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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Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria
Bron, Peter A. ; Marcelli, Barbara ; Mulder, Joyce ; Els, Simon van der; Morawska, Luiza P. ; Kuipers, Oscar P. ; Kok, Jan ; Kleerebezem, Michiel - \ 2019
Current Opinion in Biotechnology 56 (2019). - ISSN 0958-1669 - p. 61 - 68.

The ever-expanding genomic insight in natural diversity of lactic acid bacteria (LAB) has revived the industrial interest in traditional and natural genetic mobilization methodologies. Here, we review recent advances in horizontal gene transfer processes in LAB, including natural competence, conjugation, and phage transduction. In addition, we envision the possibilities for industrial strain improvement arising from the recent discoveries of molecular exchanges between bacteria through nanotubes and extracellular vesicles, as well as the constantly expanding genome editing possibilities using the CRISPR-Cas technology.

IL-37 expression reduces lean body mass in mice by reducing food intake
Kuipers, Eline N. ; Dam, Andrea D. van; Ballak, Dov B. ; Wit, Ellemiek A. de; Dinarello, Charles A. ; Stienstra, Rinke ; Diepen, Janna A. van; Rensen, Patrick C.N. ; Boon, Mariëtte R. - \ 2018
International Journal of Molecular Sciences 19 (2018)8. - ISSN 1661-6596
Energy metabolism - Food intake - High fat diet - IL-37

The human cytokine interleukin (IL)-37 is an anti-inflammatory member of the IL-1 family of cytokines. Transgenic expression of IL-37 in mice protects them from diet-induced obesity and associated metabolic complications including dyslipidemia, inflammation and insulin resistance. The precise mechanism of action leading to these beneficial metabolic effects is not entirely known. Therefore, we aimed to assess in detail the effect of transgenic IL-37 expression on energy balance, including food intake and energy expenditure. Feeding homozygous IL-37 transgenic mice and wild-type (WT) control mice a high-fat diet (HFD; 45% kcal palm fat) for 6 weeks showed that IL-37 reduced body weight related to a marked decrease in food intake. Subsequent mechanistic studies in mice with heterozygous IL-37 expression versus WT littermates, fed the HFD for 18 weeks, confirmed that IL-37 reduces food intake, which led to a decrease in lean body mass, but did not reduce fat mass and plasma lipid levels or alterations in energy expenditure independent of lean body mass. Taken together, this suggests that IL-37 reduces lean body mass by reducing food intake.

In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria
Frenzel, Elrike ; Legebeke, Jelmer ; Stralen, Atze Van; Kranenburg, Richard Van; Kuipers, Oscar P. - \ 2018
Biotechnology for Biofuels 11 (2018)1. - ISSN 1754-6834
Biotechnology - Cyan - FACS - Geobacillus sp. - GFP - In vivo application - Parageobacillus sp. - Protein engineering - sfGFP - Thermophilic bacteria - Thermostability - Yellow
Background: Fluorescent reporter proteins (FP) have become an indispensable tool for the optimization of microbial cell factories and in synthetic biology per se. The applicability of the currently available FPs is, however, constrained by species-dependent performance and misfolding at elevated temperatures. To obtain functional reporters for thermophilic, biotechnologically important bacteria such as Parageobacillus thermoglucosidasius, an in vivo screening approach based on a mutational library of superfolder GFP was applied. Results: Flow cytometry-based benchmarking of a set of GFPs, sfGFPs and species-specific codon-optimized variants revealed that none of the proteins was satisfyingly detectable in P. thermoglucosidasius at its optimal growth temperature of 60 °C. An undirected mutagenesis approach coupled to fluorescence-activated cell sorting allowed the isolation of sfGFP variants that were extremely well expressed in the chassis background at 60 °C. Notably, a few nucleotide substitutions, including silent mutations, significantly improved the functionality and brightness. The best mutant sfGFP(N39D/A179A) showed an 885-fold enhanced mean fluorescence intensity (MFI) at 60 °C and is the most reliable reporter protein with respect to cell-to-cell variation and signal intensity reported so far. The in vitro spectral and thermostability properties were unaltered as compared to the parental sfGFP protein, strongly indicating that the combination of the amino acid exchange and an altered translation or folding speed, or protection from degradation, contribute to the strongly improved in vivo performance. Furthermore, sfGFP(N39D/A179A) and the newly developed cyan and yellow derivatives were successfully used for labeling several industrially relevant thermophilic bacilli, thus proving their broad applicability. Conclusions: This study illustrates the power of in vivo isolation of thermostable proteins to obtain reporters for highly efficient fluorescence labeling. Successful expression in a variety of thermophilic bacteria proved that the novel FPs are highly suitable for imaging and flow cytometry-based studies. This enables a reliable cell tracking and single-cell-based real-time monitoring of biological processes that are of industrial and biotechnological interest.
Intermodality and synchromodality
Tavasszy, L. ; Behdani, B. ; Konings, Rob - \ 2018
In: Ports and Networks - Strategies, Operations and Perspectives / Geerlings, Harry, Kuipers, Bart, Zuidwijk, Rob, Oxon : Routledge - ISBN 9781472485007 - p. 251 - 266.
Transport networks have evolved from multimodal networks towards integrated networks allowing for intermodal transport – the carriage of a single load unit by consecutive modes in a transport chain. Synchromodality (or synchronized intermodality) – as the next stage in port/hinterland network development – can be briefly summarized as the vision of a network of well-synchronized and interconnected transport modes, which together cater for the aggregate transport demand and can dynamically adapt to the individual and instantaneous needs of network users. The objective of the chapter is to introduce the idea of Synchromodality. We discuss the current position and evolution of intermodal hinterland transport systems. Next, we describe the main elements of a synchronized intermodal transport system and the innovations that are necessary to arrive at synchromodal transport systems. We further describe the barriers for future development including technological, economical and institutional aspects.
Dairy farmers’ business strategies in Central and Eastern Europe based on evidence from Lithuania, Poland and Slovenia
Verhees, Frans ; Malak-Rawlikowska, Agatsa ; Stalgiene, Aldona ; Kuipers, Abele ; Klopčič, Marija - \ 2018
Italian Journal of Animal Science 17 (2018)3. - ISSN 1594-4077 - p. 755 - 766.
To evaluate market-oriented strategic decision-making by farmers in Central and Eastern Europe (CEE) farm development paths of dairy farmers in Slovenia, Poland and Lithuania were analysed. The influence of internal strengths and weaknesses, external opportunities and threats, and farmer goals on strategic choices and performance were explored. Principal component, hierarchical cluster and regression analyses were performed to test the conceptual framework. Seven strategic groups emerged with specific development paths, that is, Wait and see, Movers, Chain integrators, Specializers and Diversifiers. The latter two split into cooperative and independent groups. Maximisation of profit and sustainable farming ranked highest as farming goals. Availability of land and labour were weaknesses for all strategic groups in all countries. External opportunities and threats varied between countries and to a lesser degree between strategic groups. The Wait and see and Cooperating diversifier groups gave less optimistic scores than other strategic groups. The attitudes of CEE farmers towards the market and future Common Agricultural Policy remain more negative than those of a group of Western European farmers. The results of this study confirm that internal strengths and weaknesses, external opportunities and threats, together with farmers’ goals and strategies influence farmer performance, but independently of each other. Strategies do not appear to be a mediating variable between the internal and external environment of the farm and the performance of the farm. Policy makers, companies and extension workers should take the heterogeneity in strategic development into account when dealing with these and similar groups of farms.
Editorial: Lactic acid bacteria - a continuing journey in science and application
Kleerebezem, M. ; Kuipers, O.P. ; Smid, E.J. - \ 2017
FEMS Microbiology Reviews 41 (2017)Supp 1. - ISSN 0168-6445 - p. S1 - S2.
Unleashing natural competence in Lactococcus lactis by induction of the competence regulator ComX
Mulder, Joyce ; Wels, Michiel ; Kuipers, Oscar P. ; Kleerebezem, Michiel ; Bron, Peter A. - \ 2017
Applied and Environmental Microbiology 83 (2017)20. - ISSN 0099-2240 - 13 p.
Comparative genomics - Lactococcus lactis - Natural competence

In biotechnological workhorses like Streptococcus thermophilus and Bacillus subtilis, natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis, natural competence has not been established to date. However, in silico analysis of the complete genome sequences of 43 L. lactis strains revealed complete late competence gene sets in 2 L. lactis subsp. cremoris strains (KW2 and KW10) and at least 10 L. lactis subsp. lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisincontrolled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon and elicited a state of natural competence in this strain. In contrast, comX expression in L. lactis NZ9000, which was predicted to encode an incomplete competence gene set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147 abolished the comX-driven natural competence, underlining the involvement of the competence machinery. Finally, introduction of nisininducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence in these strains also, expanding this phenotype to other L. lactis strains of both subspecies.

ANGPTL4 promotes bile acid absorption during taurocholic acid supplementation via a mechanism dependent on the gut microbiota
Janssen, Aafke W.F. ; Dijk, Wieneke ; Boekhorst, Jos ; Kuipers, Folkert ; Groen, Albert K. ; Lukovac, Sabina ; Hooiveld, Guido J.E.J. ; Kersten, Sander - \ 2017
Biochimica et Biophysica Acta. Molecular and Cell Biology of Lipids 1862 (2017)10. - ISSN 1388-1981 - p. 1056 - 1067.
Angiopoietin-like 4 - Antibiotics - Bile acids - Gut microbiota - Lipoprotein lipase - Triglycerides
Angiopoietin-like 4 (ANGPTL4) raises plasma triglyceride levels by inhibiting lipoprotein lipase. A set of compounds that are able to reduce plasma triglyceride levels are bile acids (BA). Because BA have been shown to decrease ANGPTL4 secretion by intestinal cells, we hypothesized that BA lower plasma triglycerides (partly) via ANGPTL4. To test that hypothesis, wild-type and Angptl4−/− mice were fed chow supplemented with taurocholic acid (TCA) for seven days. TCA supplementation effectively lowered plasma triglycerides in wild-type and Angptl4−/− mice, indicating that ANGPTL4 is not required for plasma triglyceride-lowering by BA. Intriguingly, however, plasma and hepatic BA concentrations were significantly lower in TCA-supplemented Angptl4−/− mice than in TCA-supplemented wild-type mice. These changes in the Angptl4−/− mice were accompanied by lower BA levels in ileal scrapings and decreased expression of FXR-target genes in the ileum, including the BA transporter Slc10a2. By contrast, faecal excretion of specifically primary BA was higher in the Angptl4−/− mice, suggesting that loss of ANGPTL4 impairs intestinal BA absorption. Since the gut microbiota converts primary BA into secondary BA, elevated excretion of primary BA in Angptl4−/− mice may reflect differences in gut microbial composition and/or functionality. Indeed, colonic microbial composition was markedly different between Angptl4−/− and wild-type mice. Suppression of the gut bacteria using antibiotics abolished differences in plasma, hepatic, and faecal BA levels between TCA-supplemented Angptl4−/− and wild-type mice. In conclusion, 1) ANGPTL4 is not involved in the triglyceride-lowering effect of BA; 2) ANGPTL4 promotes BA absorption during TCA supplementation via a mechanism dependent on the gut microbiota.
Modulation of the gut microbiota impacts nonalcoholic fatty liver disease: a potential role for bile acids
Janssen, Aafke W.F. ; Houben, Tom ; Katiraei, Saeed ; Dijk, Wieneke ; Boutens, Lily ; Bolt, Nieke van der; Wang, Zeneng ; Brown, J.M. ; Hazen, Stanley L. ; Mandard, Stéphane ; Shiri-Sverdlov, Ronit ; Kuipers, Folkert ; Willems van Dijk, Ko ; Vervoort, Jacques ; Stienstra, Rinke ; Hooiveld, Guido J.E.J. ; Kersten, Sander - \ 2017
Journal of Lipid Research 58 (2017)7. - ISSN 0022-2275 - p. 1399 - 1416.
Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide, yet the pathogenesis of NAFLD is only partially understood. Here, we investigated the role of the gut bacteria in NAFLD by stimulating the gut bacteria via feeding mice the fermentable dietary fiber, guar gum (GG), and suppressing the gut bacteria via chronic oral administration of antibiotics. GG feeding profoundly altered the gut microbiota composition, in parallel with reduced diet-induced obesity and improved glucose tolerance. Strikingly, despite reducing adipose tissue mass and inflammation, GG enhanced hepatic inflammation and fibrosis, concurrent with markedly elevated plasma and hepatic bile acid levels. Consistent with a role of elevated bile acids in the liver phenotype, treatment of mice with taurocholic acid stimulated hepatic inflammation and fibrosis. In contrast to GG, chronic oral administration of antibiotics effectively suppressed the gut bacteria, decreased portal secondary bile acid levels, and attenuated hepatic inflammation and fibrosis. Neither GG nor antibiotics influenced plasma lipopolysaccharide levels. In conclusion, our data indicate a causal link between changes in gut microbiota and hepatic inflammation and fibrosis in a mouse model of NAFLD, possibly via alterations in bile acids.
Mining prokaryotes for antimicrobial compounds : From diversity to function
Tracanna, Vittorio ; Jong, Anne de; Medema, Marnix H. ; Kuipers, Oscar P. - \ 2017
FEMS Microbiology Reviews 41 (2017)3. - ISSN 0168-6445 - p. 417 - 429.
Antimicrobial - Bacteria - Biosynthetic - Evolution - Gene clusters - Genome - Mining - NRPS - PKS - RiPP

The bacterial kingdom provides a major source of antimicrobials that can either be directly applied or used as scaffolds to further improve their functionality in the host. The rapidly increasing amount of bacterial genomic, metabolomic and transcriptomic data offers unique opportunities to apply a variety of approaches to mine for existing and novel antimicrobials. Here, we discuss several powerful mining approaches to identify novel molecules with antimicrobial activity across structurally diverse natural products, including ribosomally synthesized and posttranslationally modified peptides, nonribosomal peptides and polyketides. We not only discuss the direct mining of genomes based on identification of biosynthetic gene clusters, but also describe more advanced and integrative approaches in ecology-based mining, functionality-based mining and mode-of-action-based mining. These efforts are likely to accelerate the discovery and development of novel antimicrobial drugs.

Draft whole-genome sequences of three Lactobacillus plantarum food isolates
Fernandez Ramirez, Monica ; Boekhorst, Jos ; Jong, Anne de; Kuipers, Oscar P. ; Abee, Tjakko ; Nierop Groot, Masja - \ 2016
Genome announcements 4 (2016)3. - ISSN 2169-8287
Lactobacillus plantarum is a widespread member of the Lactobacillus genus and frequently isolated from spoiled acidified food products. Here, we report the draft genome sequences of three L. plantarum food isolates.
Draft whole-genome sequences of 11 Bacillus cereus food isolates
Hayrapetyan, Hasmik ; Boekhorst, Jos ; Jong, Anne de; Kuipers, Oscar P. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2016
Genome announcements 4 (2016)3. - ISSN 2169-8287

Bacillus cereus is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we report the whole-genome sequences of 11 B. cereus food isolates.

2016 EAAP Novus Travel Award - Akke Kok
Kok, A. - \ 2016
American Dairy Science Association (Nieuwsbrief EAAP en andere congressen )
At the EAAP 2015 meeting in Warsaw, I received the Novus Travel Grant for my presentation about the effective lactation yield: a measure to compare the milk yield of cows with different dry period lengths. The grant enabled me to visit Novus International and the ADSA/JAM in 2016.

I had never been to the USA before, but I was lucky to travel with two experienced colleagues. We arrived in Salt Lake City on Tuesday afternoon. The climate outside was like being in a toaster (almost 40 C). Inside, however, air-conditioning did a good job at keeping a very(!) cool climate. The conference centre was enormous, and posters were displayed electronically in a central hall, a perfect place to meet people! The interactive posters included much information, and many small-scale oral presentations were given.

Together, my colleagues and I had 3 presentations about consequences of shortening the dry period in dairy cows, on Thursday, Friday, and Saturday. My presentation was on the last day, and I was grateful that so many people attended it. After the conference, we visited Yellowstone NP. The park was amazing: full of geysers, mud pools and other colourful 'geothermal features', and at the same time full of wildlife.

Next was a visit to Novus International headquarters, Missouri. There I attended a research meeting and had a tour around the labs and facilities. Also, I could visit the research farm Green Acres for a tour. I felt very welcome, and it was interesting that mechanisms behind the feed additives and also the effects of processing were studied.

My visit in the USA was a wonderful experience, and I would like to take this opportunity to thank Novus International (especially Heather Tucker and Barbara Repking), ADSA (especially Alois Kertz), and EAAP (especially Abele Kuipers) for making it possible.
Developments, strategies and challenges for Netherlands’ dairy sector
Veer, A. de; Boer, I.J.M. de; Kuipers, A. - \ 2016
In: Book of Abstracts of the 67st Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers - p. 24 - 24.
In 2014 the Netherlands had 18,000 dairy farms with 1.6 million cows, 12.7 billion kg of milk of which 65%
sold abroad, 23 processing companies and 60,000 jobs in the chain. This contributed 1.2% to national economy
and 9% to trade surplus. Grassland prices in period 2013-15 varied between €45.000 till 80.000/ha. Recently,
milk price is around 30 ct/kg, but for ecological milk 52 ct/kg (2% of total volume). In years preceding the
ending of quota system, policy discussions started how to guide the sector in a sustainable way into the
quota free era. A land tied dairy sector was envisioned by politics and the sector itself. This was laid down
in the so called ‘Melkveewet’ (Dairy Husbandry Law). Enlargement of no. of cattle was linked to requiring
additional land. Moreover, the national produced amount of phosphate from animal manure was already set
at 172.9 million kg in agreement with EU commission, of which 84.9 for the dairy cow population. Farmers
anticipating the quota free situation enlarged herds in 2013/2014. In 2015, the number of cows was increased
by 120.000, + 7, 5% (production + 10%). As result, three month after the abolition of quota, the Netherlands
government installed a phosphate quota on farm level, reference July 2015, restricting the sector: 4-8% flat
reduction; 10% take away by transfer; price at moment €5,000/cow. Main focus in developing the sector is on
increasing cow production efficiency, nutrient use efficiency (by introduction of a nutrient cycle planner; farm
specific P-norms are allowed), amazing grazing initiatives, including policy to increase % of cows grazed,
cow welfare (by experimenting with bedded pack barns and the innovative cow garden), improving structure
of soils, decrease in antibiotic use (partly realized) and cow health initiatives, like increasing resilience of
cows. Research in these areas will be presented. Early 2015, a commission was appointed by the government
to make a future draft of a sustainable animal sector, which results will be presented as well.
Linking Bacillus cereus genotypes and carbohydrate utilization capacity
Warda, Alicja K. ; Siezen, Roland J. ; Boekhorst, Jos ; Wells-Bennik, Marjon H.J. ; Jong, Anne de; Kuipers, Oscar P. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2016
PLoS One 11 (2016)6. - ISSN 1932-6203

We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.

Strong reactive movement response of the medium-sized European hare to elevated predation risk in short vegetation
Weterings, Martijn J.A. ; Zaccaroni, Marco ; Koore, Nikki van der; Zijlstra, Linda M. ; Kuipers, Henry J. ; Langevelde, Frank van; Wieren, Sipke E. van - \ 2016
Animal Behaviour 115 (2016). - ISSN 0003-3472 - p. 107 - 114.
Habitat characteristics - Lepus europaeus - Nonlethal predator - Risk effect - Stretch length - Vegetation structure

Reactive movement responses of prey are affected by habitat characteristics, such as cover, which determine predation risk. Open habitats with low cover facilitate predator detection, movement and escape, while closed habitats reduce the ability to detect predators and hinder movement. We performed a field experiment using nonlethal predators to study the reactive movement responses of medium-sized prey in patches with different vegetation characteristics related to elevated predation risk. Ten GPS-collared, free-ranging European hares, Lepus europaeus, were repeatedly subjected to a leashed dog and two humans in an experimental cross-over design. Linear mixed models were used to assess the effect of the treatment and its interaction with vegetation parameters on the movement behaviour of the European hare. The reactive movement response was best explained by the model that included the interaction between elevated predation risk and vegetation structure. A strong immediate response was found in short vegetation up to 1 h after the treatment ended. The effect extended beyond the duration of the treatment and was synchronized with the resting and foraging period over the next 24 h. The distance covered between resting and foraging grounds was negatively affected, while use of less risky, low-quality vegetation during resting and foraging was favoured. Medium-sized prey species exhibit strong behavioural responses to the perceived predation risk, which we demonstrate here for the European hare. An elevated predation risk, for example by dogs, can trigger costly behavioural responses in these medium-sized prey species.

Bacterial Spores in Food : Survival, Emergence, and Outgrowth
Wells-Bennik, Marjon H.J. ; Eijlander, Robyn T. ; Besten, Heidy M.W. Den; Berendsen, Erwin M. ; Warda, Alicja K. ; Krawczyk, Antonina O. ; Nierop Groot, Masja N. ; Xiao, Yinghua ; Zwietering, Marcel H. ; Kuipers, Oscar P. ; Abee, Tjakko - \ 2016
Annual Review of Food Science and Technology 7 (2016). - ISSN 1941-1413 - p. 457 - 482.
Bacillus - Clostridium - Germination - Heat resistance - Predictive modeling - Spore dormancy

Spore-forming bacteria are ubiquitous in nature. The resistance properties of bacterial spores lie at the heart of their widespread occurrence in food ingredients and foods. The efficacy of inactivation by food-processing conditions is largely determined by the characteristics of the different types of spores, whereas food composition and storage conditions determine the eventual germination and outgrowth of surviving spores. Here, we review the current knowledge on variation in spore resistance, in germination, and in the outgrowth capacity of spores relevant to foods. This includes novel findings on key parameters in spore survival and outgrowth obtained by gene-trait matching approaches using genome-sequenced Bacillus spp. food isolates, which represent notorious food spoilage and pathogenic species. Additionally, the impact of strain diversity on heat inactivation of spores and the variability therein is discussed. Knowledge and quantification of factors that influence variability can be applied to improve predictive models, ultimately supporting effective control of spore-forming bacteria in foods.

Antibiotic use in dairy herds in the Netherlands from 2005 to 2012
Kuipers, A. ; Koops, W.J. ; Wemmenhove, H. - \ 2016
Journal of Dairy Science 99 (2016)2. - ISSN 0022-0302 - p. 1632 - 1648.
Antibiotic use - Dairy farmer group - Treatment category - Variation and trend

The aim of this study was to examine the variation in antibiotic use and the effects of external factors on trends in antibiotic use at the herd level by using the number of daily dosages as an indicator for antibiotic use. For this purpose, antibiotic use was analyzed in 94 dairy herds in the Netherlands from 2005 to 2012. The herds were divided into 3 groups of farmers: one group was guided in their antibiotic use from 2008 to 2010 as part of the project, whereas the other 2 groups were not actively guided. The farms were located in 10 of the 12 provinces and were clients of 32 of the 300 veterinary practices that treat cattle. Sales invoices from the veterinary practices provided the antibiotic and cost data for the participating farmers. The number of animal-defined daily dosages (ADDD) indicates the number of days per year that the average cow in a herd is given antibiotic treatment. The average ADDD for all farms from 2005 to 2012 was 5.86 (standard deviation. = 2.14); 68% of ADDD were used for udder health, 24% for clinical mastitis and 44% for dry-cow therapy. Variation in ADDD among herds decreased during the study period. The trend in ADDD can be described as having 3 phases: (1) a period of increasing use coinciding with little public concern about antibiotic use (2005-2007), (2) a period of growing awareness and stabilization of use (2007-2010), and (3) a period of decreasing use coinciding with increasing societal concerns (2010-2012). The greatest reduction in use was for drugs other than those used to treat the udder. Drug use for mastitis treatment fell considerably in the final year of the study period, whereas farmers were reluctant to reduce use for dry-cow therapy. Almost 40% of the herds were given less than 2.5 ADDD for dry-cow therapy, which is equivalent to 2.5 tubes per average cow in the herd, and 20% used more than 3 tubes per cow. Use of third- and fourth-generation cephalosporins and fluoroquinolones dropped from 18% of ADDD during 2005 to 2010 to 1% in 2012, with a shift toward penicillins and broad spectrum drugs. The ADDD was 22% lower in 2012 than 2007, the year of the highest usage. The decrease in ADDD over time varied between the 3 groups of farmers. During the second phase of the study, the guided group began to display a reduction in use, whereas the other groups only displayed a significant reduction in the third phase. The reduction in antibiotic use has resulted in lower veterinary costs per cow in recent years.

De Amsterdamse haven draait (groen) door : Op weg naar duurzaam concurrentievoordeel door inzet op de biobased en circulaire economie
Kuipers, Bart ; Jong, Onno de; Raak, Roel van; Sanders, Frederic ; Meesters, Koen ; Dam, J.E.G. van - \ 2015
Wageningen UR - Food & Biobased Research - 112 p.
regionale economie - regionale ontwikkeling - economische ontwikkeling - kringlopen - biobased economy - havens - amsterdam - noord-holland - regional economics - regional development - economic development - cycling - harbours
In dit onderzoek is de haven van Amsterdam nader onderzocht, zijn kansen voor de ontwikkeling van zowel biobased als circulaire economie in kaart gebracht en worden 17 acties benoemd voor het Havenbedrijf Amsterdam om deze kansen te kunnen verzilveren. De auteurs concluderen dat er grote kansen zijn voor de haven van Amsterdam om de transitie naar duurzame toepassingen in de biobased en circulaire economie door te zetten, met name voor biodiesel en -gas en bouwstenen voor de biochemie. Deze kansen blijken voorts uit de sterke knooppuntfunctie van de haven: er is reeds een aantal krachtige logistieke spelers aanwezig dat zich actief bezig houdt met de behandeling van biodiesel, maar vooral de reeds bestaande agrostromen hebben potentie voor toepassing in biobased routes. Tevens is een aantal logistieke spelers actief in schroot en andere vormen van recycling in de haven aanwezig—de schroothandel laat zien dat de circulaire economie zich steeds meer op een internationaal schaalniveau ontwikkelt waarbij de inzet van zeehavens onontbeerlijk is.
Minimum Information about a Biosynthetic Gene cluster
Medema, M.H. ; Kottmann, Renzo ; Yilmaz, Pelin ; Cummings, Matthew ; Biggins, J.B. ; Blin, Kai ; Bruijn, Irene De; Chooi, Yit Heng ; Claesen, Jan ; Coates, R.C. ; Cruz-Morales, Pablo ; Duddela, Srikanth ; Düsterhus, Stephanie ; Edwards, Daniel J. ; Fewer, David P. ; Garg, Neha ; Geiger, Christoph ; Gomez-Escribano, Juan Pablo ; Greule, Anja ; Hadjithomas, Michalis ; Haines, Anthony S. ; Helfrich, Eric J.N. ; Hillwig, Matthew L. ; Ishida, Keishi ; Jones, Adam C. ; Jones, Carla S. ; Jungmann, Katrin ; Kegler, Carsten ; Kim, Hyun Uk ; Kötter, Peter ; Krug, Daniel ; Masschelein, Joleen ; Melnik, Alexey V. ; Mantovani, Simone M. ; Monroe, Emily A. ; Moore, Marcus ; Moss, Nathan ; Nützmann, Hans Wilhelm ; Pan, Guohui ; Pati, Amrita ; Petras, Daniel ; Reen, F.J. ; Rosconi, Federico ; Rui, Zhe ; Tian, Zhenhua ; Tobias, Nicholas J. ; Tsunematsu, Yuta ; Wiemann, Philipp ; Wyckoff, Elizabeth ; Yan, Xiaohui ; Yim, Grace ; Yu, Fengan ; Xie, Yunchang ; Aigle, Bertrand ; Apel, Alexander K. ; Balibar, Carl J. ; Balskus, Emily P. ; Barona-Gómez, Francisco ; Bechthold, Andreas ; Bode, Helge B. ; Borriss, Rainer ; Brady, Sean F. ; Brakhage, Axel A. ; Caffrey, Patrick ; Cheng, Yi Qiang ; Clardy, Jon ; Cox, Russell J. ; Mot, René De; Donadio, Stefano ; Donia, Mohamed S. ; Donk, Wilfred A. Van Der; Dorrestein, Pieter C. ; Doyle, Sean ; Driessen, Arnold J.M. ; Ehling-Schulz, Monika ; Entian, Karl Dieter ; Fischbach, Michael A. ; Gerwick, Lena ; Gerwick, William H. ; Gross, Harald ; Gust, Bertolt ; Hertweck, Christian ; Höfte, Monica ; Jensen, Susan E. ; Ju, Jianhua ; Katz, Leonard ; Kaysser, Leonard ; Klassen, Jonathan L. ; Keller, Nancy P. ; Kormanec, Jan ; Kuipers, Oscar P. ; Kuzuyama, Tomohisa ; Kyrpides, Nikos C. ; Kwon, Hyung Jin ; Lautru, Sylvie ; Lavigne, Rob ; Lee, Chia Y. ; Linquan, Bai ; Liu, Xinyu ; Liu, Wen ; Luzhetskyy, Andriy ; Mahmud, Taifo ; Mast, Yvonne ; Méndez, Carmen ; Metsä-Ketelä, Mikko ; Micklefield, Jason ; Mitchell, Douglas A. ; Moore, Bradley S. ; Moreira, Leonilde M. ; Müller, Rolf ; Neilan, Brett A. ; Nett, Markus ; Nielsen, Jens ; O'Gara, Fergal ; Oikawa, Hideaki ; Osbourn, Anne ; Osburne, Marcia S. ; Ostash, Bohdan ; Payne, Shelley M. ; Pernodet, Jean Luc ; Petricek, Miroslav ; Piel, Jörn ; Ploux, Olivier ; Raaijmakers, Jos M. ; Salas, José A. ; Schmitt, Esther K. ; Scott, Barry ; Seipke, Ryan F. ; Shen, Ben ; Sherman, David H. ; Sivonen, Kaarina ; Smanski, Michael J. ; Sosio, Margherita ; Stegmann, Evi ; Süssmuth, Roderich D. ; Tahlan, Kapil ; Thomas, Christopher M. ; Tang, Yi ; Truman, Andrew W. ; Viaud, Muriel ; Walton, Jonathan D. ; Walsh, Christopher T. ; Weber, Tilmann ; Wezel, Gilles P. Van; Wilkinson, Barrie ; Willey, Joanne M. ; Wohlleben, Wolfgang ; Wright, Gerard D. ; Ziemert, Nadine ; Zhang, Changsheng ; Zotchev, Sergey B. ; Breitling, Rainer ; Takano, Eriko ; Glöckner, Frank Oliver - \ 2015
Nature Chemical Biology 11 (2015)9. - ISSN 1552-4450 - p. 625 - 631.

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

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