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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Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study
Depommier, Clara ; Everard, Amandine ; Druart, Céline ; Plovier, Hubert ; Hul, Matthias Van; Vieira-Silva, Sara ; Falony, Gwen ; Raes, Jeroen ; Maiter, Dominique ; Delzenne, Nathalie M. ; Barsy, Marie de; Loumaye, Audrey ; Hermans, Michel P. ; Thissen, Jean Paul ; Vos, Willem M. de; Cani, Patrice D. - \ 2019
Nature Medicine 25 (2019)7. - ISSN 1078-8956 - p. 1096 - 1103.

Metabolic syndrome is characterized by a constellation of comorbidities that predispose individuals to an increased risk of developing cardiovascular pathologies as well as type 2 diabetes mellitus1. The gut microbiota is a new key contributor involved in the onset of obesity-related disorders2. In humans, studies have provided evidence for a negative correlation between Akkermansia muciniphila abundance and overweight, obesity, untreated type 2 diabetes mellitus or hypertension3–8. Since the administration of A. muciniphila has never been investigated in humans, we conducted a randomized, double-blind, placebo-controlled pilot study in overweight/obese insulin-resistant volunteers; 40 were enrolled and 32 completed the trial. The primary end points were safety, tolerability and metabolic parameters (that is, insulin resistance, circulating lipids, visceral adiposity and body mass). Secondary outcomes were gut barrier function (that is, plasma lipopolysaccharides) and gut microbiota composition. In this single-center study, we demonstrated that daily oral supplementation of 1010A. muciniphila bacteria either live or pasteurized for three months was safe and well tolerated. Compared to placebo, pasteurized A. muciniphila improved insulin sensitivity (+28.62 ± 7.02%, P = 0.002), and reduced insulinemia (−34.08 ± 7.12%, P = 0.006) and plasma total cholesterol (−8.68 ± 2.38%, P = 0.02). Pasteurized A. muciniphila supplementation slightly decreased body weight (−2.27 ± 0.92 kg, P = 0.091) compared to the placebo group, and fat mass (−1.37 ± 0.82 kg, P = 0.092) and hip circumference (−2.63 ± 1.14 cm, P = 0.091) compared to baseline. After three months of supplementation, A. muciniphila reduced the levels of the relevant blood markers for liver dysfunction and inflammation while the overall gut microbiome structure was unaffected. In conclusion, this proof-of-concept study (clinical trial no. NCT02637115) shows that the intervention was safe and well tolerated and that supplementation with A. muciniphila improves several metabolic parameters.

Bioelectrochemical chain elongation
Raes, Sanne M.T. - \ 2019
Wageningen University. Promotor(en): C.J.N. Buisman, co-promotor(en): Strik. D.P.B.T.B.. - Wageningen : Wageningen University - ISBN 9789463439169 - 167
Hydrophobic eutectic mixtures as volatile fatty acid extractants
Bruinhorst, Adriaan van den; Raes, Sanne ; Maesara, Sausan Atika ; Kroon, Maaike C. ; Esteves, A.C.C. ; Meuldijk, Jan - \ 2019
Separation and Purification Technology 216 (2019). - ISSN 1383-5866 - p. 147 - 157.
Deep eutectic solvents - Designer solvents - Eutectic mixtures - Liquid–liquid extraction - Volatile fatty acid recovery

Organic waste streams can be converted into volatile fatty acids (VFAs) via fermentation. VFAs can be used as intermediates in the synthesis of added-value chemicals. In this work, hydrophobic eutectic mixtures were designed for the liquid-liquid extraction of VFAs from dilute aqueous solutions. The eutectic behaviour was screened for over 100 combinations of 16 hydrophobic components that were selected based on a set of predetermined criteria. Mixtures of dihexylthiourea and trioctylphosphine oxide (TOPO) showed the best extraction performance and were stable over a wide pH range. The extraction efficiency increased with increasing hydrophobicity of the VFAs, and only undissociated acids were extracted. Upon increasing the TOPO content of the eutectic mixture, the extraction performance could be improved, confirming the tuneable nature of eutectic solvents. However, the extraction performance was less than that for solutions of TOPO in hydrophobic solvents, even though mole fractions of TOPO were higher in the eutectic mixtures. It was hypothesized that the intermolecular VFA–TOPO interactions required for extraction are suppressed by the inter-component interactions in the eutectic mixture. The inter-component interactions are responsible for the negative deviation from ideality of the melting temperature depressions that extend the liquid window of the mixtures towards the extraction temperature. Hence, the design of novel hydrophobic extractants based on eutectic mixtures was demonstrated. Their performance might be improved by selecting counterparts that interfere less with the interactions required for VFA extraction.

Water-Based Synthesis of Hydrophobic Ionic Liquids [N8888][oleate] and [P666,14][oleate] and their Bioprocess Compatibility
Raes, Sanne M.T. ; Jourdin, Ludovic ; Carlucci, Livio ; Bruinhorst, Adriaan van den; Strik, David P.B.T.B. ; Buisman, Cees J.N. - \ 2018
ChemistryOpen 7 (2018)11. - ISSN 2191-1363 - p. 878 - 884.
fatty acids - ionic liquids - microbial compatibility - toxicity - wastewater

The conversion of organic waste streams into carboxylic acids as renewable feedstocks results in relatively dilute aqueous streams. Carboxylic acids can be recovered from such streams by using liquid–liquid extraction. Hydrophobic ionic liquids (ILs) are novel extractants that can be used for carboxylic acid recovery. To integrate these ILs as in situ extractants in several biotechnological applications, the IL must be compatible with the bioprocesses. Herein the ILs [P666,14][oleate] and [N8888][oleate] were synthesized in water and their bioprocess compatibility was assessed by temporary exposure to an aqueous phase that contained methanogenic granular sludge. After transfer of the sludge into fresh medium, [P666,14][oleate]-exposed granules were completely inhibited. Granules exposed to [N8888][oleate] sustained anaerobic digestion activity, albeit moderately reduced. The IL contaminants, bromide (5–500 ppm) and oleate (10–4000 ppm), were shown not to inhibit the methanogenic conversion of acetate. [P666,14] was identified as a bioprocess-incompatible component. However, our results showed that [N8888][oleate] was bioprocess compatible and, therefore, has potential applications in bioprocesses.

A Summary of Research Activities from the AgMIP Potato Crop Modeling Intercomparison Pilot
Fleisher, D.H. ; Condori, B. ; Quiroz, R. ; Alva, A. ; Asseng, S. ; Barreda, Carolina ; Berghuijs, H.N.C. ; Bindi, M. ; Boote, K.J. ; Craigon, J. ; Fangmeier, A. ; Ferrise, Roberto ; Franke, A.C. ; Gayler, S. ; Govindakrishnan, P.M. ; Harahagazwe, Dieudonne ; Hoogenboom, G. ; Kremer, P. ; Kroes, J. ; Naresh Kumar, S. ; Merante, Paolo ; Nendel, C. ; Olesen, J.E. ; Parker, P.S. ; Pleijel, H. ; Raes, Dirk ; Raymundo, Rubi ; Reidsma, P. ; Ruana, A. ; Silva, J.V. ; Stella, T. ; Stockle, Claudio ; Supit, I. ; Evert, F.K. van; Vandermeiren, K. ; Vanuytrecht, Eline ; Vorne, V. ; Wolf, J. ; Woli, Prem - \ 2018
Activity-1 of the potato crop model intercomparison pilot was recently completed and focused on quantifying multi-model uncertainty to climate responses when using common data sets from low-and high-input management sites. Median model ensemble response outperformed any single model in terms of replicatingobserved yield across all sites. Uncertainty among models averaged 15% higher for low-versus high-input sites, with larger differences observed for evapotranspiration (ET), nitrogen uptake, and water use efficiency as compared to dry matter. A minimum of five partial, or three full, calibrated models was required for an ensemble approach to keep variability below that of common field variation. Model variation was not influenced by carbon dioxide (C), but increased as much as 41 and 23% for yield and ET respectively as temperature (T) or rainfall (W) moved away from historical levels. Increases in T accounted for the highest amount of uncertainty, suggesting that methods and parameters for T sensitivity represent a considerable unknown among models. Activity-2 research is on-going and tests the capability of multiple models to mimic effects of elevated C concentration on potato yields measured at eight different locations in Europe. A subset from observed OTC and FACE data was used to initially calibrate the models. This research will also evaluate the stability of the models’ calibration with respect to changes in geographic location, as the same variety was used in all locations. This presentation will summarize the Activity-1 results and discuss the current status of Activity-2 investigations.
Critical biofilm growth throughout unmodified carbon felts allows continuous bioelectrochemical chain elongation from CO2 up to caproate at high current density
Jourdin, Ludovic ; Raes, Sanne M.T. ; Buisman, Cees J.N. ; Strik, David P.B.T.B. - \ 2018
Frontiers in Energy Research 6 (2018)MAR. - ISSN 2296-598X
Biocatalysis - Bioelectrochemical chain elongation - Biofilm - Caproate - Carbon dioxide utilization - Microbial electrosynthesis
Current challenges for microbial electrosynthesis include the production of higher value chemicals than acetate, at high rates, using cheap electrode materials. We demonstrate here the continuous, biofilm-driven production of acetate (C2), n-butyrate (nC4), and n-caproate (nC6) from sole CO2 on unmodified carbon felt electrodes. No other organics were detected. This is the first quantified continuous demonstration of n-caproate production from CO2 using an electrode as sole electron donor. During continuous nutrients supply mode, a thick biofilm was developed covering the whole thickness of the felt (1.2-cm deep), which coincided with high current densities and organics production rates. Current density reached up to -14 kA melectrode -3 (-175 A m-2). Maximum sustained production rates of 9.8 ± 0.65 g L-1 day-1 C2, 3.2 ± 0.1 g L-1 day-1 nC4, and 0.95 ± 0.05 g L-1 day-1 nC6 were achieved (averaged between duplicates), at electron recoveries of 60-100%. Scanning electron micrographs revealed a morphologically highly diverse biofilm with long filamentous microorganism assemblies (~400 μm). n-Caproate is a valuable chemical for various industrial application, e.g., it can be used as feed additives or serve as precursor for liquid biofuels production.
Publisher Correction : Enterotypes in the landscape of gut microbial community composition
Costea, Paul I. ; Hildebrand, Falk ; Arumugam, Manimozhiyan ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O’Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
Enterotypes in the landscape of gut microbial community composition
Costea, Paul I. ; Hildebrand, Falk ; Manimozhiyan, Arumugam ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O'Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2017
Nature Microbiology 3 (2017)1. - ISSN 2058-5276 - p. 8 - 16.
Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
What determines plant species diversity in Central Africa?
Proosdij, Andreas S.J. van - \ 2017
Wageningen University. Promotor(en): M.S.M. Sosef, co-promotor(en): N. Raes; J.J. Wieringa. - Wageningen : Wageningen University - ISBN 9789463436618 - 161
plants - biodiversity - species diversity - species - distribution - biogeography - central africa - biosystematics - tropical rain forests - modeling - planten - biodiversiteit - soortendiversiteit - soorten - distributie - biogeografie - centraal-afrika - biosystematiek - tropische regenbossen - modelleren

Planet Earth hosts an incredible biological diversity. Estimated numbers of species occurring on Earth range from 5 to 11 million eukaryotic species including 400,000-450,000 species of plants. Much of this biodiversity remains poorly known and many species have not yet been named or even been discovered. This is not surprising, as the majority of species is known to be rare and ecosystems are generally dominated by a limited number of common species.

Tropical rainforests are the most species-rich terrestrial ecosystems on Earth. The general higher level of species richness is often explained by higher levels of energy near the Equator (latitudinal diversity gradient). However, when comparing tropical rainforest biomes, African rainforests host fewer plant species than either South American or Asian ones. The Central African country of Gabon is situated in the Lower Guinean phytochorical region. It is largely covered by what is considered to be the most species-rich lowland rainforest in Africa while the government supports an active conservation program. As such, Gabon is a perfect study area to address that enigmatic question that has triggered many researchers before: “What determines botanical species richness?”.

In the past 2.5 million years, tropical rainforests have experienced 21 cycles of global glaciations. They responded to this by contracting during drier and cooler glacials into larger montane and smaller riverine forest refugia and expanding again during warmer and wetter interglacials. The current rapid global climate change coupled with change of land use poses new threats to the survival of many rainforest species. The limited availability of resources for conservation forces governments and NGOs to set priorities. Unfortunately, for many plant species, lack of data on their distribution hampers well-informed decision making in conservation.

Species distribution models (SDMs) offer opportunities to bridge at least partly this knowledge gap. SDMs are correlative models that infer the spatial distribution of species using only a limited set of known species occurrence records coupled with high resolution environmental data. SDMs are widely applied to study the past, present and future distribution of species, assess the risk of invasive species, infer patterns of species richness and identify hotspots, as well as to assess the impact of climate change. The currently available methods form a pipeline, with which data are selected and cleaned, models selected, parameterized, evaluated and projected to other areas and climatic scenarios, and biodiversity patterns are computed from these SDMs. In this thesis, SDMs of all Gabonese plant species were generated and patterns of species richness and of weighted endemism were computed (chapter 4 & 5).

Although this pipeline enables the rapid generation of SDMs and inferring of biodiversity patterns, its effective use is limited by several matters of which three are specifically addressed in this thesis. Not knowing the true distribution limits the opportunities to assess the accuracy of models and assess the impact of assumptions and limitations of SDMs. The use of simulated species has been advocated as a method to systematically assess the impact of specific matters of SDMs (virtual ecologist). Following this approach, in chapter 2, I present a novel method to simulate large numbers of species that each have their own unique niche.

One matter of SDMs that is usually ignored but has been shown to be of great impact on model accuracy is the number of species occurrence records used to train a model. In chapter 2, I quantify the effect of sample size on model accuracy for species of different range size classes. The results show that the minimum number of records required to generate accurate SDMs is not uniform for species of every range size class and that larger sample sizes are required for more widespread species. By applying a uniform minimum number of records, SDMs of narrow-ranged species are incorrectly rejected and SDMs of widespread species are incorrectly accepted. Instead, I recommend to identify and apply the unique minimum numbers of required records for each individual species. The method presented here to identify the minimum number of records for species of particular range size classes is applicable to any species group and study area.

The range size or prevalence is an important plant feature that is used in IUCN Red List classifications. It is commonly computed as the Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Currently, these metrics are computed using methods based on the spatial distribution of the known species occurrences. In chapter 3, using simulated species again, I show that methods based on the distribution of species occurrences in environmental parameter space clearly outperform those based on spatial data. In this chapter, I present a novel method that estimates the range size of a species as the fraction of raster cells within the minimum convex hull of the species occurrences, when all cells from the study area are plotted in environmental parameter space. This novel method outperforms all ten other assessed methods. Therefore, the current use of EOO and AOO based on spatial data alone for the purpose of IUCN Red List classification should be reconsidered. I recommend to use the novel method presented here to estimate the AOO and to estimate the EOO from the predicted distribution based on a thresholded SDM.

In chapter 4, I apply the currently best possible methods to generate accurate SDMs and estimate the range size of species to the large dataset of Gabonese plant species records. All significant SDMs are used here to assess the unique contribution of narrow-ranged, widespread, and randomly selected species to patterns of species richness and weighted endemism. When range sizes of species are defined based on their full range in tropical Africa, random subsets of species best represent the pattern of species richness, followed by narrow-ranged species. Narrow-ranged species best represent the weighted endemism pattern. Moreover, the results show that the applied criterion of widespread and narrow-ranged is crucial. Too often, range sizes of species are computed on their distribution within a study area defined by political borders. I recommend to use the full range size of species instead. Secondly, the use of widespread species, of which often more data are available, as an indicator of diversity patterns should be reconsidered.

The effect of global climate change on the distribution patterns of Gabonese plant species is assed in chapter 5 using SDMs projected to the year 2085 for two climate change scenarios assuming either full or no dispersal. In Gabon, predicted loss of plant species ranges from 5% assuming full dispersal to 10% assuming no dispersal. However, these numbers are likely to be substantially higher, as for many rare, narrow-ranged species no significant SDMs could be generated. Predicted species turnover is as high as 75% and species-rich areas are predicted to loose many species. The explanatory power of individual future climate anomalies to predicted future species richness patterns is quantified. Species loss is best explained by increased precipitation in the dry season. Species gain and species turnover are correlated with a shift from extreme to average values of annual temperature range.

In the final chapter, the results are placed in a wider scientific context. First, the results on the methodological aspects of SDMs and their implications of the SDM pipeline are discussed. The method presented in this thesis to simulate large numbers of species offers opportunities to systematically investigate other matters of the pipeline, some of which are discussed here. Secondly, the factors that shape the current and predicted future patterns of plant species richness in Gabon are discussed including the location of centres of species richness and of weighted endemism in relation to the hypothesized location of glacial forest refugia. Factors that may contribute to the lower species richness of African rainforests compared with South American and Asian forests are discussed. I conclude by reflecting on the conservation of the Gabonese rainforest and its plant species as well as on the opportunities SDMs offer for this in the wider socio-economic context of a changing world with growing demand for food and other ecosystem services.

Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns
Proosdij, A.S.J. van; Raes, N. ; Wieringa, J.J. ; Sosef, M.S.M. - \ 2017
Species Distribution Models, centres of endemism - Species Distribution Models - centres of endemism - biodiversity hotspots - widespread - narrow-ranged - weighted endemism - species richness
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We call for a reconsideration of the use of widespread species as an indicator of diversity patterns, and advocate using the full ranges of species when assessing diversity patterns.
Continuous long-term bioelectrochemical chain elongation to butyrate
Raes, S.M.T. ; Jourdin, Ludovic ; Buisman, C.J.N. ; Strik, D.P.B.T.B. - \ 2017
ChemElectroChem 4 (2017)2. - ISSN 2196-0216 - p. 386 - 395.
We demonstrate here the long-term continuous bioelectrochemical chain elongation from CO2 and acetate by using a mixed microbial culture. The role of applied current (3.1 vs. 9.3 A m−2) on the performance was investigated. The main product was n-butyrate which was continuously produced over time. Trace amounts of propionate and n-caproate were also produced, but no alcohols were detected during the whole course of the experiment (163 days). Microbial electrosynthesis (MES) systems controlled with more current (9.3 Am−2) showed a butyrate concentration that was 4.5 times higher (maximum 0.59 g L−1) and increased volumetric production rates (0.54 g L−1 day−1) compared to the low-current reactors (0.12 g L−1 day−1), at 58.9 and 71.6 % electron recovery, respectively. Biocatalytic activity of the microbial consortia was demonstrated. This study revealed that the solid-state electrode does control the chain elongation reaction as an essential electron donor and determines the performance of MES systems. This study highlights MES as a promising alternative for acetate upgrading
A potato model intercomparison across varying climates and productivity levels
Fleisher, David H. ; Condori, Bruno ; Quiroz, Roberto ; Alva, Ashok ; Asseng, Senthold ; Barreda, Carolina ; Bindi, Marco ; Boote, Kenneth J. ; Ferrise, Roberto ; Franke, Angelinus C. ; Govindakrishnan, Panamanna M. ; Harahagazwe, Dieudonne ; Hoogenboom, Gerrit ; Naresh Kumar, Soora ; Merante, Paolo ; Nendel, Claas ; Olesen, Jorgen E. ; Parker, Phillip S. ; Raes, Dirk ; Raymundo, Rubi ; Ruane, Alex C. ; Stockle, Claudio ; Supit, Iwan ; Vanuytrecht, Eline ; Wolf, Joost ; Woli, Prem - \ 2017
Global Change Biology 23 (2017)3. - ISSN 1354-1013 - p. 1258 - 1281.
A potato crop multimodel assessment was conducted to quantify variation among models and evaluate responses to climate change. Nine modeling groups simulated agronomic and climatic responses at low-input (Chinoli, Bolivia and Gisozi, Burundi)- and high-input (Jyndevad, Denmark and Washington, United States) management sites. Two calibration stages were explored, partial (P1), where experimental dry matter data were not provided, and full (P2). The median model ensemble response outperformed any single model in terms of replicating observed yield across all locations. Uncertainty in simulated yield decreased from 38% to 20% between P1 and P2. Model uncertainty increased with interannual variability, and predictions for all agronomic variables were significantly different from one model to another (P < 0.001). Uncertainty averaged 15% higher for low- vs. high-input sites, with larger differences observed for evapotranspiration (ET), nitrogen uptake, and water use efficiency as compared to dry matter. A minimum of five partial, or three full, calibrated models was required for an ensemble approach to keep variability below that of common field variation. Model variation was not influenced by change in carbon dioxide (C), but increased as much as 41% and 23% for yield and ET, respectively, as temperature (T) or rainfall (W) moved away from historical levels. Increases in T accounted for the highest amount of uncertainty, suggesting that methods and parameters for T sensitivity represent a considerable unknown among models. Using median model ensemble values, yield increased on average 6% per 100-ppm C, declined 4.6% per °C, and declined 2% for every 10% decrease in rainfall (for nonirrigated sites). Differences in predictions due to model representation of light utilization were significant (P < 0.01). These are the first reported results quantifying uncertainty for tuber/root crops and suggest modeling assessments of climate change impact on potato may be improved using an ensemble approach.
Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns
Proosdij, A.S.J. van; Raes, N. ; Wieringa, J.J. ; Sosef, Marc - \ 2016
PLoS ONE 11 (2016)2. - ISSN 1932-6203 - 15 p.
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We call for a reconsideration of the use of widespread species as an indicator of diversity patterns, and advocate using the full ranges of species when assessing diversity patterns.
Faecal metaproteomic analysis reveals a personalized and stable functional microbiome and limited effects of a probiotic intervention in adults
Kolmeder, Carolin A. ; Salojärvi, Jarkko ; Ritari, Jarmo ; Been, Mark De; Raes, Jeroen ; Falony, Gwen ; Vieira-Silva, Sara ; Kekkonen, Riina A. ; Corthals, Garry L. ; Palva, Airi ; Salonen, Anne ; Vos, Willem M. de - \ 2016
PLoS ONE 11 (2016)4. - ISSN 1932-6203

Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.

Minimum required number of specimen records to develop accurate species distribution models
Proosdij, A.S.J. van; Sosef, M.S.M. ; Wieringa, J.J. ; Raes, N. - \ 2016
Ecography 39 (2016)6. - ISSN 0906-7590 - p. 542 - 552.
Species distribution models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence-only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre-defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The area under the curve (AUC) is commonly used as a measure of model performance. However, when applied to presence-only data it is prevalence-dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow-ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow-ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.
Minimum required number of specimen records to develop accurate species distribution models
Proosdij, A.S.J. van; Sosef, M.S.M. ; Wieringa, Jan ; Raes, N. - \ 2015
simulated species - prevalence - AUC - minimum number of records - model performance - null model - species distribution model
Species Distribution Models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence-only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre-defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The Area Under the Curve (AUC) is commonly used as a measure of model performance. However, when applied to presence-only data it is prevalence-dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow-ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow-ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.
Towards microbial fermentation metabolites as markers for health benefits of prebiotics
Verbeke, Kristin A. ; Boobis, Alan R. ; Chiodini, Alessandro ; Edwards, Christine A. ; Franck, Anne ; Kleerebezem, Michiel ; Nauta, Arjen ; Raes, Jeroen ; Tol, Eric A.F. Van; Tuohy, Kieran M. - \ 2015
Nutrition Research Reviews 28 (2015)1. - ISSN 0954-4224 - p. 42 - 66.
Metagenome - Microbial metabolites - Nutrikinetics - Prebiotic health benefits

Available evidence on the bioactive, nutritional and putative detrimental properties of gut microbial metabolites has been evaluated to support a more integrated view of how prebiotics might affect host health throughout life. The present literature inventory targeted evidence for the physiological and nutritional effects of metabolites, for example, SCFA, the potential toxicity of other metabolites and attempted to determine normal concentration ranges. Furthermore, the biological relevance of more holistic approaches like faecal water toxicity assays and metabolomics and the limitations of faecal measurements were addressed. Existing literature indicates that protein fermentation metabolites (phenol, p-cresol, indole, ammonia), typically considered as potentially harmful, occur at concentration ranges in the colon such that no toxic effects are expected either locally or following systemic absorption. The endproducts of saccharolytic fermentation, SCFA, may have effects on colonic health, host physiology, immunity, lipid and protein metabolism and appetite control. However, measuring SCFA concentrations in faeces is insufficient to assess the dynamic processes of their nutrikinetics. Existing literature on the usefulness of faecal water toxicity measures as indicators of cancer risk seems limited. In conclusion, at present there is insufficient evidence to use changes in faecal bacterial metabolite concentrations as markers of prebiotic effectiveness. Integration of results from metabolomics and metagenomics holds promise for understanding the health implications of prebiotic microbiome modulation but adequate tools for data integration and interpretation are currently lacking. Similarly, studies measuring metabolite fluxes in different body compartments to provide a more accurate picture of their nutrikinetics are needed.

Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena?
Rajilic-Stojanovic, M. ; Jonkers, D.M. ; Salonen, A. ; Hanevik, K. ; Raes, J. ; Jalanka, J. ; Vos, W.M. de; Manichanh, C. ; Golic, N. ; Enck, P. ; Philippou, E. ; Iraqi, F.A. ; Clarke, G. ; Spiller, R.C. ; Penders, J. - \ 2015
American Journal of Gastroenterology 110 (2015)2. - ISSN 0002-9270 - p. 278 - 287.
Irritable bowel syndrome (IBS) is a heterogeneous functional disorder with a multifactorial etiology that involves the interplay of both host and environmental factors. Among environmental factors relevant for IBS etiology, the diet stands out given that the majority of IBS patients report their symptoms to be triggered by meals or specific foods. The diet provides substrates for microbial fermentation, and, as the composition of the intestinal microbiota is disturbed in IBS patients, the link between diet, microbiota composition, and microbial fermentation products might have an essential role in IBS etiology. In this review, we summarize current evidence regarding the impact of diet and the intestinal microbiota on IBS symptoms, as well as the reported interactions between diet and the microbiota composition. On the basis of the existing data, we suggest pathways (mechanisms) by which diet components, via the microbial fermentation, could trigger IBS symptoms. Finally, this review provides recommendations for future studies that would enable elucidation of the role of diet and microbiota and how these factors may be (inter)related in the pathophysiology of IBS
Metagenomics meets time series analysis: unraveling microbial community dynamics
Faust, K. ; Lahti, L.M. ; Gonze, D. ; Vos, W.M. de; Raes, J. - \ 2015
Current Opinion in Microbiology 25 (2015). - ISSN 1369-5274 - p. 56 - 66.
The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.
Prioritizing West African medicinal plants for conservation and sustainable extraction studies based on market surveys and species distribution models.
Andel, T.R. van; Croft, S. ; Loon, E.E. van; Quiroz Villarreal, D.K. ; Towns, A.M. ; Raes, N. - \ 2015
Biological Conservation 181 (2015). - ISSN 0006-3207 - p. 173 - 181.
timber forest products - ecological explanation - benin - prediction - bark - commercialization - performance - disturbance - vegetation - impact
Sub-Saharan African human populations rely heavily on wild-harvested medicinal plants for their health. The trade in herbal medicine provides an income for many West African people, but little is known about the effects of commercial extraction on wild plant populations. Detailed distribution maps are lacking for even the most commonly traded species. Here we combine quantitative market surveys in Ghana and Benin with species distribution models (SDMs) to assess potential species’ vulnerability to overharvesting and to prioritize areas for sustainable extraction studies. We provide the first detailed distribution maps for 12 commercially extracted medicinal plants in West Africa. We suggest an IUCN threat status for four forest species that were not previously assessed (Sphenocentrum jollyanum, Okoubaka aubrevillei, Entada gigas and Piper guineense), which have narrow distributions in West Africa and are extensively commercialized. As SDMs estimate the extent of suitable abiotic habitat conditions rather than population size per se, their output is of limited use to assess vulnerability for overharvesting of widely distributed species. Examples of such species are Khaya senegalensis and Securidaca longipedunculata, two trees that were reported by market vendors as becoming increasingly scarce in the wild. Field surveys should start in predicted suitable habitats closest to urban areas and main roads, as commercial extraction likely occurs at the shortest cost distance to the markets. Our study provides an example of applying SDMs to conservation assessments aiming to safeguard provisioning ecosystems.
Harmonization and translation of crop modeling data to ensure interoperability
Porter, C. ; Villalobos, C. ; Holzworth, D. ; Nelson, R. ; White, J.W. ; Athanasiadis, I.N. ; Janssen, S.J.C. ; Ripoche, D. ; Cufi, J. ; Raes, D. ; Zhang, M. ; Knapen, M.J.R. ; Sahajpal, R. ; Boote, K. ; Jones, J.W. - \ 2014
Environmental Modelling & Software 62 (2014). - ISSN 1364-8152 - p. 495 - 508.
simulate yield response - systems simulation - climate-change - integration - framework - protocols - seamless - nitrogen - openmi
The Agricultural Model Intercomparison and Improvement Project (AgMIP) seeks to improve the capability of ecophysiological and economic models to describe the potential impacts of climate change on agricultural systems. AgMIP protocols emphasize the use of multiple models; consequently, data harmonization is essential. This interoperability was achieved by establishing a data exchange mechanism with variables defined in accordance with international standards; implementing a flexibly structured data schema to store experimental data; and designing a method to fill gaps in model-required input data. Researchers and modelers are able to use these tools to run an ensemble of models on a single, harmonized dataset. This allows them to compare models directly, leading ultimately to model improvements. An important outcome is the development of a platform that facilitates researcher collaboration from many organizations, across many countries. This would have been very difficult to achieve without the AgMIP data interoperability standards described in this paper.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nielsen, H.B. ; Almeida, M. ; Sierakowska Juncker, A. ; Rasmussen, S. ; Li, J. ; Sunagawa, S. ; Plichta, D.R. ; Gautier, L. ; Pedersen, A.G. ; Chatelier, E. Le; Pelletier, E. ; Bonde, I. ; Nielsen, T. ; Manichanh, C. ; Arumugam, M. ; Batto, J.M. ; Quintanilha dos Santos, M.B. ; Blom, N. ; Borruel, N. ; Burgdorf, K.S. ; Boumezbeur, F. ; Casellas, F. ; Doré, J. ; Dworzynski, P. ; Guarner, F. ; Hansen, T. ; Hildebrand, F. ; Kaas, R.S. ; Kennedy, S. ; Kristiansen, K. ; Kultima, J.R. ; Leonard, P. ; Levenez, F. ; Lund, O. ; Moumen, B. ; Paslier, D. Le; Pons, N. ; Pedersen, O. ; Prifti, E. ; Qin, J. ; Raes, J. ; Sørensen, S. ; Tap, J. ; Tims, S. ; Ussery, D.W. ; Yamada, T. ; Jamet, A. ; Mérieux, A. ; Cultrone, A. ; Torrejon, A. ; Quinquis, B. ; Brechot, C. ; Delorme, C. ; M'Rini, C. ; Vos, W.M. de; Maguin, E. ; Varela, E. ; Guedon, E. ; Gwen, F. ; Haimet, F. ; Artiguenave, F. ; Vandemeulebrouck, G. ; Denariaz, G. ; Khaci, G. ; Blottière, H. ; Knol, J. ; Weissenbach, J. ; Hylckama Vlieg, J.E. van; Torben, J. ; Parkhil, J. ; Turner, K. ; Guchte, M. van de; Antolin, M. ; Rescigno, M. ; Kleerebezem, M. ; Derrien, M. ; Galleron, N. ; Sanchez, N. ; Grarup, N. ; Veiga, P. ; Oozeer, R. ; Dervyn, R. ; Layec, S. ; Bruls, T. ; Winogradski, Y. ; Zoetendal, E.G. ; Renault, D. ; Sicheritz-Ponten, ; Bork, P. ; Wang, J. ; Brunak, S. ; Ehrlich, S.D. - \ 2014
Nature Biotechnology 32 (2014). - ISSN 1087-0156 - p. 822 - 828.
short read alignment - sequences - systems - algorithms - microbiota - protein - life - sets - tree - tool
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
Op safari in het Lichaam
Raes, J. ; Kleerebezem, M. ; Vos, W.M. de - \ 2014
Chemische Feitelijkheden 73 (2014)301. - p. 2 - 8.
Dietary vitamin A intake below the recommended daily intake during pregnancy and the risk of congenital diaphragmatic hernia in the offspring
Beurskens, L.W.J.E. ; Schrijver, L.H. ; Tibboel, D. ; Wildhagen, M.F. ; Knapen, M.F.C.M. ; Lindemans, J. ; Vries, J.H.M. de; Steegers-Theunissen, R.P.M. - \ 2013
Birth Defects Res. Part A-Clin. Mol. Teratol. 97 (2013)1. - ISSN 1542-9768 - p. 60 - 66.
BACKGROUND Vitamin A has been related to the etiology of congenital diaphragmatic hernia (CDH). We performed a case-control study to investigate whether maternal dietary vitamin A intake is related to CDH in the offspring. METHODS Thirty-one pregnancies diagnosed with CDH and 46 control pregnancies were included during the study. After CDH diagnosis and inclusion of controls by risk set sampling, maternal vitamin A intake was investigated with a food frequency questionnaire. Serum retinol and retinol-binding protein were determined. Univariable and multivariable logistic regression models were used to calculate risk estimates with adjustment for potential confounders. RESULTS We found no significant differences in the overall nutrient and vitamin A intake between case and control mothers. After stratification in body mass index (BMI) categories, case mothers with normal weight showed a lower energy adjusted vitamin A intake (685 vs. 843 mu g retinol activity equivalents [RAEs] / day; p = 0.04) and a slightly lower serum retinol (1.58 vs. 1.67 mu mol/L; p = 0.08) than control mothers. Vitamin A intake
Richness of human gut microbiome correlates with metabolic markers
Chatelier, E. Le; Nielsen, T. ; Qin, J. ; Prifti, E. ; Hildebrand, F. ; Falony, G. ; Almeida, M. ; Arumugam, M. ; Batto, J.M. ; Kennedy, S. ; Leonard, P. ; Li, J. ; Burgdorf, K. ; Grarup, N. ; Jorgensen, T. ; Branslund, I. ; Nielsen, H.B. ; Juncker, A.S. ; Bertalan, M. ; Levenez, F. ; Pons, N. ; Rasmussen, S. ; Sunagawa, S. ; Tap, J. ; Tims, S. ; Zoetendal, E.G. ; Brunak, S. ; Clement, K. ; Dore, J. ; Kleerebezem, M. ; Kristiansen, K. ; Renault, P. ; Sicheritz-Ponten, T. ; Vos, W.M. de; Zucker, J.D. ; Raes, J. ; Hansen, T. ; Bork, P. ; Wang, J. ; Ehrlich, S.D. ; Pederson, O. ; Guedon, E. ; Delorme, C. ; Layec, S. ; Khaci, G. ; Guchte, M. van de; Vandemeulebrouck, G. ; Jamet, A. ; Dervyn, R. ; Sanchez, N. ; Maguin, E. ; Haimet, F. ; Winogradski, Y. ; Cultrone, A. ; Leclerc, M. ; Juste, C. ; Blottière, H. ; Pelletier, E. ; LePaslier, D. ; Artiguenave, F. ; Bruls, T. ; Weissenbach, J. ; Turner, K. ; Parkhill, J. ; Antolin, M. ; Manichanh, C. ; Casellas, F. ; Boruel, N. ; Varela, E. ; Torrejon, A. ; Guarner, F. ; Denariaz, G. ; Derrien, M. ; Hylckama Vlieg, J.E.T. van; Veiga, P. ; Oozeer, R. ; Knol, J. ; Rescigno, M. ; Brechot, C. ; M'Rini, C. ; Mérieux, A. ; Yamada, T. - \ 2013
Nature 500 (2013)7464. - ISSN 0028-0836 - p. 541 - 546.
body-mass index - diet-induced obesity - insulin-resistance - wide association - reared apart - weight-loss - inflammation - adiposity - disease - twins
We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
Translating the human microbiome
Brown, J. ; Vos, W.M. de; Distefano, P.S. ; Doré, J. ; Huttenhower, C. ; Knight, R. ; Lawley, T.D. ; Raes, J. ; Turnbaugh, P. - \ 2013
Nature Biotechnology 31 (2013)4. - ISSN 1087-0156 - p. 304 - 308.
Over the past decade, an explosion of descriptive analyses from initiatives, such as the Human Microbiome Project (HMP) and the MetaHIT project, have begun to delineate the human microbiome. Inhabitants of the intestinal tract, nasal passages, oral cavities, skin, gastrointestinal tract and urogenital tract have been identified using whole genome sequencing, cultivation, metagenomics, metatranscriptomics, metaproteomics and metabolomics. Generation of these data has led to an improved understanding of the contribution of the human microbiome to physiology, health and disease. Nature Biotechnology approached several experts to seek their views on what steps need to be taken to move from descriptive microbiome biology to targeted therapies that tackle diseases in which microbiome dysfunction is a contributory factor
In search of the perfect aphrodisiac: Parallel use of bitter tonics in West Africa and the Caribbean
Andel, T.R. van; Mitchell, S. ; Volpato, G. ; Vandebroek, I. ; Swier, J. ; Ruysschaert, S. ; Rentería Jiménez, C.A. ; Raes, N. - \ 2012
Journal of Ethnopharmacology 143 (2012)3. - ISSN 0378-8741 - p. 840 - 850.
male-rats - ethnobotany - medicine - cameroon
Ethnopharmacological relevance Enslaved Africans in the Americas had to reinvent their medicinal flora in an unknown environment by adhering to plants that came with them, learning from Amerindians and Europeans, using their Old World knowledge and trial and error to find substitutes for their homeland herbs. This process has left few written records, and little research has been done on transatlantic plant use. We used the composition of aphrodisiac mixtures across the black Atlantic to discuss the adaptation of herbal medicine by African diaspora in the New World. Since Africans are considered relatively recent migrants in America, their healing flora is often said to consist largely of pantropical and cultivated species, with few native trees. Therefore, we expected Caribbean recipes to be dominated by taxa that occur in both continents, poor in forest species and rich in weeds and domesticated exotics. Materials and methods To test this hypothesis, we compared botanical ingredients of 35 African and 117 Caribbean mixtures, using Dentrended Correspondence Analysis, Cluster Analysis, Indicator Species Analysis and Mann–Whitney U tests. Results Very few of the 324 ingredients were used on both continents. A slightly higher overlap on generic and family level showed that Africans did search for taxa that were botanically related to African ones, but largely selected new, unrelated plants with similar taste, appearance or pharmacological properties. Recipes from the forested Guianas contained more New World, wild and forest species than those from deforested Caribbean islands. We recorded few ‘transatlantic genera’ and weeds never dominated the recipes, so we rejected our hypothesis. Conclusions The popularity of bitter tonics in the Caribbean suggests an African heritage, but the inclusion of Neotropical species and vernacular names of plants and mixtures indicate Amerindian and European influence. We show that enslaved Africans have reinvented their herbal medicine wherever they were put to work, using the knowledge and flora that was available to them with great creativity and flexibility. Our analysis reveals how transplanted humans adapt their traditional medical practises in a new environment.
Corresponding Mitochondrial DNA and Niche Divergence for Crested Newt Candidate Species
Wielstra, B.M. ; Beukema, W. ; Arntzen, J.W. ; Skidmore, A.K. ; Toxopeus, A.G. ; Raes, N. - \ 2012
PLoS ONE 7 (2012)9. - ISSN 1932-6203
absence data - models - phylogeography - delimitation - speciation - ecology - areas
Genetic divergence of mitochondrial DNA does not necessarily correspond to reproductive isolation. However, if mitochondrial DNA lineages occupy separate segments of environmental space, this supports the notion of their evolutionary independence. We explore niche differentiation among three candidate species of crested newt (characterized by distinct mitochondrial DNA lineages) and interpret the results in the light of differences observed for recognized crested newt species. We quantify niche differences among all crested newt (candidate) species and test hypotheses regarding niche evolution, employing two ordination techniques (PCA-env and ENFA). Niche equivalency is rejected: all (candidate) species are found to occupy significantly different segments of environmental space. Furthermore, niche overlap values for the three candidate species are not significantly higher than those for the recognized species. As the three candidate crested newt species are, not only in terms of mitochondrial DNA genetic divergence, but also ecologically speaking, as diverged as the recognized crested newt species, our findings are in line with the hypothesis that they represent cryptic species. We address potential pitfalls of our methodology.
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
Zoetendal, E.G. ; Raes, J. ; Bogert, B. van den; Arumugam, M. ; Booijink, C.C.G.M. ; Troost, F.J. ; Borkent, P. ; Wels, M.W.W. ; Vos, W.M. de; Kleerebezem, M. - \ 2012
ISME Journal 6 (2012)7. - ISSN 1751-7362 - p. 1415 - 1426.
human gastrointestinal-tract - fragment-length-polymorphism - gut microbiome - bacterial diversity - microarray analysis - sequence data - human ileal - samples - twins - mucosa
The human gastrointestinal tract (GI tract) harbors a complex community of microbes. The microbiota composition varies between different locations in the GI tract, but most studies focus on the fecal microbiota, and that inhabiting the colonic mucosa. Consequently, little is known about the microbiota at other parts of the GI tract, which is especially true for the small intestine because of its limited accessibility. Here we deduce an ecological model of the microbiota composition and function in the small intestine, using complementing culture-independent approaches. Phylogenetic microarray analyses demonstrated that microbiota compositions that are typically found in effluent samples from ileostomists (subjects without a colon) can also be encountered in the small intestine of healthy individuals. Phylogenetic mapping of small intestinal metagenome of three different ileostomy effluent samples from a single individual indicated that Streptococcus sp., Escherichia coli, Clostridium sp. and high G+C organisms are most abundant in the small intestine. The compositions of these populations fluctuated in time and correlated to the short-chain fatty acids profiles that were determined in parallel. Comparative functional analysis with fecal metagenomes identified functions that are overrepresented in the small intestine, including simple carbohydrate transport phosphotransferase systems (PTS), central metabolism and biotin production. Moreover, metatranscriptome analysis supported high level in-situ expression of PTS and carbohydrate metabolic genes, especially those belonging to Streptococcus sp. Overall, our findings suggest that rapid uptake and fermentation of available carbohydrates contribute to maintaining the microbiota in the human small intestine
Soils on exposed Sunda Shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia
Slik, J.W.F. ; Aiba, S.I. ; Bastian, M. ; Brearley, F.Q. ; Cannon, C.H. ; Eichhorn, K.A.O. ; Fredriksson, G. ; Kartawinata, K. ; Laumonier, Y. ; Mansor, A. ; Marjokorpi, A. ; Meijaard, E. ; Morley, R.J. ; Nagamasu, H. ; Nilus, R. ; Nurtjahya, E. ; Payne, J. ; Permana, A. ; Poulsen, A.D. ; Raes, N. ; Riswan, S. ; Schaik, C.P. ; Sheil, D. ; Sidiyasa, K. ; Suzuki, E. ; Valkenburg, J.L.C.H. van; Webb, C.O. ; Wich, S. ; Yoneda, T. ; Zakaria, R. ; Zweifel, N. - \ 2011
Proceedings of the National Academy of Sciences of the United States of America 108 (2011)30. - ISSN 0027-8424 - p. 12343 - 12347.
last glacial maximum - carbon stocks - vegetation - east - sea - environments - biodiversity - indicators - climate - borneo
The marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland is surprising given the long time that these areas have formed a single landmass. A dispersal barrier in the form of a dry savanna corridor during glacial maxima has been proposed to explain this disparity. However, the short duration of these dry savanna conditions make it an unlikely sole cause for the biogeographic pattern. An additional explanation might be related to the coarse sandy soils of central Sundaland. To test these two nonexclusive hypotheses, we performed a floristic cluster analysis based on 111 tree inventories from Peninsular Malaysia, Sumatra, and Borneo. We then identified the indicator genera for clusters that crossed the central Sundaland biogeographic boundary and those that did not cross and tested whether drought and coarse-soil tolerance of the indicator genera differed between them. We found 11 terminal floristic clusters, 10 occurring in Borneo, 5 in Sumatra, and 3 in Peninsular Malaysia. Indicator taxa of clusters that occurred across Sundaland had significantly higher coarse-soil tolerance than did those from clusters that occurred east or west of central Sundaland. For drought tolerance, no such pattern was detected. These results strongly suggest that exposed sandy sea-bed soils acted as a dispersal barrier in central Sundaland. However, we could not confirm the presence of a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distributions within Sundaland, including possible migration routes for early humans, need to be reevaluated.
A novel soluble immune-type receptor (SITR) in teleost fish: carp SITR is involved in the nitric oxide-mediated response to a protozoan parasite
Ribeiro, C.M.S. ; Raes, G. ; Ghassabeh, G.H. ; Schijns, V.E.J.C. ; Pontes, M.J.S.L. ; Savelkoul, H.F.J. ; Wiegertjes, G.F. - \ 2011
PLoS ONE 6 (2011)1. - ISSN 1932-6203 - 20 p.
immunoglobulin-like transcripts - ig-like domains - cyprinus-carpio - trypanoplasma-borreli - gene-cluster - monoclonal-antibodies - natural cytotoxicity - evolution - molecules - recognition
Background- The innate immune system relies upon a wide range of germ-line encoded receptors including a large number of immunoglobulin superfamily (IgSF) receptors. Different Ig-like immune receptor families have been reported in mammals, birds, amphibians and fish. Most innate immune receptors of the IgSF are type I transmembrane proteins containing one or more extracellular Ig-like domains and their regulation of effector functions is mediated intracellularly by distinct stimulatory or inhibitory pathways. Methodology/Principal Findings - Carp SITR was found in a substracted cDNA repertoire from carp macrophages, enriched for genes up-regulated in response to the protozoan parasite Trypanoplasma borreli. Carp SITR is a type I protein with two extracellular Ig domains in a unique organisation of a N-proximal V/C2 (or I-) type and a C-proximal V-type Ig domain, devoid of a transmembrane domain or any intracytoplasmic signalling motif. The carp SITR C-proximal V-type Ig domain, in particular, has a close sequence similarity and conserved structural characteristics to the mammalian CD300 molecules. By generating an anti-SITR antibody we could show that SITR protein expression was restricted to cells of the myeloid lineage. Carp SITR is abundantly expressed in macrophages and is secreted upon in vitro stimulation with the protozoan parasite T. borreli. Secretion of SITR protein during in vivo T. borreli infection suggests a role for this IgSF receptor in the host response to this protozoan parasite. Overexpression of carp SITR in mouse macrophages and knock-down of SITR protein expression in carp macrophages, using morpholino antisense technology, provided evidence for the involvement of carp SITR in the parasite-induced NO production. Conclusion/Significance - We report the structural and functional characterization of a novel soluble immune-type receptor (SITR) in a teleost fish and propose a role for carp SITR in the NO-mediated response to a protozoan parasite.
Heterogeneity of macrophage activation in fish
Forlenza, M. ; Fink, I.R. ; Raes, G. ; Wiegertjes, G.F. - \ 2011
Developmental and Comparative Immunology 35 (2011)12. - ISSN 0145-305X - p. 1246 - 1255.
tumor-necrosis-factor - cyprinus-carpio l. - trout oncorhynchus-mykiss - nitric-oxide synthase - toll-like receptors - interferon-gamma genes - carassius-auratus l. - expression analysis - rainbow-trout - factor-alpha
In this review, we focus on four different activation states of fish macrophages. In vitro, stimulation with microbial ligands induces the development of innate activated macrophages whereas classically activated macrophages can be induced by stimulation with LPS in combination with (recombinant) IFN¿. Both types of macrophages show elevated phagocytic activity, expression of pro-inflammatory cytokine genes and radical production. Alternatively activated macrophages require the cytokines IL-4/IL-13 for induction of, among others, arginase activity. Until in vitro studies identify the effects of putative IL-4 and IL-13 homologues on fish macrophages, arginase enzyme activity remains the most reliable marker for the presence of alternatively activated macrophages in fish. The best evidence for the existence of regulatory macrophages, associated with the presence of IL-10, comes from in vivo studies, for example during parasitic infections of carp. Altogether, differentially activated macrophages in fish largely resemble the phenotypes of mammalian macrophages. However, the presence of fish-specific ligand recognition by TLRs and of duplicated genes coding for proteins with particular activities, poses additional challenges for the characterization of phenotype-specific gene signatures and cell surface markers.
Comparison of spatio-temporal patterns of droughts in Malawi and el Nino Oscillation index
Corzo Perez, G. ; Fiwa, L. ; Wiyo, K. ; Raes, D. ; Vanutrecht, E. ; Geerts, S. ; Lanen, H.A.J. van - \ 2011
A human gut microbial gene catalogue established by metagenomic sequencing
Qin, J. ; Li, R. ; Raes, J. ; Arumugam, M. ; Tims, S. ; Vos, W.M. de; Zoetendal, E.G. ; Kleerebezem, M. - \ 2010
Nature 464 (2010). - ISSN 0028-0836 - p. 59 - 65.
16s ribosomal-rna - intestinal microbiota - communities - host - diversity - obesity - fermentation - environment - alignment - networks
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ~150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively
Mitochondrial (dys)function in adipocyte (de)-differentiation and systemic metabolic alterations
Pauw, A. de; Tejerina, S. ; Raes, M. ; Keijer, J. ; Arnould, T. - \ 2009
American Journal of Pathology 175 (2009)3. - ISSN 0002-9440 - p. 927 - 939.
white adipose-tissue - active antiretroviral therapy - polyunsaturated fatty-acids - receptor corepressor rip140 - element-binding protein - necrosis-factor-alpha - insulin-resistance - transgenic mice - uncoupling protein-3 - 3t3-l1 adipocytes
In mammals, adipose tissue, composed of BAT and WAT, collaborates in energy partitioning and performs metabolic regulatory functions. It is the most flexible tissue in the body, because it is remodeled in size and shape by modifications in adipocyte cell size and/or number, depending on developmental status and energy fluxes. Although numerous reviews have focused on the differentiation program of both brown and white adipocytes as well as on the pathophysiological role of white adipose tissues, the importance of mitochondrial activity in the differentiation or the dedifferentiation programs of adipose cells and in systemic metabolic alterations has not been extensively reviewed previously. Here, we address the crucial role of mitochondrial functions during adipogenesis and in mature adipocytes and discuss the cellular responses of white adipocytes to mitochondrial activity impairment. In addition, we discuss the increase in scientific knowledge regarding mitochondrial functions in the last 10 years and the recent suspicion of mitochondrial dysfunction in several 21st century epidemics (ie, obesity and diabetes), as well as in lipodystrophy found in HIV-treated patients, which can contribute to the development of new therapeutic strategies targeting adipocyte mitochondria
Influence of management and genetic merit for milk yield on the oxidative status of plasma in heifers
Wullepit, N. ; Raes, B. ; Beerda, B. ; Veerkamp, R.F. ; Fremaut, D. ; Smet, S. de - \ 2009
Livestock Science 123 (2009)2-3. - ISSN 1871-1413 - p. 276 - 282.
transition dairy-cows - vitamin-e - early lactation - energy-balance - antioxidant status - alpha-tocopherol - metabolic status - beta-carotene - stress - health
This study was part of a larger study that addressed whether milk production levels affect health risks in dairy cows as influenced by genetic merit for milk yield and management factors. Plasma samples were collected from 80 Holstein Friesian heifers at 2 weeks pre-partum and at 4 and 8 weeks post-partum in a 2 × 2 × 2 factorial arrangement design with the factors breeding value for milk production (high or low), milking frequency (2 or 3 times a day) and feed energy density (high or low). The following parameters indicative of the oxidative status were measured in plasma: ferric reducing ability of plasma (FRAP), a-tocopherol level, glutathione peroxidase activity (GSH-Px), superoxide dismutase activity (SOD), thiobarbituric acid reactive substances (TBARS) concentration and paraoxonase activity (PON). There was a significant effect of time for FRAP, a-tocopherol, GSH-Px and SOD, indicating changes in the plasma oxidative status around parturition. A high merit for milk yield, three-times-daily milking and especially feeding the high energy feed all stimulated milk production level. However, the influence on oxidative status parameters was minimal. Only the FRAP value was significantly lower in the high compared to the low energy group. Cows seem to undergo some oxidative stress around parturition, which can make them more susceptible to disorders. However, there were no clear indications that breeding value, milk frequency or feed energy level jeopardizes heifers in a way oxidative stress became critical
The global impact of ozone on agricultural crop yields under current and future air quality legislation
Dingenen, R. van; Dentener, F.J. ; Raes, F. ; Krol, M.C. ; Emberson, L. ; Cofala, J. - \ 2009
Atmospheric Environment 43 (2009)3. - ISSN 1352-2310 - p. 604 - 618.
surface ozone - tropospheric ozone - climate-change - semiarid site - ambient ozone - united-states - urban site - india - pollution - europe
In this paper we evaluate the global impact of surface ozone on four types of agricultural crop. The study is based on modelled global hourly ozone fields for the year 2000 and 2030, using the global 1°×1° 2-way nested atmospheric chemical transport model (TM5). Projections for the year 2030 are based on the relatively optimistic ¿current legislation (CLE) scenario¿, i.e. assuming that currently approved air quality legislation will be fully implemented by the year 2030, without a further development of new abatement policies. For both runs, the relative yield loss due to ozone damage is evaluated based on two different indices (accumulated concentration above a 40 ppbV threshold and seasonal mean daytime ozone concentration respectively) on a global, regional and national scale. The cumulative metric appears to be far less robust than the seasonal mean, while the seasonal mean shows satisfactory agreement with measurements in Europe, the US, China and Southern India and South-East Asia. Present day global relative yield losses are estimated to range between 7% and 12% for wheat, between 6% and 16% for soybean, between 3% and 4% for rice, and between 3% and 5% for maize (range resulting from different metrics used). Taking into account possible biases in our assessment, introduced through the global application of ¿western¿ crop exposure¿response functions, and through model performance in reproducing ozone-exposure metrics, our estimates may be considered as being conservative. Under the 2030 CLE scenario, the global situation is expected to deteriorate mainly for wheat (additional 2¿6% loss globally) and rice (additional 1¿2% loss globally). India, for which no mitigation measures have been assumed by 2030, accounts for 50% of these global increase in crop yield loss. On a regional-scale, significant reductions in crop losses by CLE-2030 are only predicted in Europe (soybean) and China (wheat). Translating these assumed yield losses into total global economic damage for the four crops considered, using world market prices for the year 2000, we estimate an economic loss in the range $14¿$26 billion. About 40% of this damage is occurring in China and India. Considering the recent upward trends in food prices, the ozone-induced damage to crops is expected to offset a significant portion of the GDP growth rate, especially in countries with an economy based on agricultural production
Influence of future air pollution mitigation strategies on total aerosol radiative forcing
Kloster, S. ; Dentener, F. ; Feichter, J. ; Raes, F. ; Aardenne, J.A. van; Roeckner, E. ; Lohmann, U. ; Stier, P. ; Swart, R.J. - \ 2008
Atmospheric Chemistry and Physics 8 (2008)21. - ISSN 1680-7316 - p. 6405 - 6437.
climate model echam5-ham - global sulfate distribution - cloud microphysics - greenhouse-gas - sulfur cycle - emissions - impact - simulation - albedo - flux
We apply different aerosol and aerosol precursor emission scenarios reflecting possible future control strategies for air pollution in the ECHAM5-HAM model, and simulate the resulting effect on the Earth's radiation budget. We use two opposing future mitigation strategies for the year 2030: one in which emission reduction legislation decided in countries throughout the world are effectively implemented (current legislation; CLE 2030) and one in which all technical options for emission reductions are being implemented independent of their cost (maximum feasible reduction; MFR 2030). We consider the direct, semi-direct and indirect radiative effects of aerosols. The total anthropogenic aerosol radiative forcing defined as the difference in the top-of-the-atmosphere radiation between 2000 and pre-industrial times amounts to -2.00 W/m2. In the future this negative global annual mean aerosol radiative forcing will only slightly change (+0.02 W/m2) under the "current legislation" scenario. Regionally, the effects are much larger: e.g. over Eastern Europe radiative forcing would increase by +1.50 W/m2 because of successful aerosol reduction policies, whereas over South Asia it would decrease by -1.10 W/m2 because of further growth of emissions. A "maximum feasible reduction" of aerosols and their precursors would lead to an increase of the global annual mean aerosol radiative forcing by +1.13 W/m2. Hence, in the latter case, the present day negative anthropogenic aerosol forcing could be more than halved by 2030 because of aerosol reduction policies and climate change thereafter will be to a larger extent be controlled by greenhouse gas emissions. We combined these two opposing future mitigation strategies for a number of experiments focusing on different sectors and regions. In addition, we performed sensitivity studies to estimate the importance of future changes in oxidant concentrations and the importance of the aerosol microphysical coupling within the range of expected future changes. For changes in oxidant concentrations caused by future air pollution mitigation, we do not find a significant effect for the global annual mean radiative aerosol forcing. In the extreme case of only abating SO2 or carbonaceous emissions to a maximum feasible extent, we find deviations from additivity for the radiative forcing over anthropogenic source regions up to 10% compared to an experiment abating both at the same time.
Are national greenhouse gas emissions reports scientifically valid
Swart, R.J. ; Bergamaschi, P. ; Pulles, T. ; Raes, F. - \ 2007
Climate Policy 7 (2007)6. - ISSN 1469-3062 - p. 535 - 538.
While countries have recently been accused of misreporting greenhouse gas emissions for their benefit, internationally agreed procedures minimize such possibilities and allow for new scientific results to be taken into account in a stepwise manner.
Climate assessment: what's next?
Raes, F. ; Swart, R.J. - \ 2007
Science 318 (2007)5855. - ISSN 0036-8075 - p. 1386 - 1386.
Making integration of adaption and mitigation work: mainstreaming into sustainable development policies?
Swart, R.J. ; Raes, F. - \ 2007
Climate Policy 7 (2007)4. - ISSN 1469-3062 - p. 288 - 303.
climate-change policy - capacity
Can an integrated approach to mitigation and adaptation offer opportunities for a more effective response to climate change than the current strategies? The nature of the linkages depends on the dimensions: economic, institutional or environmental, and on the scale. Differences are pervasive: adaptation and mitigation usually have different temporal and spatial scales and are mostly relevant for different economic sectors, so that costs and benefits are distributed differently. The article concludes that generally the global, regional and - in most countries - national potential of synergetic options to mitigate and adapt to climate change is relatively low, and both strategies should be considered as complementary. However, a few notable exceptions are identified in the land and water management and urban planning sectors, in particular in countries or locations where these sectors provide important adaptation and mitigation opportunities. What is the theoretically most efficient and least expensive mixture of adaptation and mitigation policies may not be a very urgent policy question. Instead, five pragmatic ways of broadening climate policy are suggested, while taking into account the linkages between adaptation and mitigation: (1) avoiding trade-offs - when designing policies for mitigation or adaptation, (2) identifying synergies, (3) enhancing response capacity, (4) developing institutional links between adaptation and mitigation - e.g. in national institutions and in international negotiations, and (5) mainstreaming adaptation and mitigation considerations into broader sustainable development policies
A search for parasite-associated molecular patterns stimulating carp macrophages
Ribeiro, C.M.S. ; Veen, J. van der; Raes, G. ; Ghassabeh, G.H. ; Savelkoul, H.F.J. ; Wiegertjes, G.F. - \ 2007
In: Proceedings of the 7th Nordic Symposium on Fish Immunology abstracts and programme, Stirling, Scotland, UK, 19 - 22 June, 2007. - - p. 65 - 65.
A good climate for clean air: linkages between climate change and air pollution
Swart, R. ; Amann, M. ; Raes, F. ; Tuinstra, W. - \ 2004
Climatic Change 66 (2004)3. - ISSN 0165-0009 - p. 263 - 269.
mortality - europe - ozone
Dietary and milk fatty acid composition in relation to the use of forages from semi-natural grasslands
Fievez, V. ; Vlaeminck, B. ; Raes, K. ; Chow, T.T. ; Smet, S. de; Demeyer, D. ; Bruinenberg, M.H. - \ 2002
In: Multi-function grasslands: Quality forages, animal products and landscapes : 19th General Meeting European Grassland Federation, La Rochelle 2002 / Durand, J.L., Emile, J.C., Huyghe, C., Lemaire, G., Poitiers : P. Oudin - ISBN 9782950411037 - p. 558 - 559.
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