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Governance arrangements in the European forest sector : Shifts towards ‘new governance’ or maintenance of state authority?
Sergent, Arnaud ; Arts, Bas ; Edwards, Peter - \ 2018
Land Use Policy 79 (2018). - ISSN 0264-8377 - p. 968 - 976.
Forest policy - Governance - Networks - Power

This article analyzes the variety of governance arrangements in the forest sector by examining the situation in ten European countries. At the national level, governance arrangements in the forest sector are analysed as a specific set of ideas, rules and relationships that shape and steer the decision-making process and determine (i) the policy framework, (ii) the forms of authority and power distribution, and (iii) the mediation pattern and network relationships. The study reveals that network governance, new policy instruments and ideational innovation have definitely emerged in the European forest sector, but, at its core, state forestry still dominates. That finding puts the shift from government to governance into perspective as well as the extent to which new forestry discourses are being put into practice. The article concludes that recent (gradual) changes in governance arrangements in the forest sector result from macro political trends, such as global and European discourses and guidelines on sustainability and good governance, on the one hand, and from the maintenance of the strategic key position of national states in European forest policies on the other.

Assessing rumen microbial composition and fibre attachment in dairy cows
Vaidya, Jueeli Deepak - \ 2018
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): Caroline Plugge; Joan Edwards. - Wageningen : Wageningen University - ISBN 9789463433587 - 181
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.

Using 'omic approaches to compare temporal bacterial colonization of lolium perenne, lotus corniculatus, and trifolium pratensein the Rumen
Elliott, Christopher L. ; Edwards, Joan E. ; Wilkinson, Toby J. ; Allison, Gordon G. ; McCaffrey, Kayleigh ; Scott, Mark B. ; Rees-Stevens, Pauline ; Kingston-Smith, Alison H. ; Huws, Sharon A. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X - 16 p.
16S rRNA gene - Birds foot trefoil - CowPI - FTIR - Microbiome - Perennial ryegrass - Red clover - Rumen

Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

Priorities for protected area research
Dudley, Nigel ; Hockings, Marc ; Stolton, Sue ; Amend, Thora ; Badola, Ruchi ; Bianco, Mariasole ; Chettri, Nakul ; Cook, Carly ; Day, Jon C. ; Dearden, Phil ; Edwards, Mary ; Ferraro, Paul ; Foden, Wendy ; Gambino, Roberto ; Gaston, Kevin J. ; Hayward, Natalie ; Hickey, Valerie ; Irving, Jason ; Jeffries, Bruce ; Karapetyan, Areg ; Kettunen, Marianne ; Laestadius, Lars ; Laffoley, Dan ; Lham, Dechen ; Lichtenstein, Gabriela ; Makombo, John ; Marshall, Nina ; McGeoch, Melodie ; Nguyen, Dao ; Nogué, Sandra ; Paxton, Midori ; Rao, Madhu ; Reichelt, Russell ; Rivas, Jorge ; Roux, Dirk ; Rutte, Claudia ; Schreckenberg, Kate ; Sovinc, Andrej ; Sutyrina, Svetlana ; Utomo, Agus ; Vallauri, Daniel ; Vedeld, Pål Olav ; Verschuuren, Bas ; Waithaka, John ; Woodley, Stephen ; Wyborn, Carina ; Zhang, Yan - \ 2018
PARKS: the International of Protected Areas and Conservation 24 (2018)1. - ISSN 0960-233X - p. 35 - 50.
Managers - Protected areas - Research priorities - Researchers - Stakeholder assessment

A hundred research priorities of critical importance to protected area management were identified by a targeted survey of conservation professionals; half researchers and half practitioners. Respondents were selected to represent a range of disciplines, every continent except Antarctica and roughly equal numbers of men and women. The results analysed thematically and grouped as potential research topics as by both practitioners and researchers. Priority research gaps reveal a high interest to demonstrate the role of protected areas within a broader discussion about sustainable futures and if and how protected areas can address a range of conservation and socio-economic challenges effectively. The paper lists the hundred priorities structured under broad headings of management, ecology, governance and social (including political and economic issues) and helps contribute to setting future research agendas.

CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, Joan E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
16S amplicon - CowPI - Function - PICRUSt - Rumen

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 and is provided to the wider scientific community for use in the study of the rumen microbiome.

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Vaidya, Jueeli D. ; Bogert, Bartholomeus van den; Edwards, J.E. ; Boekhorst, Jos ; Gastelen, S. van; Saccenti, Edoardo ; Plugge, Caroline M. ; Smidt, Hauke - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
454 pyrosequencing - Archaea - Bacteria - DNA extraction methods - Fibrous content - Fungi - QPCR - Rumen fluid
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method (p < 0.001) and fraction (p < 0.001). The 260/280 ratio was not affected by extraction (p = 0.08) but was affected by fraction (p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method (p < 0.001) but not affected by fraction (p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction (p = 0.012), and that PBB (p = 0.012) and FDSS (p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both. In summary, the comprehensive assessment of observed communities of bacteria, archaea and anaerobic fungi described here provides insight into a rational basis for selecting an optimal methodology to obtain a representative picture of the rumen microbiota.
The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Vaidya, J.D. ; Bogert, B. van den; Edwards, J.E. ; Boekhorst, Jos ; Gastelen, S. van; Saccenti, E. ; Plugge, C.M. ; Smidt, H. - \ 2017
PRJEB22996 - ERP104729
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed four diets with different ratios of grass and maize silage.
The rumen microbiome : An underexplored resource for novel antimicrobial discovery
Oyama, Linda B. ; Girdwood, Susan E. ; Cookson, Alan R. ; Fernandez-Fuentes, Narcis ; Privé, Florence ; Vallin, Hannah E. ; Wilkinson, Toby J. ; Golyshin, Peter N. ; Golyshina, Olga V. ; Mikut, Ralf ; Hilpert, Kai ; Richards, Jennifer ; Wootton, Mandy ; Edwards, Joan E. ; Maresca, Marc ; Perrier, Josette ; Lundy, Fionnuala T. ; Luo, Yu ; Zhou, Mei ; Hess, Matthias ; Mantovani, Hilario C. ; Creevey, Christopher J. ; Huws, Sharon A. - \ 2017
npj Biofilms and Microbiomes 3 (2017)1. - ISSN 2055-5008
Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.
Developing a Research Strategy to Better Understand, Observe, and Simulate Urban Atmospheric Processes at Kilometer to Subkilometer Scales
Barlow, J. ; Best, M. ; Bohnenstengel, S. ; Clark, P. ; Grimmond, S. ; Lean, H. ; Christen, A. ; Emeis, S. ; Haeffelin, M. ; Harman, I.N. ; Lemonsu, A. ; Martilli, A. ; Pardyjak, E. ; Rotach, M.W. ; Ballard, S. ; Boutle, I. ; Brown, A. ; Cai, X. ; Carpentieri, M. ; Coceal, O. ; Crawford, B. ; Sabatino, S. Di; Dou, J. ; Drew, D.R. ; Edwards, J.M. ; Fallmann, J. ; Fortuniak, K. ; Gornall, J. ; Gronemeier, T. ; Halios, C.H. ; Hertwig, D. ; Hirano, K. ; Holtslag, A.A.M. ; Luo, Z. ; Mills, G. ; Nakayoshi, M. ; Pain, K. ; Schlünzen, K.H. ; Smith, S. ; Soulhac, L. ; Steeneveld, G.J. ; Sun, T. ; Theeuwes, N.E. ; Thomson, D. ; Voogt, J.A. ; Ward, H.C. ; Xie, Z.T. ; Zhong, J. - \ 2017
Bulletin of the American Meteorological Society 98 (2017)10. - ISSN 0003-0007 - p. ES261 - ES264.
PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi : Insights, challenges and opportunities
Edwards, Joan E. ; Forster, Robert J. ; Callaghan, Tony M. ; Dollhofer, Veronika ; Dagar, Sumit S. ; Cheng, Yanfen ; Chang, Jongsoo ; Kittelmann, Sandra ; Fliegerova, Katerina ; Puniya, Anil K. ; Henske, John K. ; Gilmore, Sean P. ; O'Malley, Michelle A. ; Griffith, Gareth W. ; Smidt, Hauke - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 27 p.
(meta) transcriptomics - Anaerobic fungi - Genomics - Metabolomics - Neocallimastigomycota - Phylogeny - Proteomics - Rumen

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

Linseed oil and DGAT1 K232A polymorphism: Effects on methane emission, energy and nitrogen metabolism, lactation performance, ruminal fermentation, and rumen microbial composition of Holstein-Friesian cows
Gastelen, S. van; Visker, M.H.P.W. ; Edwards, J.E. ; Antunes Fernandes, E.C. ; Hettinga, K.A. ; Alferink, S.J.J. ; Hendriks, W.H. ; Bovenhuis, H. ; Smidt, H. ; Dijkstra, J. - \ 2017
Journal of Dairy Science 100 (2017)11. - ISSN 0022-0302 - p. 8939 - 8957.
diary cow - enteric methane production - Linseed oil - DGAT1 K232A polymorphism
Complex interactions between rumen microbiota, cow genetics, and diet composition may exist. Therefore, the effect of linseed oil, DGAT1 K232A polymorphism (DGAT1), and the interaction between linseed oil and DGAT1 on CH4 and H2 emission, energy and N metabolism, lactation performance, ruminal fermentation, and rumen bacterial and archaeal composition was investigated. Twenty-four lactating Holstein-Friesian cows (i.e., 12 with DGAT1 KK genotype and 12 with DGAT1 AA genotype) were fed 2 diets in a crossover design: a control diet and a linseed oil diet (LSO) with a difference of 22 g/kg of dry matter (DM) in fat content between the 2 diets. Both diets consisted of 40% corn silage, 30% grass silage, and 30% concentrates (DM basis). Apparent digestibility, lactation performance, N and energy balance, and CH4 emission were measured in climate respiration chambers, and rumen fluid samples were collected using the oral stomach tube technique. No linseed oil by DGAT1 interactions were observed for digestibility, milk production and composition, energy and N balance, CH4 and H2 emissions, and rumen volatile fatty acid concentrations. The DGAT1 KK genotype was associated with a lower proportion of polyunsaturated fatty acids in milk fat, and with a higher milk fat and protein content, and proportion of saturated fatty acids in milk fat compared with the DGAT1 AA genotype, whereas the fat- and protein-corrected milk yield was unaffected by DGAT1. Also, DGAT1 did not affect nutrient digestibility, CH4 or H2 emission, ruminal fermentation or ruminal archaeal and bacterial concentrations. Rumen bacterial and archaeal composition was also unaffected in terms of the whole community, whereas at the genus level the relative abundances of some bacterial genera were found to be affected by DGAT1. The DGAT1 KK genotype was associated with a lower metabolizability (i.e., ratio of metabolizable to gross energy intake), and with a tendency for a lower milk N efficiency compared with the DGAT1 AA genotype. The LSO diet tended to decrease CH4 production (g/d) by 8%, and significantly decreased CH4 yield (g/kg of DM intake) by 6% and CH4 intensity (g/kg of fat- and protein-corrected milk) by 11%, but did not affect H2 emission. The LSO diet also decreased ruminal acetate molar proportion, the acetate to propionate ratio, and the archaea to bacteria ratio, whereas ruminal propionate molar proportion and milk N efficiency increased. Ruminal bacterial and archaeal composition tended to be affected by diet in terms of the whole community, with several bacterial genera found to be significantly affected by diet. These results indicate that DGAT1 does not affect enteric CH4 emission and production pathways, but that it does affect traits other than lactation characteristics, including metabolizability, N efficiency, and the relative abundance of Bifidobacterium. Additionally, linseed oil reduces CH4 emission independent of DGAT1 and affects the rumen microbiota and its fermentative activity.
Domesticated equines have fundamental differences in faecal microbial concentrations
Edwards, J.E. ; Berg, Paul van den; Burden, F. ; Doorn, D.A. van; Pellikaan, W.F. ; Dijkstra, J. ; Everts, H. ; Smidt, H. - \ 2017
- 2 p.
Domesticated equines have fundamental differences in faecal microbial concentrations
Edwards, J.E. ; Berg, Paul van den; Burden, F. ; Doorn, D.A. van; Pellikaan, W.F. ; Dijkstra, J. ; Everts, H. ; Smidt, H. - \ 2017
Nutritional studies have shown that horses and donkeys differ, with donkeys having a higher dry matter digestibility (DMD) of dietary material and a longer gut retention time of dietary particles1,2. As analysis of the equine gut microbiome to date has primarily focussed on horses3, however, it is unclear to what extent these differences are mediated by differences in the physiology and/or hindgut microbiota of these domesticated equines (Figure 1). A preliminary study was therefore conducted in order to assess the faecal concentrations of bacteria, archaea and anaerobic fungi in horses, donkeys and hybrids (mules & hinnies) .
Buwchitin : A ruminal peptide with antimicrobial potential against Enterococcus faecalis
Oyama, Linda B. ; Crochet, Jean Adrien ; Edwards, Joan E. ; Girdwood, Susan E. ; Cookson, Alan R. ; Fernandez-Fuentes, Narcis ; Hilpert, Kai ; Golyshin, Peter N. ; Golyshina, Olga V. ; Privé, Florence ; Hess, Matthias ; Mantovani, Hilario C. ; Creevey, Christopher J. ; Huws, Sharon A. - \ 2017
Frontiers in Chemistry 5 (2017)JUL. - ISSN 2296-2646
Antibiotic resistance - Antimicrobial activity - Antimicrobial peptides - Enterococcus faecalis - Metagenomics - Microbiome - Rumen bacteria
Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.
Addressing complex challenges using a co-innovation approach : Lessons from five case studies in the New Zealand primary sector
Vereijssen, Jessica ; Srinivasan, M.S. ; Dirks, Sarah ; Fielke, Simon ; Jongmans, C.T. ; Agnew, Natasha ; Klerkx, Laurens ; Pinxterhuis, Ina ; Moore, John ; Edwards, Paul ; Brazendale, Rob ; Botha, Neels ; Turner, James A. - \ 2017
Outlook on Agriculture 46 (2017)2. - ISSN 0030-7270 - p. 108 - 116.
Agricultural innovation systems - Co-innovation principles - Innovation projects - Primary industries - Transdisciplinary research

Co-innovation can be effective for complex challenges – involving interactions amongst multiple stakeholders, viewpoints, perceptions, practices and interests across programmes, sectors and national systems. Approaches to challenges in the primary sector have tended to be linear, where tools and outputs are developed by a few, mostly scientists/researchers, and then extended to stakeholders. A co-innovation approach first deciphers and delineates the biophysical, societal, regulatory, policy, economic and environmental drivers, constraints and controls influencing these challenges at multiple levels. Second, stakeholder interactions and perspectives can inform and change the focus as well as help in co-developing solutions to deliver agreed outcomes. However, there is limited systematic and comparative research on how co-innovation works out in different projects. Here we analyse the results of applying a co-innovation approach to five research projects in the New Zealand primary sector. The projects varied in depth and breadth of stakeholder engagement, availability of ready-made solutions and prevalence of interests and conflicts. The projects show how and why co-innovation approaches in some cases contributed to a shared understanding of complex problems. Our results confirm the context specificity of co-innovation practices.

Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen
Lingen, Henk J. van; Edwards, Joan E. ; Vaidya, Jueeli D. ; Gastelen, Sanne van; Saccenti, Edoardo ; Bogert, Bartholomeus van den; Bannink, André ; Smidt, Hauke ; Plugge, Caroline M. ; Dijkstra, Jan - \ 2017
Frontiers in Microbiology 8 (2017)MAR. - ISSN 1664-302X
Bacteria - Dairy cow - Hydrogen - Linseed oil - Methane - Methanogenic archaea - Volatile fatty acids
Diurnal patterns of ruminal fermentation metabolites and microbial communities are not commonly assessed when investigating variation in ruminal CH4 production. The aims of this study were to monitor diurnal patterns of: (i) gaseous and dissolved metabolite concentrations in the bovine rumen, (ii) H2 and CH4 emitted, and (iii) the rumen microbiota. Furthermore, the effect of dietary inclusion of linseed oil on these patterns was assessed. Four rumen cannulated multiparous cows were used in a cross-over design with two 17 days periods and two dietary treatments: a control diet and a linseed oil supplemented diet [40% maize silage, 30% grass silage, 30% concentrate on dry matter (DM) basis for both diets; fat contents of 33 vs. 56 g/kg of DM]. On day 11, rumen contents were sampled for 10 h after morning feeding to profile gaseous and dissolved metabolite concentrations and microbiota composition. H2 and CH4 emission (mass per unit of time) was measured in respiration chambers from day 13 to 17. A 100-fold increase in ruminal H2 partial pressure (contribution to the total pressure of rumen headspace gases) was observed at 0.5 h after feeding. This peak was followed by a decline to basal level. Qualitatively similar patterns after feeding were also observed for H2 and CH4 emission, ethanol and lactate concentrations, and propionate molar proportion, although the opposite pattern was seen for acetate molar proportion. Associated with these patterns, a temporal biphasic change in the microbial composition was observed as based on 16S ribosomal RNA with certain taxa specifically associated with each phase. Bacterial concentrations (log10 16S ribosomal RNA gene copies based) were affected by time, and were increased by linseed oil supplementation. Archaeal concentrations (log10 16S ribosomal RNA gene copies based) tended to be affected by time and were not affected by diet, despite linseed oil supplementation decreasing CH4 emission, tending to decrease the partial pressure of CH4, and tending to increase propionate molar proportion. Linseed oil supplementation affected microbiota composition, and was most associated with an uncultivated Bacteroidales taxon. In summary, our findings support the importance of diurnal dynamics for the understanding of VFA, H2, and CH4 production.
Denial of long-term issues with agriculture on tropical peatlands will have devastating consequences
Wijedasa, Lahiru S. ; Jauhiainen, Jyrki ; Könönen, Mari ; Lampela, Maija ; Vasander, Harri ; Leblanc, Marie-Claire ; Evers, Stephanie ; Smith, Thomas E.L. ; Yule, Catherine M. ; Varkkey, Helena ; Lupascu, Massimo ; Parish, Faizal ; Singleton, Ian ; Clements, Gopalasamy R. ; Aziz, Sheema Abdul ; Harrison, Mark E. ; Cheyne, Susan ; Anshari, Gusti Z. ; Meijaard, Erik ; Goldstein, Jenny E. ; Waldron, Susan ; Hergoualc'h, Kristell ; Dommain, Rene ; Frolking, Steve ; Evans, Christopher D. ; Posa, Mary Rose C. ; Glaser, Paul H. ; Suryadiputra, Nyoman ; Lubis, Reza ; Santika, Truly ; Padfield, Rory ; Kurnianto, Sofyan ; Hadisiswoyo, Panut ; Lim, Teck Wyn ; Page, Susan E. ; Gauci, Vincent ; Meer, Peter J. Van Der; Buckland, Helen ; Garnier, Fabien ; Samuel, Marshall K. ; Choo, Liza Nuriati Lim Kim ; O'reilly, Patrick ; Warren, Matthew ; Suksuwan, Surin ; Sumarga, Elham ; Jain, Anuj ; Laurance, William F. ; Couwenberg, John ; Joosten, Hans ; Vernimmen, Ronald ; Hooijer, Aljosja ; Malins, Chris ; Cochrane, Mark A. ; Perumal, Balu ; Siegert, Florian ; Peh, Kelvin S.H. ; Comeau, Louis-Pierre ; Verchot, Louis ; Harvey, Charles F. ; Cobb, Alex ; Jaafar, Zeehan ; Wösten, Henk ; Manuri, Solichin ; Müller, Moritz ; Giesen, Wim ; Phelps, Jacob ; Yong, Ding Li ; Silvius, Marcel ; Wedeux, Béatrice M.M. ; Hoyt, Alison ; Osaki, Mitsuru ; Hirano, Takashi ; Takahashi, Hidenori ; Kohyama, Takashi S. ; Haraguchi, Akira ; Nugroho, Nunung P. ; Coomes, David A. ; Quoi, Le Phat ; Dohong, Alue ; Gunawan, Haris ; Gaveau, David L.A. ; Langner, Andreas ; Lim, Felix K.S. ; Edwards, David P. ; Giam, Xingli ; Werf, Guido Van Der; Carmenta, Rachel ; Verwer, Caspar C. ; Gibson, Luke ; Gandois, Laure ; Graham, Laura Linda Bozena ; Regalino, Jhanson ; Wich, Serge A. ; Rieley, Jack ; Kettridge, Nicholas ; Brown, Chloe ; Pirard, Romain ; Moore, Sam ; Capilla, B.R. ; Ballhorn, Uwe ; Ho, Hua Chew ; Hoscilo, Agata ; Lohberger, Sandra ; Evans, Theodore A. ; Yulianti, Nina ; Blackham, Grace ; Onrizal, O. ; Husson, Simon ; Murdiyarso, Daniel ; Pangala, Sunita ; Cole, Lydia E.S. ; Tacconi, Luca ; Segah, Hendrik ; Tonoto, Prayoto ; Lee, Janice S.H. ; Schmilewski, Gerald ; Wulffraat, Stephan ; Putra, Erianto Indra ; Cattau, Megan E. ; Clymo, R.S. ; Morrison, Ross ; Mujahid, Aazani ; Miettinen, Jukka ; Liew, Soo Chin ; Valpola, Samu ; Wilson, David ; Arcy, Laura D'; Gerding, Michiel ; Sundari, Siti ; Thornton, Sara A. ; Kalisz, Barbara ; Chapman, Stephen J. ; Su, Ahmad Suhaizi Mat ; Basuki, Imam ; Itoh, Masayuki ; Traeholt, Carl ; Sloan, Sean ; Sayok, Alexander K. ; Andersen, Roxane - \ 2017
Global Change Biology 23 (2017)3. - ISSN 1354-1013 - p. 977 - 982.
The first International Peat Congress (IPC) held in the tropics – in Kuching (Malaysia) – brought together over 1000 international peatland scientists and industrial partners from across the world (“International Peat Congress with over 1000 participants!,” 2016). The congress covered all aspects of peatland ecosystems and their management, with a strong focus on the environmental, societal and economic challenges associated with contemporary large-scale agricultural conversion of tropical peat.
Anaerobic fungi are a key unexplored taxon for optimizing fibre utilisation in equines
Edwards, J.E. ; Doorn, D.A. van; Pellikaan, W.F. ; Everts, H. ; Burden, F. ; Smidt, H. - \ 2016
Diurnal dynamics of metabolites and microbes in the bovine rumen: implications for the control of fermentation pathways
Edwards, J.E. ; Lingen, H.J. van; Vaidya, J.D. ; Gastelen, S. van; Bogert, Bartholomeus van den; Bannink, A. ; Plugge, C.M. ; Dijkstra, J. ; Smidt, H. - \ 2016
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