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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Sigma B stress response in the genus Bacillus - Stressosome proteins, RsbK signalling pathways and predicted regulons
Yeak, K.Y. ; Boekhorst, Jos ; Abee, T. ; Wells-Bennik, Marjon H.J. - \ 2018
T lymphocytes actively suppress intestinal pathobionts in zebrafish
Lopez Nadal, Adria ; Boekhorst, Jos ; Timmerman, Harro M. ; Kleerebezem, M. ; Brugman, S. - \ 2018
- 1 p.
Reliability of a participant-friendly fecal collection method for microbiome analyses : A step towards large sample size investigation
Szopinska, Joanna W. ; Gresse, Raphaële ; Marel, Saskia van der; Boekhorst, Jos ; Lukovac, Sabina ; Swam, Iris van; Franke, Barbara ; Timmerman, Harro ; Belzer, Clara ; Vasquez, Alejandro Arias - \ 2018
BMC Microbiology 18 (2018)1. - ISSN 1471-2180
Bacterial DNA extraction - Fecal collection and storage method - Microbiome - Next generation sequencing - OMNIgene•GUT

Background: The effects of gut microbiota on human traits are expected to be small to moderate and adding the complexity of the human diseases, microbiome research demands big sample sizes. Fecal samples for such studies are mostly self-collected by participants at home. This imposes an extra level of complexity as sample collection and storage can be challenging. Effective, low-burden collection and storage methods allowing fecal samples to be transported properly and ensuring optimal quality and quantity of bacterial DNA for upstream analyses are necessary. Moreover, accurate assessment of the microbiome composition also depends on bacterial DNA extraction method. The aim of this study was to evaluate the reliability and efficiency of the OMNIgene•GUT kit as a participant-fecal friendly collection method (storage at room temperature for 24 h (O24h) or 7 days (O7d)) in comparison to the standard collection method (Fresh, storage at 4 °C for less than 24 h) in terms of amount of variability and information content accounting for two common DNA extraction methods. Results: Fourteen fecal samples were collected from healthy individuals (7 males, 7 females). Collection and storage methods did not differ significantly in terms of DNA concentration and Shannon diversity index. Phylum relative abundance showed significant differences for Bacteroidetes, Actinobacteria and Cyanobacteria. The differences were observed between control (Fresh) and O24h methods, but not between Fresh and O7d. These differences were not seen when performing bacterial DNA quantification based on three bacterial groups: Bacteroides spp., Bifidobacterium spp. and Clostridium cluster IV, which represent three major phyla: Bacteroidetes, Actinobacteria and Firmicutes respectively. The two DNA extraction methods differ in terms of DNA quantity, quality, bacterial diversity and bacterial relative abundance. Furthermore, principal component analysis revealed differences in microbial structure, which are driven by the DNA extraction methods more than the collection/storage methods. Conclusion: Our results have highlighted the potential of using the OMNIgene•GUT kit for collection and storage at ambient temperature, which is convenient for studies aiming to collect large samples by giving participants the possibility to send samples by post. Importantly, we revealed that the choice of DNA extraction method have an impact on the microbiome profiling.

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Vaidya, Jueeli D. ; Bogert, Bartholomeus van den; Edwards, J.E. ; Boekhorst, Jos ; Gastelen, S. van; Saccenti, Edoardo ; Plugge, Caroline M. ; Smidt, Hauke - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
454 pyrosequencing - Archaea - Bacteria - DNA extraction methods - Fibrous content - Fungi - QPCR - Rumen fluid
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method (p < 0.001) and fraction (p < 0.001). The 260/280 ratio was not affected by extraction (p = 0.08) but was affected by fraction (p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method (p < 0.001) but not affected by fraction (p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction (p = 0.012), and that PBB (p = 0.012) and FDSS (p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both. In summary, the comprehensive assessment of observed communities of bacteria, archaea and anaerobic fungi described here provides insight into a rational basis for selecting an optimal methodology to obtain a representative picture of the rumen microbiota.
The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Vaidya, J.D. ; Bogert, B. van den; Edwards, J.E. ; Boekhorst, Jos ; Gastelen, S. van; Saccenti, E. ; Plugge, C.M. ; Smidt, H. - \ 2017
PRJEB22996 - ERP104729
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed four diets with different ratios of grass and maize silage.
Representation and inclusion in SCAR : Task 1.1 Analysis of the key factors of involvement and representativeness
Boekhorst, Dorri te - \ 2017
H2020 CSA CASA - 61 p.
SCAR - CASA - representation - Inclusion - representativeness - Bioeconomy - Research agenda - European Research Area - Common agricultural
Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis
Rogier, Rebecca ; Ederveen, Thomas H.A. ; Boekhorst, Jos ; Wopereis, Harm ; Scher, Jose U. ; Manasson, Julia ; Frambach, Sanne J.C.M. ; Knol, Jan ; Garssen, Johan ; Kraan, Peter M. van der; Koenders, Marije I. ; Berg, Wim B. van den; Hijum, Sacha A.F.T. van; Abdollahi-Roodsaz, Shahla - \ 2017
Microbiome 5 (2017)1. - ISSN 2049-2618 - p. 63 - 63.
Autoimmune arthritis - IL-1 receptor antagonist - Microbiota - T helper 17 cells - Toll-like receptors
BACKGROUND: Perturbation of commensal intestinal microbiota has been associated with several autoimmune diseases. Mice deficient in interleukin-1 receptor antagonist (Il1rn -/- mice) spontaneously develop autoimmune arthritis and are susceptible to other autoimmune diseases such as psoriasis, diabetes, and encephalomyelitis; however, the mechanisms of increased susceptibility to these autoimmune phenotypes are poorly understood. We investigated the role of interleukin-1 receptor antagonist (IL-1Ra) in regulation of commensal intestinal microbiota, and assessed the involvement of microbiota subsets and innate and adaptive mucosal immune responses that underlie the development of spontaneous arthritis in Il1rn -/- mice.RESULTS: Using high-throughput 16S rRNA gene sequencing, we show that IL-1Ra critically maintains the diversity and regulates the composition of intestinal microbiota in mice. IL-1Ra deficiency reduced the intestinal microbial diversity and richness, and caused specific taxonomic alterations characterized by overrepresented Helicobacter and underrepresented Ruminococcus and Prevotella. Notably, the aberrant intestinal microbiota in IL1rn -/- mice specifically potentiated IL-17 production by intestinal lamina propria (LP) lymphocytes and skewed the LP T cell balance in favor of T helper 17 (Th17) cells, an effect transferable to WT mice by fecal microbiota. Importantly, LP Th17 cell expansion and the development of spontaneous autoimmune arthritis in IL1rn -/- mice were attenuated under germ-free condition. Selective antibiotic treatment revealed that tobramycin-induced alterations of commensal intestinal microbiota, i.e., reduced Helicobacter, Flexispira, Clostridium, and Dehalobacterium, suppressed arthritis in IL1rn -/- mice. The arthritis phenotype in IL1rn -/- mice was previously shown to depend on Toll-like receptor 4 (TLR4). Using the ablation of both IL-1Ra and TLR4, we here show that the aberrations in the IL1rn -/- microbiota are partly TLR4-dependent. We further identify a role for TLR4 activation in the intestinal lamina propria production of IL-17 and cytokines involved in Th17 differentiation preceding the onset of arthritis.CONCLUSIONS: These findings identify a critical role for IL1Ra in maintaining the natural diversity and composition of intestinal microbiota, and suggest a role for TLR4 in mucosal Th17 cell induction associated with the development of autoimmune disease in mice.
Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures
Timmerman, Harro M. ; Rutten, Nicole B.M.M. ; Boekhorst, Jos ; Saulnier, Delphine M. ; Kortman, Guus A.M. ; Contractor, Nikhat ; Kullen, Martin ; Floris, Esther ; Harmsen, Hermie J.M. ; Vlieger, Arine M. ; Kleerebezem, Michiel ; Rijkers, Ger T. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322

The establishment of the infant gut microbiota is a highly dynamic process dependent on extrinsic and intrinsic factors. We characterized the faecal microbiota of 4 breastfed infants and 4 formula-fed infants at 17 consecutive time points during the first 12 weeks of life. Microbiota composition was analysed by a combination of 16S rRNA gene sequencing and quantitative PCR (qPCR). In this dataset, individuality was a major driver of microbiota composition (P = 0.002) and was more pronounced in breastfed infants. A developmental signature could be distinguished, characterized by sequential colonisation of i) intrauterine/vaginal birth associated taxa, ii) skin derived taxa and other typical early colonisers such as Streptococcus and Enterobacteriaceae, iii) domination of Bifidobacteriaceae, and iv) the appearance of adultlike taxa, particularly species associated with Blautia, Eggerthella, and the potential pathobiont Clostridium difficile. Low abundance of potential pathogens was detected by 16S profiling and confirmed by qPCR. Incidence and dominance of skin and breast milk associated microbes were increased in the gut microbiome of breastfed infants compared to formula-fed infants. The approaches in this study indicate that microbiota development of breastfed and formula-fed infants proceeds according to similar developmental stages with microbiota signatures that include stage-specific species.

ANGPTL4 promotes bile acid absorption during taurocholic acid supplementation via a mechanism dependent on the gut microbiota
Janssen, Aafke W.F. ; Dijk, Wieneke ; Boekhorst, Jos ; Kuipers, Folkert ; Groen, Albert K. ; Lukovac, Sabina ; Hooiveld, Guido J.E.J. ; Kersten, Sander - \ 2017
Biochimica et Biophysica Acta. Molecular and Cell Biology of Lipids 1862 (2017)10. - ISSN 1388-1981 - p. 1056 - 1067.
Angiopoietin-like 4 - Antibiotics - Bile acids - Gut microbiota - Lipoprotein lipase - Triglycerides
Angiopoietin-like 4 (ANGPTL4) raises plasma triglyceride levels by inhibiting lipoprotein lipase. A set of compounds that are able to reduce plasma triglyceride levels are bile acids (BA). Because BA have been shown to decrease ANGPTL4 secretion by intestinal cells, we hypothesized that BA lower plasma triglycerides (partly) via ANGPTL4. To test that hypothesis, wild-type and Angptl4−/− mice were fed chow supplemented with taurocholic acid (TCA) for seven days. TCA supplementation effectively lowered plasma triglycerides in wild-type and Angptl4−/− mice, indicating that ANGPTL4 is not required for plasma triglyceride-lowering by BA. Intriguingly, however, plasma and hepatic BA concentrations were significantly lower in TCA-supplemented Angptl4−/− mice than in TCA-supplemented wild-type mice. These changes in the Angptl4−/− mice were accompanied by lower BA levels in ileal scrapings and decreased expression of FXR-target genes in the ileum, including the BA transporter Slc10a2. By contrast, faecal excretion of specifically primary BA was higher in the Angptl4−/− mice, suggesting that loss of ANGPTL4 impairs intestinal BA absorption. Since the gut microbiota converts primary BA into secondary BA, elevated excretion of primary BA in Angptl4−/− mice may reflect differences in gut microbial composition and/or functionality. Indeed, colonic microbial composition was markedly different between Angptl4−/− and wild-type mice. Suppression of the gut bacteria using antibiotics abolished differences in plasma, hepatic, and faecal BA levels between TCA-supplemented Angptl4−/− and wild-type mice. In conclusion, 1) ANGPTL4 is not involved in the triglyceride-lowering effect of BA; 2) ANGPTL4 promotes BA absorption during TCA supplementation via a mechanism dependent on the gut microbiota.
Reply to Meisel et al.
Zeeuwen, Patrick L.J.M. ; Boekhorst, Jos ; Ederveen, Thomas H.A. ; Kleerebezem, Michiel ; Schalkwijk, Joost ; Hijum, Sacha A.F.T. van; Timmerman, Harro M. - \ 2017
Journal of Investigative Dermatology 137 (2017)4. - ISSN 0022-202X - p. 961 - 962.
Analysis of germination capacity and germinant receptor (sub)clusters of genomesequenced Bacillus cereus environmental isolates and model strains
Warda, Alicja K. ; Xiao, Yinghua ; Boekhorst, Jos ; Wells-Bennik, Marjon H.J. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2017
Applied and Environmental Microbiology 83 (2017)4. - ISSN 0099-2240
Bacillus cereus - Germination - Sporeformer - Spores

Spore germination of 17 Bacillus cereus food isolates and reference strains was evaluated using flow cytometry analysis in combination with fluorescent staining at a single-spore level. This approach allowed for rapid collection of germination data under more than 20 conditions, including heat activation of spores, germination in complex media (brain heart infusion [BHI] and tryptone soy broth [TSB]), and exposure to saturating concentrations of single amino acids and the combination of alanine and inosine. Whole-genome sequence comparison revealed a total of 11 clusters of operons encoding germinant receptors (GRs): GerK, GerI, and GerL were present in all strains, whereas GerR, GerS, GerG, GerQ, GerX, GerF, GerW, and GerZ (sub)clusters showed a more diverse presence/absence in different strains. The spores of tested strains displayed high diversity with regard to their sensitivity and responsiveness to selected germinants and heat activation. The two laboratory strains, B. cereus ATCC 14579 and ATCC 10987, and 11 food isolates showed a good germination response under a range of conditions, whereas four other strains (B. cereus B4085, B4086, B4116, and B4153) belonging to phylogenetic group IIIA showed a very weak germination response even in BHI and TSB media. Germination responses could not be linked to specific (combinations of) GRs, but it was noted that the four group IIIA strains contained pseudogenes or variants of subunit C in their gerL cluster. Additionally, two of those strains (B4086 and B4153) carried pseudogenes in the gerK and gerRI (sub)clusters that possibly affected the functionality of these GRs.

Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin : Letter to the editor
Zeeuwen, Patrick L.J.M. ; Ederveen, Thomas H.A. ; Krieken, Danique A. van der; Niehues, Hanna ; Boekhorst, Jos ; Kezic, Sanja ; Hanssen, Daniëlle A.T. ; Otero, Marisol E. ; Hanssen, Daniëlle A.T. ; Rodijk-Olthuis, Diana ; Falcone, Denise ; Bogaard, Ellen H.J. van den; Kamsteeg, Marijke ; Koning, Heleen D. de; Zeeuwen-Franssen, Manon E.J. ; Steensel, Maurice A.M. van; Kleerebezem, Michiel ; Timmerman, Harro M. ; Hijum, Sacha A.F.T. van; Schalkwijk, Joost - \ 2017
Journal of Allergy and Clinical Immunology 139 (2017)4. - ISSN 0091-6749 - p. 1368 - 1371.
Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups
Steegenga, Wilma T. ; Mischke, Mona ; Lute, Carolien ; Boekschoten, Mark V. ; Lendvai, Agnes ; Pruis, Maurien G.M. ; Verkade, Henkjan J. ; Heijning, Bert J.M. van de; Boekhorst, Jos ; Timmerman, Harro M. ; Plösch, Torsten ; Müller, Michael ; Hooiveld, Guido J.E.J. - \ 2017
Molecular Nutrition & Food Research 61 (2017)1. - ISSN 1613-4125
Gut development - Maternal diet - Microbiota composition - Offspring - Transcriptomics

Scope: The long-lasting consequences of nutritional programming during the early phase of life have become increasingly evident. The effects of maternal nutrition on the developing intestine are still underexplored. Methods and results: In this study, we observed (1) altered microbiota composition of the colonic luminal content, and (2) differential gene expression in the intestinal wall in 2-week-old mouse pups born from dams exposed to a Western-style (WS) diet during the perinatal period. A sexually dimorphic effect was found for the differentially expressed genes in the offspring of WS diet-exposed dams but no differences between male and female pups were found for the microbiota composition. Integrative analysis of the microbiota and gene expression data revealed that the maternal WS diet independently affected gene expression and microbiota composition. However, the abundance of bacterial families not affected by the WS diet (Bacteroidaceae, Porphyromonadaceae, and Lachnospiraceae) correlated with the expression of genes playing a key role in intestinal development and functioning (e.g. Pitx2 and Ace2). Conclusion: Our data reveal that maternal consumption of a WS diet during the perinatal period alters both gene expression and microbiota composition in the intestinal tract of 2-week-old offspring.

Draft whole-genome sequences of three Lactobacillus plantarum food isolates
Fernandez Ramirez, Monica ; Boekhorst, Jos ; Jong, Anne de; Kuipers, Oscar P. ; Abee, Tjakko ; Nierop Groot, Masja - \ 2016
Genome Announcements 4 (2016)3. - ISSN 2169-8287
Lactobacillus plantarum is a widespread member of the Lactobacillus genus and frequently isolated from spoiled acidified food products. Here, we report the draft genome sequences of three L. plantarum food isolates.
Report of the kick off meeting of the Knowledge Network on Sustainable Intensification (KNSI), 3 June 2016, Wageningen
Bura, M. ; Boekhorst, D. te - \ 2016
FACCE-JPI
FACCE - FACCE JPI - KNSI - Sustainable intensification - knowlegde network - agriculture - food security - climate change - knowledge network - sustainable intensification - FACCE-JPI - Bioeconomy
Report of DG AGRI Conference on Agriculture and Innovation - Pre-Event on International Soil Research: Opportunities for Synergy and Cooperation with FACCE-JPI, 27 January 2016, Brussels
Aller Moran, P. ; McKhann, H. ; Boekhorst, D. te - \ 2016
FACCE-JPI - 6 p.
agriculture - food security - climate change - innovation - soil - FACCE-JPI - Climate change - soil - DG AGRI - conference - FACCE JPI - Bioeconomy
Draft whole-genome sequences of 11 Bacillus cereus food isolates
Hayrapetyan, Hasmik ; Boekhorst, Jos ; Jong, Anne de; Kuipers, Oscar P. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2016
Genome Announcements 4 (2016)3. - ISSN 2169-8287

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

FACCE JPI Implementation Plan 2016 - 2018
Gøtke, Niels ; McKhann, Heather ; Albouy, I. ; Bunthof, C.J. ; Bura, M. ; Lesser, C. ; Aller Moran, P. ; Boekhorst, D. te; Wiley, P. - \ 2016
FACCE-JPI - 16 p.
Implementation - Plan - FACCE JPI - FACCE - JPI - agriculture - food security - climate change - implementation plan - FACCE-JPI - Bioeconomy - policy
Workshop phenotyping, genotyping, breeding, reproduction techniques and evaluating alternative crop species for adaptation to climate change - State-of-art and opportunities for further cooperation, 27-28 October 2016, Wageningen : Final report
Boekhorst, D. te - \ 2016
FACCE-JPI - 15 p.
agriculture - food security - climate change - FACCE JPI - Adaptation to climate change - breeding techniques - FACCE-JPI - Bioeconomy - phenotyping - Genotyping - breeding - Climate change adaptation
The workshop highlighted opportunities, gaps, needs and priorities for novel breeding techniques like phenotyping for resilience under climate change. Starting with four key presentations, the scene was set from the perspectives of policy, end-users and science, accompanied by an overview of phenotyping initiatives. In five presentations several other initiatives were introduced, after which dedicated discussion sessions identified priorities in opportunies, needs and gaps. This resulted in the following ten priorities:
Phenotyping needs multi- and transdisciplinary research, but fundamental research with regard to gene-environment-management interactions is also essential;
High quality open data speeds up research, but policy also needs to deal with the associated risks and legal issues (big data questions);
Regulation of funding needs to be adapted: linkages are needed between (more structural) project funding and infrastructure funding;
Phenotyping needs long-term research;
More focus is needed on breeding for climate change: widening up genetic traits;
More focus is needed on breeding for climate change: crops - also ‘multi-valorization’ and perennial crops;
Climate change research and phenotyping research needs te be connected; this also includes phenotyping research on different management systems;
Phenotyping for whole value chain approach, including aspects related to quality, is needed;
Public-private cooperation could strengthen research and accelerate impact;
Management of expectations and views of the public at large.
Draft genome sequences of four thermophilic spore formers isolated from a dairy-processing environment
Caspers, M.P.M. ; Boekhorst, J. ; Jong, A. de; Kort, R. ; Nierop Groot, M.N. ; Abee, T. - \ 2016
Genome Announcements 4 (2016)4. - ISSN 2169-8287
Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. Here, we report draft genome sequences of four thermophilic strains from a milk-processing plant or standard milk, namely, a Geobacillus thermoglucosidans isolate (TNO-09.023), Geobacillus stearothermophilus TNO-09.027, and two Anoxybacillus flavithermus isolates (TNO-09.014 and TNO-09.016).
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