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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How fertile are earthworm casts? A meta-analysis
Groenigen, J.W. van; Groenigen, Kees Jan Van; Koopmans, G.F. ; Stokkermans, Lotte ; Vos, M.J. ; Lubbers, I.M. - \ 2018
Geoderma (2018). - ISSN 0016-7061 - 11 p.
It has long been established that earthworms beneficially affect plant growth. This is to a large extent due to the high fertility of their casts. However, it is not clear how fertile casts are compared to bulk soil, and how their fertility varies between earthworm feeding guilds and with physico-chemical soil properties. Using meta-analysis, we quantified the fertility of earthworm casts and identi
fied its controlling factors. Our analysis included 405 observations from 81 articles, originating from all continents except Antarctica. We quantified cast fertility by determining the enrichment of earthworm casts relative to the bulk soil (“relative cast fertility”; RCF) for total organic carbon (TOC), total phosphorus (P) and total nitrogen (N) concentrations, as well as for plant available pools of N (total mineral N) and P (available P: P-Olsen, P-Bray or comparable metrics), C-to-N ratio and microbial biomass C. In addition to these response variables, we studied four additional ones closely related to soil fertility: pH-H2O, clay content, cation exchange capacity (CEC), and base saturation. With the exception of C-to-N ratio, microbial C and clay content, all studied response variables were significantly increased in casts compared to the bulk soil. Increases in total elemental concentrations (TOC, total P and total N), which are the result of preferential feeding or concentration processes, were comparable and ranged between 40 and 48%. Nutrient availability, which is to a large extent the result of (bio)chemical transformation processes in the earthworm gut, was increased more strongly than total elemental concentrations (241% and 84% for mineral N and available P, respectively). Increases in pH (0.5 pH units), cation exchange capacity (40%), and base saturation (27%) were also large and significant. None of the soil-related possible controlling factors could satisfactorily explain the
variation in RCF; plant presence (or other sources of organic C input such as residue application) was the only controlling factor that consistently increased RCF across soil properties. With the exception of available P, none of the studied response variables could be linked to earthworm feeding guild. Our results show that earthworm casts are much more fertile than bulk soil for almost all analysed cast fertility properties. However, these positive RCFs are to a large extent dependent upon the presence of plants. In general, earthworm feeding guild or specific physico-chemical soil properties could not explain the large variability in RCF for the various response variables. Therefore, we hypothesize that RCF e
ffects depend on intricate interactions between earthworm species traits and specific soil properties. Understanding these interactions requires trait-based approaches combined with mechanistic modelling of biochemical processes in the earthworm gut and casts.
Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent
Gerritsen, Jacoline ; Umanets, Alexander ; Staneva, Ivelina ; Hornung, Bastian ; Ritari, Jarmo ; Paulin, Lars ; Rijkers, Ger T. ; Vos, Willem M. de; Smidt, Hauke - \ 2018
International Journal of Systematic and Evolutionary Microbiology 68 (2018)11. - ISSN 1466-5026 - p. 3479 - 3486.
Clostridium - human intestine - ileostoma effluent - Peptostreptococcaceae - Romboutsia

A Gram-stain-positive, motile, rod-shaped, obligately anaerobic bacterium, designated FRIFIT, was isolated from human ileostoma effluent and characterized. On the basis of 16S rRNA gene sequence similarity, strain FRIFIT was most closely related to the species Romboutsia ilealis CRIBT (97.7 %), Romboutsia lituseburensis DSM 797T (97.6 %) and Romboutsia sedimentorum LAM201T (96.6 %). The level of DNA-DNA relatedness between strain FRIFIT and R. ilealis CRIBT was 13.9±3.3 % based on DNA-DNA hybridization. Whole genome sequence-based average nucleotide identity between strain FRIFIT and closely related Romboutsia strains ranged from 78.4-79.1 %. The genomic DNA G+C content of strain FRIFIT was 27.8 mol%. The major cellular fatty acids of strain FRIFIT were saturated and unsaturated straight-chain C12-C19 fatty acids as well as cyclopropane fatty acids, with C16 : 0 being the predominant fatty acid. The polar lipid profile comprised five phospholipids and six glycolipids. These results, together with differences in phenotypic features, support the proposal that strain FRIFIT represents a novel species within the genus Romboutsia, for which the name Romboutsiahominis sp. nov. is proposed. The type strain is FRIFIT (=DSM 28814T=KCTC 15553T).

Counter-Mapping against oil palm plantations : reclaiming village territory in Indonesia with the 2014 Village Law
Vos, Rosanne de - \ 2018
Critical Asian Studies (2018). - ISSN 1467-2715
2014 Indonesia Village Law - counter-mapping - land conflict - oil palm - spatial planning

This paper explores how villagers in Sambas District of West Kalimantan, Indonesia, attempt to protect their land rights against oil palm companies by engaging in mapping and spatial planning, in the context of the implementation of Indonesia's 2014 Village Law. Drawing on theoretical debates about counter-territorialization and counter-mapping, this paper considers how villagers use the Village Law to legitimate control over their territory. Although village-level spatial planning and mapping initiatives do not guarantee that land rights will be protected in the long term, spatial plans and maps can serve as leverage in negotiations with oil palm companies and government officials. Moreover, mapping and spatial planning help to organize people and boost discussions about land rights and different aspirations for land use. Proactive village-level spatial planning is necessary to find ways to maintain pre-existing ways of using land, and to counter notions of empty land, available for companies to claim.

Intestinal Microbiota in Hirschsprung Disease
Neuvonen, Malla I. ; Korpela, Katri ; Kyrklund, Kristiina ; Salonen, Anne ; Vos, Willem de; Rintala, Risto J. ; Pakarinen, Mikko P. - \ 2018
Journal of Pediatric Gastroenterology and Nutrition 67 (2018)5. - ISSN 0277-2116 - p. 594 - 600.
OBJECTIVES: The aim of the study was to characterize the microbiota profiles of patients with Hirschsprung disease (HD) and to evaluate this in relation to postoperative bowel function and the incidence of Hirschsprung-associated enterocolitis (HAEC). METHODS: All patients operated on for HD at our center between 1987 and 2011 were invited to answer questionnaires on bowel function and to participate in a clinical follow-up for laboratory investigations, including fecal DNA extraction, fecal calprotectin (FC), and brush border lactase (LCT) genotyping. The microbiota compositions of patients with HD were compared with those of healthy controls aged between 2 and 7 years. RESULTS: The microbiota composition of eligible patients with HD (n = 34; median age 12 [range, 3-25] years) differed from the healthy controls (n = 141), showing decreased overall microbial richness (P < 0.005). Seventy-seven percent had experienced HAEC. Normal maturation of the intestinal flora was not observed, but patients had a significantly increased abundance of Proteobacteria among other taxa (P < 0.005) resulting in a reduced carbohydrate degradation potential, as predicted by the taxonomic composition. Genetic lactase deficiency was present in 17% and did not correlate with bowel symptoms. No patients reported active HAEC at the time of sampling and FC was within the normal range in all samples. CONCLUSIONS: Patients with HD and HAEC had a significantly altered intestinal microbiome compared to healthy individuals, characterized by a lack of richness and pathologic expansions of taxa, particularly Enterobacteria and Bacilli. Further evaluation is needed to identify whether these observations are intrinsic to HD or secondary to the recurrent use of antibiotics during early childhood.
Literatuurstudie effecten van duurzame kaas op gezondheid en smaak
Vos, Claire - \ 2018
Ecosysteemdiensten Hart van Holland
Vos, Claire - \ 2018
presentatie
Bacteriën eten tegen overgewicht : Start-up A-Mansia voedingssupplementen op de markt brengen
Vos, Willem de - \ 2018
Eating bacteria to combat overweight : startup A-Mansia wants to market nutritional supplements
Vos, Willem de - \ 2018
Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants
Korpela, Katri ; Salonen, Anne ; Vepsäläinen, Outi ; Suomalainen, Marjo ; Kolmeder, Carolin ; Varjosalo, Markku ; Miettinen, Sini ; Kukkonen, Kaarina ; Savilahti, Erkki ; Kuitunen, Mikael ; Vos, Willem M. de - \ 2018
Microbiome 6 (2018)1. - ISSN 2049-2618
Bifidobacteria - Early-life microbiota - Lactobacilli - Metagenomics - Metaproteomics

Background: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches. Results: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced. Conclusions: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding. Trial registration: clinicaltrials.gov NCT00298337. Registered March 2, 2006.

Meer zorg nodig voor de Veenkoloniale bodem
Hoekzema, Gerard - \ 2018
Keuzes maken in Veenkoloniale akkerbouw
Hoekzema, Gerard - \ 2018
Communicatie over duurzame vis in de visdetailhandel
Janssens, S.R.M. ; Vos, B.I. de - \ 2018
Wageningen : Wageningen University & Research, Wetenschapswinkel (Wetenschapswinkel rapport 329) - ISBN 9789463432283 - 54
Ecosysteemdiensten Hart van Holland : een bonus voor diversiteit
Vos, Claire ; Meeuwsen, Henk ; Woltjer, I. - \ 2018
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2902) - 47
Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?
Tytgat, Hanne L.P. ; Nobrega, Franklin L. ; Oost, John van der; Vos, Willem M. de - \ 2018
Trends in Microbiology (2018). - ISSN 0966-842X
biofilm - colorectal cancer - microbiota - tipping points

Bacterial communities are known to impact human health and disease. Mixed species biofilms, mostly pathogenic in nature, have been observed in dental and gastric infections as well as in intestinal diseases, chronic gut wounds and colon cancer. Apart from the appendix, the presence of thick polymicrobial biofilms in the healthy gut mucosa is still debated. Polymicrobial biofilms containing potential pathogens appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut mucosa. Key biofilm-forming pathogens and associated molecules hold promise as biomarkers. Criteria to distinguish microcolonies from biofilms are crucial to provide clarity when reporting biofilm-related phenomena in health and disease in the gut.

Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota
Korpela, Katri ; Salonen, Anne ; Hickman, Brandon ; Kunz, Clemens ; Sprenger, Norbert ; Kukkonen, Kaarina ; Savilahti, Erkki ; Kuitunen, Mikael ; Vos, Willem M. de - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

One of the most abundant components in human milk is formed by oligosaccharides, which are poorly digested by the infant. The oligosaccharide composition of breast milk varies between mothers, and is dependent on maternal secretor (FUT2) genotype. Secretor mothers produce milk containing α1-2 fucosylated human milk oligosaccharides, which are absent in the milk of non-secretor mothers. Several strains of bacteria in the infant gut have the capacity to utilise human milk oligosaccharides (HMOs). Here we investigate the differences in infant gut microbiota composition between secretor (N = 76) and non-secretor (N = 15) mothers, taking into account birth mode. In the vaginally born infants, maternal secretor status was not associated with microbiota composition. In the caesarean-born, however, many of the caesarean-associated microbiota patterns were more pronounced among the infants of non-secretor mothers compared to those of secretor mothers. Particularly bifidobacteria were strongly depleted and enterococci increased among the caesarean-born infants of non-secretor mothers. Furthermore, Akkermansia was increased in the section-born infants of secretor mothers, supporting the suggestion that this organism may degrade HMOs. The results indicate that maternal secretor status may be particularly influential in infants with compromised microbiota development, and that these infants could benefit from corrective supplementation.

Sex differences in lipid metabolism are affected by presence of the gut microbiota
Baars, Annemarie ; Oosting, Annemarie ; Lohuis, Mirjam ; Koehorst, Martijn ; Aidy, Sahar El; Hugenholtz, Floor ; Smidt, Hauke ; Mischke, Mona ; Boekschoten, Mark V. ; Verkade, Henkjan J. ; Garssen, Johan ; Beek, Eline M. van der; Knol, Jan ; Vos, Paul de; Bergenhenegouwen, Jeroen van; Fransen, Floris - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Physiological processes are differentially regulated between men and women. Sex and gut microbiota have each been demonstrated to regulate host metabolism, but it is unclear whether both factors are interdependent. Here, we determined to what extent sex-specific differences in lipid metabolism are modulated via the gut microbiota. While male and female Conv mice showed predominantly differential expression in gene sets related to lipid metabolism, GF mice showed differences in gene sets linked to gut health and inflammatory responses. This suggests that presence of the gut microbiota is important in sex-specific regulation of lipid metabolism. Further, we explored the role of bile acids as mediators in the cross-talk between the microbiome and host lipid metabolism. Females showed higher total and primary serum bile acids levels, independent of presence of microbiota. However, in presence of microbiota we observed higher secondary serum bile acid levels in females compared to males. Analysis of microbiota composition displayed sex-specific differences in Conv mice. Therefore, our data suggests that bile acids possibly play a role in the crosstalk between the microbiome and sex-specific regulation of lipid metabolism. In conclusion, our data shows that presence of the gut microbiota contributes to sex differences in lipid metabolism.

What is the role of the model in socio-hydrology? Discussion of “Prediction in a socio-hydrological world”*
Melsen, Lieke Anna ; Vos, Jeroen ; Boelens, Rutgerd - \ 2018
Hydrological Sciences Journal 63 (2018)9. - ISSN 0262-6667 - p. 1435 - 1443.
modelling - prediction - socio-hydrology - socio-natural relationships - transdisciplinarity

Srinivasan et al. provide an interesting overview of the challenges for long-term socio-hydrological predictions. Although agreeing with most of the statements made, we argue for the need to take socio-hydrological analysis a step further and add some fundamental considerations, especially concerning the crucial importance of many (conscious and unconscious) assumptions made upfront of the modelling exercise. Eventual assumptions of technological determinism need correction: Models are not “value-free”, but uncertain, subjective and a product of the society in which they were shaped. It is important to acknowledge this uncertainty and bias when making decisions based on socio-hydrological models, considering also that these models are “social and political actors” in and by themselves. Furthermore, socio-hydrological models require a transdisciplinary approach, since physical water availability is only one of the boundary conditions for society. Last but not least, interaction with stakeholders remains important to enable understanding of what the variable of interest is.

Adhesion of emulsified oil droplets to hydrophilic and hydrophobic surfaces-effect of surfactant charge, surfactant concentration and ionic strength
Dickhout, Janneke M. ; Kleijn, J.M. ; Lammertink, Rob G.H. ; Vos, Wiebe M. De - \ 2018
Soft Matter 14 (2018)26. - ISSN 1744-683X - p. 5452 - 5460.

Adhesion of emulsified oil droplets to a surface plays an important role in processes such as crossflow membrane filtration, where the oil causes fouling. We present a novel technique, in which we study oil droplets on a model surface in a flow cell under shear force to determine the adhesive force between droplets and surface. We prepared an emulsion of hexadecane and used hydrophilic and hydrophobic glass slides as model surfaces. Different surfactants were used as emulsifiers: negatively charged sodium dodecyl sulphate (SDS), positively charged hexadecyltrimethylammonium bromide (CTAB) and nonionic Triton X-100. We evaluate the role of the surfactant, the glass surface properties and the ionic strength of the emulsion. We found a minimum in the adhesion force between droplets and surface as a function of surfactant concentration. The charged surfactants cause a lower droplet adhesion compared to the nonionic surfactant. The flow cell technique presented here proved to be very useful in understanding the interaction between oil droplets and a surface.

Spaces for participation and resistance : gendered experiences of oil palm plantation development
Vos, Rosanne de; Delabre, Izabela - \ 2018
Geoforum 96 (2018). - ISSN 0016-7185 - p. 217 - 226.
Gender - Micro-politics - Palm oil - Positionality - Resistance - Spaces for participation

In this paper, we explore the gendered experiences of, and responses to, socio-economic and environmental change evoked by processes of land acquisition for oil palm plantation development. Drawing upon ethnographic fieldwork in West Kalimantan, Indonesia, we examine the heterogeneous and differentiated nature of women's lived experiences in resisting, accepting and enacting agrarian change. We find that impacts stretch beyond livelihood opportunities, access to land and resources, and labour conditions: plantation development also affects and changes social relations, leading to insecurity and anxiety and new forms of solidarity. Using an analytical framework of ‘spaces for participation’ we highlight how women are excluded from participation during negotiations and contestations around land acquisition for the development of oil palm plantations. Yet, women also challenge their exclusion by claiming space for participation in different ways, including by engaging in alternative, more subtle forms of resistance that frequently go unnoticed by policies and practices that aim to empower women.

Organic acid production from starchy waste by gut derived microorganisms
Palakawong Na Ayudthaya, Susakul - \ 2018
University. Promotor(en): Fons Stams; Willem de Vos, co-promotor(en): Caroline Plugge. - Wageningen : Wageningen University - ISBN 9789463437882 - 219
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