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.

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Microbiome data science
Shetty, Sudarshan A. ; Lahti, Leo - \ 2019
Journal of Biosciences 44 (2019)5. - ISSN 0250-5991
Bioinformatics - data science - microbiome - open science - research software

Best practices from open data science are spreading across research fields, providing new opportunities for research and education. Open data science emphasizes the view that digitalization is enabling new forms of resource sharing, collaboration and outreach. This has the potential to improve the overall transparency and efficiency of research. Microbiome bioinformatics is a rapidly developing area that can greatly benefit from this progress. The concept of microbiome data science refers to the application of best practices from open data science to microbiome bioinformatics. The increasing availability of open data and new opportunities to collaborate online are greatly facilitating the development of this field. A microbiome data science ecosystem combines experimental research data with open data processing and analysis and reproducible tutorials that can also serve as an educational resource. Here, we provide an overview of the current status of microbiome data science from a community developer perspective and propose directions for future development of the field.

Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models
Jurburg, Stephanie D. ; Cornelissen, Jan J.B.W.J. ; Boer, Paulo de; Smits, Mari A. ; Rebel, Johanna M.J. - \ 2019
Frontiers in Cellular and Infection Microbiology 9 (2019). - ISSN 2235-2988 - 11 p.
animal models - bacteria - Clostridium difficile - microbiome - pig

Clostridium difficile infections (CDI) are a major cause of antibiotic-associated diarrhea. It is hypothesized that CDI develops due to the antibiotic-induced disruption of the intestinal microbial community structure, which allows C. difficile to flourish. Here, we pre-treated weaned pigs with the antibiotics Clindamycin or Ciprofloxacin for 1 day, and subsequently inoculated them with a human and pig enteropathogenic C. difficile strain 078 spores. Body temperature, clinical signs of disease, and the fecal microbiome were monitored daily for 15 days. Clindamycin had a stronger effect on the pigs than Ciprofloxacin, resulting in drastic shifts in the fecal microbiome, decreases in microbial diversity and significant increases in body temperature, even in the absence of C. difficile. Fecal shedding of C. difficile was detectable for 3 and 9 days in Ciprofloxacin and Clindamycin treated pigs inoculated with C. difficile, respectively, and in both cases decreased cell proliferation rates were detected in colon tissue. The timing of C. difficile shedding coincided with the decrease in a large cluster of Firmicutes following Clindamycin treatment, a pattern which was also independent of C. difficile inoculation. The observed community patterns suggest that successional dynamics following antibiotic treatment facilitate C. difficile establishment. The similarities between the microbiome responses observed in our study and those previously reported in CDI-infected humans further support the utility of adult pigs as models for the study of CDI.

Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants
Borewicz, Klaudyna ; Gu, Fangjie ; Saccenti, Edoardo ; Arts, I.C.W. ; Penders, John ; Thijs, Carel ; Leeuwen, Sander S. van; Lindner, Cordula ; Nauta, Arjen ; Leusen, Ellen van; Schols, Henk A. ; Smidt, Hauke - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
breastfeeding - human milk oligosaccharide - microbial clusters - microbiome

Scope: Understanding the biological functions of human milk oligosaccharides (HMOs) in shaping gastrointestinal (GI) tract microbiota during infancy is of great interest. A link between HMOs in maternal milk and infant fecal microbiota composition is examined and the role of microbiota in degrading HMOs within the GI tract of healthy, breastfed, 1-month-old infants is investigated. Methods and results: Maternal breast milk and infant feces are from the KOALA Birth Cohort. HMOs are quantified in milk and infant fecal samples using liquid chromatography-mass spectrometry. Fecal microbiota composition is characterized using Illumina HiSeq 16S rRNA gene amplicon sequencing. The composition is associated with gender, delivery mode, and milk HMOs: Lacto-N-fucopentaose I and 2′-fucosyllactose. Overall, Bifidobacterium, Bacteroides, Escherichia–Shigella, and Parabacteroides are predominating genera. Three different patterns in infant fecal microbiota structure are detected. GI degradation of HMOs is strongly associated with fecal microbiota composition, and there is a link between utilization of specific HMOs and relative abundance of various phylotypes (operational taxonomic units). Conclusions: HMOs in maternal milk are among the important factors shaping GI tract microbiota in 1-month-old breastfed infants. An infant's ability to metabolize different HMOs strongly correlates with fecal microbiota composition and specifically with phylotypes within genera Bifidobacterium, Bacteroides, and Lactobacillus.

Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage-specific microbial signatures
Lokesh, Jep ; Kiron, Viswanath ; Sipkema, Detmer ; Fernandes, Jorge M.O. ; Moum, Truls - \ 2019
MicrobiologyOpen 8 (2019)4. - ISSN 2045-8827
amplicon sequencing - Atlantic salmon (Salmo salar) - developmental stages - intestine - microbiome

Host-associated microbiota undergoes a continuous transition, from the birth to adulthood of the host. These developmental stage-related transitions could lead to specific microbial signatures that could impact the host biological processes. In this study, the succession of early-life and intestinal bacterial communities of Atlantic salmon (starting from embryonic stages to 80-week post hatch; wph) was studied using amplicon sequencing of 16S rRNA. Stage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities showed lower richness and diversity (Shannon and PD whole tree) compared to the hatchlings. A marked transition of the intestinal communities also occurred during the development; Proteobacteria were dominant in the early stages (both embryonic and intestinal), though the abundant genera under this phylum were stage-specific. Firmicutes were the most abundant group in the intestine of late freshwater; Weissella being the dominant genus at 20 wph and Anaerofilum at 62 wph. Proteobacteria regained its dominance after the fish entered seawater. Furthermore, LEfSe analysis identified genera under the above - mentioned phyla that are significant features of specific stages. The environmental (water) bacterial community was significantly different from that of the fish, indicating that the host is a determinant of microbial assemblage. Overall the study demonstrated the community dynamics during the development of Atlantic salmon.

Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome
Cortes, Laetitia ; Wopereis, Harm ; Tartiere, Aude ; Piquenot, Julie ; Gouw, Joost W. ; Tims, Sebastian ; Knol, Jan ; Chelsky, Daniel - \ 2019
International Journal of Molecular Sciences 20 (2019)6. - ISSN 1661-6596
fecal - infants - intestinal - mass spectrometry - metabolism - metacluster - microbiome

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.

The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls
Jalanka, Jonna ; Major, Giles ; Murray, Kathryn ; Singh, Gulzar ; Nowak, Adam ; Kurtz, Caroline ; Silos-Santiago, Inmaculada ; Johnston, Jeffrey M. ; Vos, Willem M. de; Spiller, Robin - \ 2019
International Journal of Molecular Sciences 20 (2019)2. - ISSN 1661-6596
constipation - ispaghula - microbiome - prebiotics - transit

Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We performed two randomised, placebo-controlled, double-blinded trials comparing 7 days of psyllium with a placebo (maltodextrin) in 8 healthy volunteers and 16 constipated patients respectively. We measured the patients' gastrointestnal (GI) transit, faecal water content, short-chain fatty acid (SCFA) and the stool microbiota composition. While psyllium supplement had a small but significant effect on the microbial composition of healthy adults (increasing Veillonella and decreasing Subdoligranulum), in constipated subjects there were greater effects on the microbial composition (increased Lachnospira, Faecalibacterium, Phascolarctobacterium, Veillonella and Sutterella and decreased uncultured Coriobacteria and Christensenella) and alterations in the levels of acetate and propionate. We found several taxa to be associated with altered GI transit, SCFAs and faecal water content in these patients. Significant increases in three genera known to produce butyrate, Lachnospira, Roseburia and Faecalibacterium, correlated with increased faecal water. In summary, psyllium supplementation increased stool water and this was associated with significant changes in microbiota, most marked in constipated patients.

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, J.E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
rumen - microbiome - metataxonomics - metagenomics
Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome
Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces
Shetty, Sudarshan A. ; Zuffa, Simone ; Bui, Thi Phuong Nam ; Aalvink, Steven ; Smidt, Hauke ; Vos, Willem M. De - \ 2018
International Journal of Systematic and Evolutionary Microbiology 68 (2018)12. - ISSN 1466-5026 - p. 3741 - 3746.
Anaerobutyricum hallii comb. nov. - Eubacterium hallii - microbiome - microbiota

A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0-98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA-DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7T was 38.6 mol%. The major fatty acids were C16 : 0, C16 : 1cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7T had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353T. Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353T is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353T=ATCC 27751T) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7T should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7T (=DSM 17630T=KCTC 15707T).

Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle
Løvendahl, P. ; Difford, G.F. ; Li, B. ; Chagunda, M.G.G. ; Huhtanen, P. ; Lidauer, M.H. ; Lassen, J. ; Lund, P. - \ 2018
Animal 12 (2018)s2. - ISSN 1751-7311 - p. s336 - s349.
digestibility - genetics - holobiont - microbiome - ranking

It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.

Data from: Intestinal Ralstonia pickettii augments glucose intolerance in obesity
Udayappan, Shanthadevi D. ; Kovatcheva-Datchary, Petia ; Bakker, Guido J. ; Havik, Stefan R. ; Herrema, Hilde ; Cani, Patrice D. ; Bouter, Kristien E. ; Belzer, C. ; Witjes, Julia J. ; Vrieze, Anne ; Sonnaville, Noor De; Chaplin, Alice ; Raalte, Daniël H. van; Aalvink, S. ; Dallinga-Thie, Geesje M. ; Heilig, G.H.J. ; Bergström, Göran ; Meij, Suzan Van Der; Wagensveld, Bart A. Van; Hoekstra, Joost B.L. ; Holleman, Frits ; Stroes, Erik S.G. ; Groen, Albert K. ; Bäckhed, Fredrik ; Vos, W.M. de; Nieuwdorp, Max - \ 2017
microbiome - obesity - glucose intolerance - inflammation - Ralstonia pickettii
An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA from the Gram-negative species Ralstonia was most prevalent. Interestingly, fecal abundance of Ralstonia pickettii was increased in obese subjects with pre-diabetes and T2DM. To assess if R. pickettii was causally involved in development of obesity and T2DM, we performed a proof-of-concept study in diet-induced obese (DIO) mice. Compared to vehicle-treated control mice, R. pickettii-treated DIO mice had reduced glucose tolerance. In addition, circulating levels of endotoxin were increased in R. pickettii-treated mice. In conclusion, this study suggests that intestinal Ralstonia is increased in obese human subjects with T2DM and reciprocally worsens glucose tolerance in DIO mice.
Microbes and asthma : Opportunities for intervention
Smits, Hermelijn H. ; Hiemstra, Pieter S. ; Prazeres Da Costa, Clarissa ; Ege, Markus ; Edwards, Michael ; Garn, Holger ; Howarth, Peter H. ; Jartti, Tuomas ; Jong, Esther C. De; Maizels, Rick M. ; Marsland, Ben J. ; McSorley, Henry J. ; Müller, Anne ; Pfefferle, Petra I. ; Savelkoul, Huub ; Schwarze, Jürgen ; Unger, Wendy W.J. ; Mutius, Erika Von; Yazdanbakhsh, Maria ; Taube, Christian - \ 2016
Journal of Allergy and Clinical Immunology 137 (2016)3. - ISSN 0091-6749 - p. 690 - 697.
asthma - helminths - Hygiene hypothesis - immune regulation - microbes - microbiome - sensitization - viruses

The worldwide incidence and prevalence of asthma continues to increase. Asthma is now understood as an umbrella term for different phenotypes or endotypes, which arise through different pathophysiologic pathways. Understanding the many factors contributing to development of the disease is important for the identification of novel therapeutic targets for the treatment of certain asthma phenotypes. The hygiene hypothesis has been formulated to explain the increasing prevalence of allergic disease, including asthma. This hypothesis postulates that decreased exposure at a young age to certain infectious agents as a result of improved hygiene, increased antibiotic use and vaccination, and changes in lifestyle and dietary habits is associated with changes in the immune system, which predispose subjects to allergy. Many microbes, during their coevolution with human subjects, developed mechanisms to manipulate the human immune system and to increase their chances of survival. Improving models of asthma, as well as choosing adequate end points in clinical trials, will lead to a more complete understanding of the underlying mechanisms, thus providing an opportunity to devise primary and secondary interventions at the same time as identifying new molecular targets for treatment. This article reports the discussion and conclusion of a workshop under the auspices of the Netherlands Lung Foundation to extend our understanding of how modulation of the immune system by bacterial, parasitic, and viral infections might affect the development of asthma and to map out future lines of investigation.

Unfermented recalcitrant polysaccharide structures from rapeseed (Brassica napus) meal in pigs
Pustjens, A.M. ; Vries, S. de; Bakuwel, M. ; Gruppen, H. ; Gerrits, W.J.J. ; Kabel, M.A. - \ 2014
Industrial Crops and Products 58 (2014). - ISSN 0926-6690 - p. 271 - 279.
cell-wall polysaccharides - nonstarch polysaccharides - canola-meal - growing pigs - poultry - digestibility - xyloglucan - enzyme - oligosaccharides - microbiome
Unprocessed and acid-extruded rapeseed meal (RSM) was fed to pigs as the only source of non-starch polysaccharides (NSP) and protein. Unfermented carbohydrate structures were analyzed. Acid-extrusion seemed to increase rigidness of the NSP-matrix in vivo, without affecting NSP-fermentability. Water-soluble NSP were almost completely fermented in the colon. From the water-insoluble unfermented carbohydrates 46–68% (w/w) was analyzed as the polysaccharides rhamnogalacturonan, (branched) arabinan, XXXG-type xyloglucan, linear xylan, galactomannan, and cellulose. A major fraction (35–54% w/w) of the unfermented carbohydrates was unexpectedly released as small uronyl-rich carbohydrates (
Genomics: A gut prediction
Vos, W.M. de; Nieuwdorp, M. - \ 2013
Nature 498 (2013)7452. - ISSN 0028-0836 - p. 48 - 49.
microbiome
Microbial cells make up the majority of cells in the human body, and most of these reside in the intestinal tract. Researchers have long recognized that some intestinal microorganisms are associated with health, but the beneficial impact of most of the gut's microbes on human metabolism has been discovered only relatively recently
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