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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Addressing global ruminant agricultural challenges through understanding the rumen microbiome : Past, present, and future
Huws, Sharon A. ; Creevey, Christopher J. ; Oyama, Linda B. ; Mizrahi, Itzhak ; Denman, Stuart E. ; Popova, Milka ; Muñoz-Tamayo, Rafael ; Forano, Evelyne ; Waters, Sinead M. ; Hess, Matthias ; Tapio, Ilma ; Smidt, Hauke ; Krizsan, Sophie J. ; Yáñez-Ruiz, David R. ; Belanche, Alejandro ; Guan, Leluo ; Gruninger, Robert J. ; McAllister, Tim A. ; Newbold, C.J. ; Roehe, Rainer ; Dewhurst, Richard J. ; Snelling, Tim J. ; Watson, Mick ; Suen, Garret ; Hart, Elizabeth H. ; Kingston-Smith, Alison H. ; Scollan, Nigel D. ; Prado, Rodolpho M. Do; Pilau, Eduardo J. ; Mantovani, Hilario C. ; Attwood, Graeme T. ; Edwards, Joan E. ; McEwan, Neil R. ; Morrisson, Steven ; Mayorga, Olga L. ; Elliott, Christopher ; Morgavi, Diego P. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X
Diet - Host - Methane - Microbiome - Omics - Production - Rumen

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Towards standards for human fecal sample processing in metagenomic studies
Costea, Paul I. ; Zeller, Georg ; Sunagawa, Shinichi ; Pelletier, Eric ; Alberti, Adriana ; Levenez, Florence ; Tramontano, Melanie ; Driessen, Marja ; Hercog, Rajna ; Jung, Ferris Elias ; Kultima, Jens Roat ; Hayward, Matthew R. ; Coelho, Luis Pedro ; Allen-Vercoe, Emma ; Bertrand, Laurie ; Blaut, Michael ; Brown, Jillian R.M. ; Carton, Thomas ; Cools-Portier, Stéphanie ; Daigneault, Michelle ; Derrien, Muriel ; Druesne, Anne ; Vos, Willem M. De; Finlay, B.B. ; Flint, Harry J. ; Guarner, Francisco ; Hattori, Masahira ; Heilig, Hans ; Luna, Ruth Ann ; Hylckama Vlieg, Johan Van; Junick, Jana ; Klymiuk, Ingeborg ; Langella, Philippe ; Chatelier, Emmanuelle Le; Mai, Volker ; Manichanh, Chaysavanh ; Martin, Jennifer C. ; Mery, Clémentine ; Morita, Hidetoshi ; O'Toole, Paul W. ; Orvain, Céline ; Patil, Kiran Raosaheb ; Penders, John ; Persson, Søren ; Pons, Nicolas ; Popova, Milena ; Salonen, Anne ; Saulnier, Delphine ; Scott, Karen P. ; Singh, Bhagirath ; Slezak, Kathleen ; Veiga, Patrick ; Versalovic, James ; Zhao, Liping ; Zoetendal, Erwin G. ; Ehrlich, S.D. ; Dore, Joel ; Bork, Peer - \ 2017
Nature Biotechnology 35 (2017)11. - ISSN 1087-0156 - p. 1069 - 1076.
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
Rearing complexity affects fearfulness and use of vertical space in adult laying hens
Brandsaeter, M. ; Nordgreen, J. ; Rodenburg, T.B. ; Tahamtani, F.M. ; Popova, A. ; Janczak, A.M. - \ 2016
In: Proceedings of the 50th congress of the International Society for Applied Ethology. - Wageningen, The Netherlands : Wageningen Academic Publishers - ISBN 9789086862870 - p. 201 - 201.
e complexity of the rearing environment is important for behavioral development in layinghens. is study aimed to test the hypothesis that laying hens reared in a complex aviarysystem would be less fearful and less sensitive to stress as adults than hens reared in barrencage environments. Laying hens (n=160) were reared in the same house, either kept insidethe aviary rows to imitate cages (n=80) or in the conventional aviary system (n=80). ebirds were then transported to the experimental facilities at 16 weeks of age and mix-housedin custom built pens. Two birds per treatment per pen where tested in human approach andnovel objct tests at 19 and 23 weeks of age. e results were analyzed by ANOVA on scores for afearfulness-related principal component, generated using principal component analysis. Flightresponses and the relationship between €ight response and fearfulness score were analyzed bylogistic regression. Use of vertical space was analyzed by Wilcoxon matched pairs signed ranktest. Aviary-reared (AV) birds had lower levels of fearfulness compared with cage-reared (C)birds both at 19 weeks (mean±std AV: 0.24±1.56; C: 0.74±1.72; F(1,19)=5.66; P=0.03) and at23 weeks (AV: -0.69±1.62; C: 0.19±2.11; F(1,19)=4.49; P=0.05) of age. At 19 weeks of age, moreaviary-reared birds tended to show a €ight response compared to cage-reared birds (OR=2.4;P=0.09) when initially exposed to a novel object. Rearing complexity did not a‚ect the €ightresponse at 23 weeks of age (OR=1.4; P=0.6). e odds ratio of showing a €ight response whenexposed to the novel object was not in€uenced by the principal component fearfulness score(OR=0.89; P=0.2). At 19 weeks of age, more aviary-reared birds spent time on the low perch(median, 25th-75th percentile AV: 20.8, 14.4-23.0; C: 12.5, 10.4-18.4; P=0.01), the elevatedplatform (AV: 19.2, 13.0-25; C: 12.1, 6.3-22.1; P=0.01) and upper perch (AV: 16.7, 10.4-23.0; C:5.2, 2.1-14.1; P<0.0001) compared to the cage-reared birds. However, at 23 weeks of age, thesedi‚erences were not detected (P>0.0001). Conclusively, increased environmental complexityduring rearing reduced fearfulness at 19 and 23 weeks of age and increased vertical space useat 19 weeks of age in laying hens.
Exposure to increased environmental complexity during rearing reduces fearfulness and increases use of three-dimensional space in laying hens (Gallus gallus domesticus)
Brantsæter, Margrethe ; Nordgreen, Janicke ; Rodenburg, T.B. ; Tahamtani, Fernanda M. ; Popova, Anastasija ; Janczak, Andrew Michael - \ 2016
Frontiers in Veterinary Science 3 (2016). - ISSN 2297-1769 - 10 p.
The complexity of the rearing environment is important for behavioral development and fearfulness. The aim of this study was to test the hypothesis that laying hens reared in a complex aviary system with exposure to mild intermittent stressors would be less fearful, less sensitive to stress, and would use elevated areas of the pen more often as adults than hens reared in a barren cage environment. Laying hens (N = 160) were housed in the same rearing house; half of the birds (n = 80) in an aviary and the other half (n = 80) in cages. At 16 weeks of age, the birds were transported to the experimental facilities. Their behavior was recorded at 19 and 23 weeks of age and analyzed by analysis of variance on individual scores for a fearfulness-related principal component generated using principal component analysis. The results indicate that aviary-reared birds have lower levels of fearfulness compared with cage-reared birds both at 19 weeks and at 23 weeks of age. When comparing the response induced by initial exposure to a novel object at 19 and 23 weeks of age, more aviary-reared birds tended to fly up at 19 weeks compared to the cage-reared birds, indicating a tendency toward a more active behavioral response in the aviary-reared birds than in cage-reared birds. There was no difference between treatments in the flight response at 23 weeks. The groups did not differ in defecation frequency or the concentration of fecal corticosterone metabolites at either age. At 19 weeks, observation of the spatial distribution in the home pens indicated that more aviary-reared birds spent time on the low perch, the elevated platform, and the upper perch, compared to the cage-reared birds. However, at 23 weeks of age, these differences were no longer detected. The results of this study support the hypothesis that increased environmental complexity during rearing reduces fearfulness of adult laying hens.
Upscaling methane emissions to regional scale using remotely sensed proxies - spectral and spatial indentification of arctic tundra vegetation types
Schaepman-Strub, G. ; Popova, M. ; Bartholomeus, H. - \ 2010
Consumer evalulations of food risk management in Russia
Popova, K. ; Frewer, L.J. ; Jonge, J. de; Fischer, A.R.H. ; Kleef, E. van - \ 2010
British Food Journal 112 (2010)9. - ISSN 0007-070X - p. 934 - 948.
expert attitudes - focus groups - trust - safety - perceptions - health - benefits - communication - hazards - determinants
Purpose – Consumer perceptions regarding what constitutes best food risk management (FRM) practice may vary as a consequence of cross-cultural differences in consumer perceptions, cultural contexts, and historical differences in governance practices and occurrence of food safety incidents. The purpose of this paper is to compare the views of Russian consumers with those of consumers in European Union member states. Design/methodology/approach – A survey previously conducted in five EU member states was replicated using a Russian consumer sample (n ¼ 460, SEM analysis). Psychological factors underpinning consumer evaluations of food risk management quality (FRMQ) were identified. A qualitative study (consumer focus group, n ¼ 9) allowed for in-depth interpretation of the quantitative results. Findings – Russian consumers hold similar views to consumers in EU member states regarding their perceptions of what constitutes effective FRM practices. However, the perceived honesty of food chain actors was an important determinant of perceived FRMQ only for Russian consumers, who also perceived that they were primarily responsible for their own food-related health protection. EU consumers attributed more responsibility to food chain actors and the authorities. Research limitations/implications – The analysis compared Russian consumers with consumers in five different EU member states. The results cannot be extended to compare Russian consumers with the entire EU. Practical implications – An international risk communication policy is likely to be impractical, and should be developed at a national or regional level. Given that Russian consumers take personal responsibility for their own health protection, information needs to be provided to enable them to do so. Originality/value – To the authors knowledge, this is the first comparative analysis of the determinants of perceptions of effective FRM held by Russian consumers with consumers from within the EU regulatory area
Microbiological and biochemical parameters - Criteria for evaluating the quality of the composts
Arkhipchenko, I.A. ; Barbolona, I.I. ; Popova, J.N. ; Solntseva, I.E. ; Derikx, P.J.L. - \ 1999
In: Abstract International Composting Symposium, 19-23 Sept., Halifax, Nova Scotia (Canada), 1 pp
On the search of disease resistant biotypes within the population of Russian and Dutch reproductions of European winterwheat varieties.
Temirbekova, S.K. ; Popova, E.V. ; Buys, J. ; Mansvelt, J.D. van - \ 1995
In: European Journal of Plant Pathology, XIII International Plant Protection Congress, The Hague, The Netherlands, (1995) 1055 pp
Cicer L., a monograph of the genus, with special reference to the chickpea (Cicer arietinum L.), its ecology and cultivation
Maessen, L.J.G. van der - \ 1972
Landbouwhogeschool Wageningen. Promotor(en): J.D. Ferwerda; H.C.D. de Wit. - Wageningen : Veenman - 341
cicer arietinum - kekererwten - papilionoideae - economische botanie - fabaceae - plantenanatomie - plantenmorfologie - plantenecologie - wilde planten - flora - plantengeografie - plantkunde - erwten - chickpeas - economic botany - plant anatomy - plant morphology - plant ecology - wild plants - phytogeography - botany - peas
<p/>1. The history of the chickpea or gram, <em>Cicer arietinum</em> L., <em></em> has been described from Homer's time and the earliest finds, 5450 B.C. in Hacilar, Turkey, up to the present day. The crop was first domesticated in Asia Minor and was introduced in India either from Central Asia or Asia Minor, the two main centres of origin. Some forms were even introduced rather recently. Ethiopia is a secondary centre of domestication; connections with Egypt or Asia remain speculative. Several pieces of evidence oppose the opinion of DE CANDOLLE (1882) that the ancient Egyptians and Jews had only known the chickpea for two millenia.<p/>Medical uses, no longer widely practised, are discussed. The spread to the present areas of cultivation is described and mapped.<p/>2. The genus <em>Cicer</em> L. has been revised. Popov (1929) accepted 22 species, now 39 species (8 annual, 31 perennial) are known. One species is described for the first time: <em>C. multijugum</em> from Afghanistan. A key to the species is prepared. The species, arranged alphabetically, are described and accompanied by detailed illustrations. The synonymy and typifications are given, as well as notes on geography, ecology and morphology. The geographical distribution of each species of the genus, occurring in Central Asia, Asia Minor and the Medi terranean, is presented in maps. It is stressed that the variability and geography of many species is not known sufficiently. The poor availability of fresh material of the wild species is a handicap to research.<p/>The relation to the other genera in <em>Vicieae</em> is discussed. <em>Cicer</em> occupies a somewhat peculiar place with its glandular hairs, inflated fruits and seed shape. The infraspecific classification in the cultivated species is reviewed; an informal classification is presented on base of the work of POPOVA (1937) without rejecting the older varieties distinguished by JAUBERT and SPACH, and ALEFELD.<p/>3. The importance of the chickpea as the third pulse crop in the world after beans and peas is presented in a map, graphs and tables. The crop ranks l5th among all crops in area occupied yearly. Yields, at present an average of about 700 kg per ha, are highest in Egypt (1670 kg) and Turkey (1220 kg). About 83 of the world production is in the Indian subcontinent.<p/>The weather is the main reason for fluctuation in area. The partial recession in area, due to the expanding new cereal cultivars, will be met by higher yields per unit area and aided by higher prices.<p/>4. Some anatomical particulars, e.g. the glandular hairs, are shortly reviewed.<p/>5. The chickpea is generally cultivated in a traditional way. The resistance to drought (deep roots) and ability to grow in poor soils has not increased the care of the crop. However, with good soil preparation, proper sowing on rows, cultivation and fertilization the crop can yield reasonably. The sowing date is very important. Sowing early in the growth season is to be preferred, except in case of wilt disease. Plant density, sowing depth and sowing seed are discussed. Irrigations, needed in some countries, should be practised with care so as not to induce soil anaeroby.<p/>Often the chickpea is grown mixed with wheat or mustard, against crop failures and for utilization of different soil layers. In rotation the chickpea is a well esteemed crop. It has maintained soil fertility at a certain level for centuries in the densely populated areas of India. The plants are harvested mainly by hand. Threshing machines need good adjustment to prevent breakage of seeds. Storage is an important problem, since much loss may occur.<p/>6. Ecological trials were carried out on light, daylength, temperature and relative humidity. The photosynthesis rate varied from 250-500 μg CO <sub><font size="-1">2</font></sub> -uptake per cm <sup><font size="-1">2</font></SUP>and per h at about 26°C, but at 18°C, the rate was not much less. Leaves of two-weeks old are the most effective in photosynthesis and may use twice as much CO <sub><font size="-1">2</font></sub> as the four-week old leaves. Estimated calculated production appeared to be 12-14 tons of total dry matter, or about 5-7 tons of grains, similar to the highest yield ever obtained on a small plot.<p/>The chickpea is a quantitative LD plant. Under 16-h days the flowering was advanced by e.g. 20-35 days, if compared with 9-h days. Short days did not prevent flowering. Dry matter yield was improved in LD. The influence of the photoperiodic effect alone of the daylengths following different sowing dates on flowering and yield is small. Increasing photoperiods appeared to be more favourable than decreasing ones.<p/>The optimum temperature for early vegetative growth ranges from 21-29°C (night and day) to 24-32°C for different cultivars. Over the entire growth period the optimum temperature is somewhat lower, 18-26°C and 21-29°C, which is also optimum for flowering.<p/>The relative humidity was found to have little influence on fruit-setting. A decrease in light intensity of 25 % of the available amount during May and June, however, was found to decrease the number of pods by 25-50%.<p/>Data on soils and nutrients are summarized. As yet the chickpea does not respond to dressings of more than 10 kg N and 30 kg P <sub><font size="-1">2</font></sub> O <sub><font size="-1">5</font></sub> per ha. Moderately heavy soils are preferred, but both heavy and light soils are used in some areas.<p/>Growth substances usually have a negative influence on the growth of chickpeas. Scarcity of practical trials prohibits any recommendation.<p/>Topping appears to be an old practice to stimulate branching. Regeneration, however, takes a long time and is only sufficient under optimum conditions and if applied at an early stage.<p/>7. Breeding has not yet improved yields over large areas. A review on cytogenetics is given. Some new reports on the somatic number of chromosomes of some wild species are added. As crossing technique is a delicate operation, hybridization on a large scale is at present not possible, but pollination at an early stage without emasculation may be a solution. The introduction of new cultivars has not been very successful because they have not shown large differ ences with local cultivars.<p/>8. The most important insect pests of the chickpea are the podborer and the pulse beetles, which are described in some detail. Geographical distribution and way of control is given. All reported pests are mentioned. Nematode attacks seem to be underestimated at present. Rats may cause important damage in stores.<p/>9. The diseases of the chickpea, their occurrence, possible way of control are described. Most damage is done by wilt, caused by both a soil fungus and by physiological drought, and blight. Several other diseases such as rust and foot rots are not yet serious over large areas. As for pests, chemical control is often uneconomic.<p/>10. The chickpea is mainly used as human food, whether fresh, boiled, or roasted in many preparations. As a part of balanced foods it can form an important supplement to the protein nutrition of children. The proteins of chickpea constitute an important part of the protein intake in India. The chemical composition of the seeds (e.g. up to nearly 30% of protein) is given, as well as the amounts of essential amino acids.<p/>Except sometimes for methionine and for tryptophan the chickpea appears to be an excellent source of amino acids.
Une recherche sur l'utilisation de la methode vacuum pour la determination prealable du degre de contamination des pommes avec Gloeoesporium et du traitement thermique pour reduire la maladie
Stenvers, N. ; Popova, L.E. - \ 1969
Wageningen : [s.n.] (Rapport / Sprenger instituut no. 1660) - 4
appels - malus - plantenziekteverwekkende schimmels - plantaardige producten - behandeling - apples - plant pathogenic fungi - plant products - treatment
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