamrongyoswittayakul, C. ; Aiumlamai, S. ; Wachirapakom, C. ; Everts, H. ; Hendriks, W.H. - \ 2013
    Livestock Science 155 (2013)2-3. - ISSN 1871-1413 - p. 197 - 204.
    physically effective fiber - neutral detergent fiber - ruminal ph - milk-yield - cattle - forage - rumen - protein - lesions - digestibility
    The objective of this study was to evaluate the importance of dietary crude protein (CP) content, dietary neutral detergent fiber (NDF) content and feeding regime as well as other factors related to management and demographics on the occurrence of (subclinical) laminitis under practical Thai feeding conditions. Hemorrhage of the white line and the sole, sole ulcer and white-line fissure of all four claws of milking cows (n=119) on 25 farms (selected based on the occurrence of lameness) were macroscopically assessed to calculate the prevalence of subclinical laminitis (SCL) on each farm. Data were collected on farm characteristics, feed and feeding management, floor type and hoof care. Dry matter intake was assessed on each farm and feed ingredients collected and analyzed for dry matter (DM), CP and NDF. No significant differences were found for farm characteristics such as herd size, number of milking cows, parity and body condition scoring between farms with a low (25%) of SCL. Percentages of DM and CP content of the rations did not differ, whereas mean NDF content in the ration was significantly higher in the low compared to the high prevalence farms. Multiple regression analysis of the data showed that a ration low in NDF content and/or in combination with the separate feeding of roughage and concentrate was associated with a high SCL prevalence. The results suggest that mixing concentrate with a substantial part of the roughage is an important strategy to prevent SCL in smallholder dairy farms under Thai feeding conditions. In addition, the dietary NDF content but not the dietary CP level is associated with SCL prevalence in dairy cows under Thai feeding conditions.
    Passage kinetics of concentrates in dairy cows measured with carbon stable isotopes
    Warner, D. ; Dijkstra, J. ; Tamminga, S. ; Pellikaan, W.F. - \ 2013
    Animal 7 (2013)12. - ISSN 1751-7311 - p. 1935 - 1943.
    neutral detergent fiber - rumen - digestion - marker - model - ruminants - excretion - ratios - impact - matter
    Fractional passage rates form a fundamental element within modern feed evaluation systems for ruminants, but knowledge on feed-specific fractional passage is largely lacking. Commonly applied tracer techniques based on externally applied markers, such as chromium-mordanted neutral detergent fibre (Cr-NDF), have been criticised for behaving differently to feed particles. This study describes the use of the carbon stable isotope ratio (13C : 12C) as an internal digesta marker to quantify the fractional passage rate of concentrates through the digestive tract of dairy cows. In a crossover study, five dairy cows were fed low (24.6%) and high (52.6%) levels of concentrates (dry matter (DM) basis) and received a pulse-dosed Cr-NDF and 13C isotopes. The latter was administered orally by exchanging part of the dietary concentrates of low 13C natural abundance with a pulse dose of maize bran-based concentrates of high 13C natural abundance. Fractional passage rates from the rumen (K1) and from the large intestine (K2) were determined from faecal marker concentrations of Cr-NDF and of 13C in the DM (13C-DM), NDF (13C-NDF) and neutral detergent soluble (13C-NDS). No differences in K1 estimates were found for the two concentrate levels fed but significant differences between markers (P
    Stable isotope labeled n-alkanes to assess digesta passage kinetics through the digestive tract of ruminants
    Warner, D. ; Ferreira, L.M.M. ; Breuer, M.J.H. ; Dijkstra, J. ; Pellikaan, W.F. - \ 2013
    PLoS ONE 8 (2013)10. - ISSN 1932-6203 - 9 p.
    marker excretion patterns - carbon-isotope - dairy-cows - enrichments delta-c-13 - botanical composition - particle-size - in-vitro - rumen - herbivores - cattle
    We describe the use of carbon stable isotope (13C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha-1) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the d13C (i.e. the ratio 13C:12C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C27–C36) and passage kinetics were determined for the most abundant C29, C31 and C33 n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p=0.002) increase with carbon chain length. K1 estimates were comparable to those of the 13C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to 0.71; p=0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of 13C versus 12C. Our results suggest that 13C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the d13C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics.
    A modified rinsing method for the determination of the S, W-S and D + U fraction of protein and starch in feedstuff within the in situ technique
    Jonge, L.H. de; Laar, H. van; Hendriks, W.H. ; Dijkstra, J. - \ 2013
    Animal 7 (2013)8. - ISSN 1751-7311 - p. 1289 - 1297.
    rumen - degradability - degradation - electrophoresis - ruminants - profiles - extent - sacco
    A modified rinsing method for the in situ technique was developed to separate, isolate and characterise the soluble (S), the insoluble washout (W–S) and the non-washout fractions (D1U) within one procedure. For non-incubated bags ( t50 h), this method was compared with the conventional, Combined Fractionation (CF) method that measures the D1U and S fractions in separate steps and subsequently calculates the W–S fraction. The modified method was based on rinsing of nylon bags in a closed vessel containing a buffer solution (pH 6.2) during 1 h, where shaking speeds of 40, 100, and 160 strokes per minutes (spm) were evaluated, and tested for six feed ingredients (faba beans, maize, oats, peas, soya beans and wheat) and four forages (two ryegrass silages and two maize silages). The average recoveries as the sum of all fractions were 0.97260.041 for N and 0.99060.050 for starch (mean6s.d.). The mean W–S fraction increased with increasing shaking speed and varied between 0.017 (N) and 0.083 (starch) at 40 spm and 0.078 (N) and 0.303 (starch) at 160 spm, respectively. For ryegrass silages, the W–S fraction was absent at all shaking speeds, but was present in the CF method. The modified method, in particular at 40 and 100 spm, reduced the loss of small particles during rinsing, resulting in lower W–S and higher D1U fractions for N and starch compared with the CF method. For soya beans and ryegrass silage, the modified method reduced the S fraction of N compared with the CF method. The results obtained at 160 spm showed the best comparison with those from the CF method. The W–S fraction of the feedstuff obtained at 160 spm contained mainly particles smaller than 40 mm (0.90860.086). In most feedstuff, starch was the most abundant chemical component in the W–S fraction and its content (726675 g/kg DM) was higher than in the D1U fraction (4056177 g/kg DM). Alkaline-soluble proteins were the dominant N-containing components in the W–S fraction of dry feed ingredients and its relative content (0.7960.18 of total N in W–S) was higher than in the D1U fraction (0.5960.07 of total N in D1U) for all feedstuff except maize. The molecular weight distribution of the alkaline-soluble proteins differed between the W–S and the D1U fractions of all dry feed ingredients, except soya beans and wheat.
    Evaluation of a feeding strategy to reduce greenhouse gas emissions from dairy farming: The level of analysis matters
    Middelaar, C.E. van; Berentsen, P.B.M. ; Dijkstra, J. ; Boer, I.J.M. de - \ 2013
    Agricultural Systems 121 (2013). - ISSN 0308-521X - p. 9 - 22.
    life-cycle assessment - enteric methane emissions - milk-production - carbon footprint - grazing behavior - eco-efficiency - new-zealand - land-use - model - rumen
    The dairy sector contributes to climate change through emission of greenhouse gases (GHGs), via mainly carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Replacing grass silage with maize silage is a feeding strategy to reduce enteric CH4 emission. The effect of this strategy on GHG emissions can be analyzed at three different levels: animal, farm, and chain level. The level of analysis might affect results and conclusions, because the strategy affects not only enteric CH4 emissions at animal level, but also other GHG emissions at farm and chain levels. The objective of this study was to determine if the level of analysis influences conclusions about the GHG reduction potential of increasing maize silage at the expense of grass and grass silage in a dairy cow’s diet. First, we used a linear programming (LP, maximizing labor income) dairy farm model to define a typical Dutch dairy farm on sandy soils without a predefined feeding strategy (i.e. reference situation). Second, we combined mechanistic modeling of enteric fermentation and life cycle assessment to quantify GHG emissions at all three levels. Third, continuing from the diet derived in the reference situation, maize silage was increased by 1 kg DM per cow per day at the expense of grass (summer), or grass silage (winter). Next, the dairy farm model was used again to determine a new optimal farm plan including the feeding strategy, and GHGs were quantified again at the three levels. Finally, we compared GHG emissions at the different levels between the reference situation and the situation including the feeding strategy. We performed this analysis for a farm with an average intensity (13,430 kg milk/ha) and for a more intensive farm (14,788 kg milk/ha). Results show that the level of analysis strongly influences results and conclusions. At animal level, the strategy reduced annual emissions by 12.8 kg CO2e per ton of fat-and-protein-corrected-milk (FPCM). Analysis at farm and chain level revealed first of all that the strategy is not feasible on the farm with an average intensity because this farm cannot reduce its grassland area because of compliance with the EU derogation regulation (a minimum of 70% grassland). This is reality for many Dutch dairy farms with an intensity up to the average. For the more intensive farm, that can reduce its area of grassland, annual emissions reduced by 17.8 kg CO2e per ton FPCM at farm level, and 20.9 kg CO2e per ton FPCM at chain level. Ploughing grassland into maize land, however, resulted in non-recurrent emissions of 913 kg CO2e per ton FPCM. At farm and chain levels, therefore, the strategy does not immediately reduce GHG emissions as opposed to what results at animal level may suggest; at chain level it takes 44 years before annual emission reduction has paid off emissions from land use change.
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