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.
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