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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    Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches : a review
    Swanson, K.S. ; Vos, W.M. de; Martens, E.C. ; Gilbert, J.A. ; Menon, R.S. ; Soto-Vaca, A. ; Hautvast, J. ; Meyer, P.D. ; Borewicz, K. ; Vaughan, E.E. ; Slavin, J.L. - \ 2020
    Beneficial Microbes 11 (2020)2. - ISSN 1876-2883 - p. 101 - 129.
    health - intestine - inulin - microbiota - nutrition

    The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest. Research and collective initiatives to determine the composition and diversity of the human gut microbiota have increased over the past decade due to great advances in high-throughput technologies, particularly the 16S ribosomal RNA (rRNA) sequencing. Here we reviewed the application of 16S rRNA-based molecular technologies, both community wide (sequencing and phylogenetic microarrays) and targeted methodologies (quantitative PCR, fluorescent in situ hybridisation) to study the effect of chicory inulin-type fructans, NDOs and specific added fibres, such as resistant starches, on the human intestinal microbiota. Overall, such technologies facilitated the monitoring of microbiota shifts due to prebiotic/fibre consumption, though there are limited community-wide sequencing studies so far. Molecular studies confirmed the selective bifidogenic effect of fructans and galactooligosaccharides (GOS) in human intervention studies. Fructans only occasionally decreased relative abundance of Bacteroidetes or stimulated other groups. The sequencing studies for various resistant starches, polydextrose and beta-glucan showed broader effects with more and different types of gut microbial species being enhanced, often including phylotypes of Ruminococcaceae. There was substantial variation in terms of magnitude of response and in individual responses to a specific fibre or NDO which may be due to numerous factors, such as initial presence and relative abundance of a microbial type, diet, genetics of the host, and intervention parameters, such as intervention duration and fibre dose. The field will clearly benefit from a more systematic approach that will support defining the impact of prebiotics and fibres on the gut microbiome, identify biomarkers that link gut microbes to health, and address the personalised response of an individual's microbiota to prebiotics and dietary fibres.

    Multiple pressures and their combined effects in Europe's seas
    Korpinen, Samuli ; Klancnik, Katja ; Peterlin, Monika ; Nurmi, Marco ; Laamanen, Leena ; Zupancic, Gasper ; Murray, Ciaran ; Harvey, Therese ; Andersen, Jesper H. ; Zenetos, Argyro ; Stein, Ulf ; Tunesi, Leonardo ; Abhold, Katrina ; Piet, G.J. ; Kallenbach, Emilie ; Agnesi, Sabrina ; Bolman, B.C. ; Vaughan, David ; Reker, J. ; Gelabert, Eva Royo - \ 2020
    European Topic Centre on Inland, Coastal and Marine waters (Report / ETC/ICM 4/2019) - ISBN 9783944280653 - 164 p.
    This report presents for the first time in Europe an overview of anthropogenic pressures and their combined effects in Europe’s seas. The assessment covers the period of 2011-2016 but also presents how human activities and pressures at sea have changed over a longer time horizon. Practically the entire European marine area is under multiple pressures – such as hazardous substances, fish stock exploitation, climate change, underwater noise, non-indigenous species, seafloor damage, marine litter and nutrient enrichment. Shelf areas and coastal zone are affected by physical disturbance of seabed, eutrophication and non-indigenous species. The highest potential combined effects are found along coastal areas of the North Sea, Southern Baltic Sea, Adriatic and Western Mediterranean. The good news from this assessment is that many of the dangerous trends seem to have reversed. We have shown that the nutrient levels, hazardous substances, northern fish stocks and tuna stocks in the open seas show improvement. However, extensive pressures from several human activities still threaten the marine ecosystem, such as disturbance of seabed, and no trend reversal was seen in this assessment.
    Dawn of the pyrocene
    Stoof, Cathelijne - \ 2019
    The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life
    Borewicz, Klaudyna ; Suarez-Diez, Maria ; Hechler, Christine ; Beijers, Roseriet ; Weerth, Carolina de; Arts, Ilja ; Penders, John ; Thijs, Carel ; Nauta, Arjen ; Lindner, Cordula ; Leusen, Ellen Van; Vaughan, Elaine E. ; Smidt, Hauke - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    Gastrointestinal (GI) microbiota composition differs between breastfed and formula-fed infants. Today’s infant formulas are often fortified with prebiotics to better mimic properties of human milk with respect to its effect on GI microbiota composition and function. We used Illumina HiSeq sequencing of PCR-amplified 16S rRNA gene fragments to investigate the composition of faecal microbiota in 2–12 week old infants receiving either breastmilk, infant formulas fortified with prebiotics, or mixed feeding. We compared these results with results from infants fed traditional formulas used in the Netherlands in 2002–2003, which contained no added prebiotics. We showed that today’s formulas supplemented with either scGOS (0.24–0.50 g/100 ml) or scGOS and lcFOS (at a 9:1 ratio; total 0.6 g/100 ml) had a strong bifidogenic effect as compared to traditional formulas, and they also resulted in altered patterns of microbial colonisation within the developing infant gastrointestinal tract. We identified three microbial states (or developmental stages) in the first 12 weeks of life, with a gradual transition pattern towards a bifidobacteria dominated state. In infants receiving only fortified formulas, this transition towards the bifidobacteria dominated state was accelerated, whereas in infants receiving mixed feeding the transition was delayed, as compared to exclusively breastfed infants.

    Karyotype evolution in Fusarium
    Waalwijk, C. ; Taga, M. ; Zheng, S.L. ; Proctor, R.H. ; Vaughan, M.M. ; O'Donnell, K. - \ 2018
    IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 13 - 33.
    ACCESSORY - CHROMOSOME - GENOME - NOR - PATHOGEN - PHYLOGENY - QPCR - RPB1 - RPB2 - SUPERNUMERARY
    The germ tube burst method (GTBM) was employed to examine karyotypes of 33 Fusarium species representative of 11 species complexes that span the phylogenetic breadth of the genus. The karyotypes revealed that the nucleolar organizing region (NOR), which includes the ribosomal rDNA region, was telomeric in the species where it was discernible. Variable karyotypes were detected in eight species due to variation in numbers of putative core and/or supernumerary chromosomes. The putative core chromosome number (CN) was most variable in the F. solani (CN = 9‒12) and F. buharicum (CN = 9+1 and 18-20) species complexes. Quantitative real-time PCR and genome sequence analysis rejected the hypothesis that the latter variation in CN was due to diploidization. The core CN in six other species complexes where two or more karyotypes were obtained was less variable or fixed. Karyotypes of 10 species in the sambucinum species complex, which is the most derived lineage of Fusarium, revealed that members of this complex possess the lowest CN in the genus. When viewed in context of the species phylogeny, karyotype evolution in Fusarium appears to have been dominated by a reduction in core CN in five closely related complexes that share a most recent common ancestor (tricinctum and incarnatum-equiseti CN = 8-9, chlamydosporum CN = 8, heterosporum CN = 7, sambucinum CN = 4-5) but not in the sister to these complexes (nisikadoi CN = 11, oxysporum CN = 11 and fujikuroi CN = 10-12). CN stability is best illustrated by the F. sambucinum subclade, where the only changes observed since it diverged from other fusaria appear to have involved two independent putative telomere to telomere fusions that reduced the core CN from five to four, once each in the sambucinum and graminearum subclades. Results of the present study indicate a core CN of 4 may be fixed in the latter subclade, which is further distinguished by the absence of putative supernumerary chromosomes. Karyotyping of fusaria in the not too distant future will be done by whole-genome sequencing such that each scaffold represents a complete chromosome from telomere to telomere. The CN data presented here should be of value to assist such full genome assembling.
    The effect of fiber and prebiotics on children’s gastrointestinal disorders and microbiome
    Wegh, Carrie A.M. ; Schoterman, Margriet H.C. ; Vaughan, Elaine E. ; Belzer, Clara ; Benninga, Marc A. - \ 2017
    Expert Review of Gastroenterology and Hepatology 11 (2017)11. - ISSN 1747-4124 - p. 1031 - 1045.
    children - dietary fiber - functional gastrointestinal disorders - Gut microbiota - oligosaccharides - prebiotics

    Introduction: The bacteria received upon birth are the start of colonization of the approximately 1014 bacteria that are present in the mature human gastrointestinal tract, better known as the microbiota. The gut microbiota is implicated in gastrointestinal health, nutrient metabolism and benefits such as prevention of infection. Dietary fiber, including prebiotics, escape digestion in the small intestine and reach the colon intact, where they are partially or completely fermented by the gut microbiota. Areas covered: The possible interactions between dietary fiber, prebiotics and microbiota are discussed as well as how this relates to functional gastrointestinal disorders. During the first years of life the microbiota have not yet reached a stable state and is sensitive to disturbance by environmental factors. An imbalance in the microbiota early in life is found to be associated with several functional gastrointestinal disorders such as colic, functional abdominal pain, irritable bowel syndrome and constipation. Expert commentary: A better understanding of how gut microbial changes in early-life can impact gastrointestinal health might lead to new treatments or disease prevention. Nutritional strategies with fiber or prebiotics may support health due to modification of colonic microbiota composition and metabolic activity, for example by growth stimulation of Bifidobacterium and Lactobacillus.

    Population-based nutrikinetic modelling of phytochemical exposure
    Velzen, E.J.J. van; Westerhuis, J.A. ; Grün, C.H. ; Duynhoven, J.P.M. van; Jacobs, D.M. ; Eilers, P.H.C. ; Mulder, T.P. ; Foltz, M. ; Garczarek, U. ; Kemperman, R. ; Vaughan, E.E. ; Smilde, A.K. - \ 2014
    Metabolomics 10 (2014)6. - ISSN 1573-3882 - p. 1059 - 1073.
    red wine/grape juice - black tea - dietary polyphenols - phenolic metabolites - nutrition research - food sources - human plasma - green tea - gut model - pharmacokinetics
    The beneficial health effects of fruits and vegetables have been attributed to their polyphenol content. These compounds undergo many bioconversions in the body. Modeling polyphenol exposure of humans upon intake is a prerequisite for understanding the modulating effect of the food matrix and the colonic microbiome. This modeling is not a trivial task and requires a careful integration of measuring techniques, modeling methods and experimental design. Moreover, both at the population level as well as the individual level polyphenol exposure has to be quantified and assessed. We developed a strategy to quantify polyphenol exposure based on the concept of nutrikinetics in combination with population-based modeling. The key idea of the strategy is to derive nutrikinetic model parameters that summarize all information of the polyphenol exposure at both individual and population level. This is illustrated by a placebo-controlled crossover study in which an extract of wine/grapes and black tea solids was administered to twenty subjects. We show that urinary and plasma nutrikinetic time-response curves can be used for phenotyping the gut microbial bioconversion capacity of individuals. Each individual harbours an intrinsic microbiota composition converting similar polyphenols from both test products in the same manner and stable over time. We demonstrate that this is a novel approach for associating the production of two gut-mediated ¿-valerolactones to specific gut phylotypes. The large inter-individual variation in nutrikinetics and ¿-valerolactones production indicated that gut microbial metabolism is an essential factor in polyphenol exposure and related potential health benefits
    Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health
    Duynhoven, J.P.M. van; Vaughan, E.E. ; Dorsten, F. van; Gomez-Roldan, V. ; Vos, R. de; Vervoort, J.J.M. ; Hooft, J.J.J. van der; Roger, L. ; Draijer, R. ; Jacobs, D.M. - \ 2013
    American Journal of Clinical Nutrition 98 (2013)6. - ISSN 0002-9165 - p. 1631S - 1641S.
    red wine/grape juice - density-lipoprotein oxidation - coronary-artery-disease - vein endothelial-cells - human fecal microbiota - in-vitro - phenolic-acids - green tea - ellagitannin metabolites - dietary polyphenols
    Epidemiologic studies have convincingly associated consumption of black tea with reduced cardiovascular risk. Research on the bioactive molecules has traditionally been focused on polyphenols, such as catechins. Black tea polyphenols (BTPs), however, mainly consist of high-molecular-weight species that predominantly persist in the colon. There, they can undergo a wide range of bioconversions by the resident colonic microbiota but can in turn also modulate gut microbial diversity. The impact of BTPs on colon microbial composition can now be assessed by microbiomics technologies. Novel metabolomics platforms coupled to de novo identification are currently available to cover the large diversity of BTP bioconversions by the gut microbiota. Nutrikinetic modeling has been proven to be critical for defining nutritional phenotypes related to gut microbial bioconversion capacity. The bioactivity of circulating metabolites has been studied only to a certain extent. Bioassays dedicated to specific aspects of gut and cardiovascular health have been used, although often at physiologically irrelevant concentrations and with limited coverage of relevant metabolite classes and their conjugated forms. Evidence for cardiovascular benefits of BTPs points toward antiinflammatory and blood pressure–lowering properties and improvement in platelet and endothelial function for specific microbial bioconversion products. Clearly, more work is needed to fill in existing knowledge gaps and to assess the in vitro and in vivo bioactivity of known and newly identified BTP metabolites. It is also of interest to assess how phenotypic variation in gut microbial BTP bioconversion capacity relates to gut and cardiovascular health predisposition.
    Gut Microbial Metabolism of Polyphenols from Black Tea and Red Wine/Grape Juice Is Source-Specific and Colon-Region Dependent
    Dorsten, F.A. van; Peters, S. ; Gross, G. ; Gomez-Roldan, V. ; Klinkenberg, M. ; Vos, Ric de; Vaughan, E.E. ; Duynhoven, J.P.M. van; Possemiers, S. ; Wiele, T. van der; Jacobs, D.M. - \ 2012
    Journal of Agricultural and Food Chemistry 60 (2012)45. - ISSN 0021-8561 - p. 11331 - 11342.
    chain fatty-acids - dietary polyphenols - phenolic-acids - intestinal microbiota - fermentation products - fecal microflora - food sources - flavonoids - degradation - identification
    The colonic microbial degradation of a polyphenol-rich black tea extract (BTE) and red wine/grape juice extract (RWGE) was compared in a five-stage in vitro gastrointestinal model (TWINSHIME). Microbial metabolism of BTE and RWGE polyphenols in the TWINSHIME was studied subsequently in single- and continuous-dose experiments. A combination of liquid or gas chromatography with mass spectrometry (LC-MS or GC-MS) and NMR-based metabolic profiling was used to measure selected parent polyphenols, their microbial degradation into phenolic acids, and the production of short-chain fatty acids (SCFAs) in different colon compartments. Acetate production was increased by continuous feeding of BTE but not RWGE. During RWGE feeding, gallic acid and 4-hydroxyphenylpropionic acid remained elevated throughout the colon, while during BTE feeding, they were consumed in the distal colon, while 3-phenylpropionic acid was strongly produced. Gut microbial production of phenolics and SCFAs is dependent on colon location and polyphenol source, which may influence potential health benefits.
    Carl Schmitt and the concept of the border
    Minca, C. ; Vaughan-Williams, N. - \ 2012
    Geopolitics 17 (2012)4. - ISSN 1465-0045 - p. 756 - 772.
    biopolitics - security
    The paper investigates the promise of Carl Schmitt's concept of ‘nomos’ for developing new spatial imaginaries apposite to the study of ‘the border’ in contemporary political life, as per the aims of the ‘Lines in the Sand’ research agenda. Schmitt introduced the idea of a ‘nomos of the earth’ to refer to the fundamental relation between space and political order. There have been various historical expressions of the nomos, from the Respublica Christiana, to the jus publicum Europaeum, to a post–World War II (dis)order yet to be adequately theorised. We aim to explore the relatively overlooked spatial ontology of Schmitt's work and suggest ways in which it might prompt alternative ways of thinking about borders and bordering practices as representative of broader dynamics in the relation between space and political order.
    The fecal bifidobacterial transcriptome of adults: A microarray approach
    Klaassens, E.S. ; Vriesema, A.J.M. ; Amor, K. Ben; Vaughan, E.E. ; Vos, W.M. de - \ 2011
    Gut Microbes 2 (2011)4. - ISSN 1949-0976 - p. 217 - 226.
    Bifidobacteria are a predominant group present among adult human intestinal microbiota and are considered to be beneficial to host health. Both the dynamics and functional activity of bifidobacteria from the intestinal tract of four adults, following ingestion of a mix consisting of short chain galactooligosaccharides, long chain fructooligosaccharides and acidic oligosaccharides from pectin hydrolysate (GFP), was investigated. The percentage of total bifidobacteria, monitored by quantitative real time PCR, was not significantly altered but marked species-specific changes occurred in all individuals over time, indicating a dynamic bifidobacterial community. Insight into the functional activity of the bifidobacteria was acquired using a clone library-based microarray comprising the genomes of various bifidobacteria to reveal the bifidobacterial transcriptome within the fecal community. Total RNA from the fecal microbial community was hybridized to the microarray and 310 clones were selected for sequencing which revealed genes belonging to a wide range of functional groups demonstrating substantial metabolic activity. While the intake of GFP did not have a significant effect on the overall change in gene expression, 82 genes showed a significant change. Most of the predicted genes were involved in metabolism of carbohydrates of plant origin, house keeping functions such as DNA replication and transcription, followed by membrane transport of a wide variety of substrates including sugars and metals and amino acid metabolism. Other genes were involved in transport, nucleotide metabolism, amino acid metabolism, environmental information processing and cellular processes and signalling. A smaller number of genes were involved in general metabolism, glycan metabolism, energy metabolism, lipid metabolism and cell surface. These results support the notion that bifidobacteria utilize mainly indigestible polysaccharides as their main source of energy and biosynthesis of cellular components
    Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes?
    Diamant, M. ; Vaughan, E.E. ; Vos, W.M. de - \ 2011
    Obesity Reviews 12 (2011)4. - ISSN 1467-7881 - p. 272 - 281.
    glucagon-like peptide-1 - gastrointestinal-tract microbiota - protein-coupled receptor - human colonic microbiota - chain fatty-acids - healthy humans - adipose-tissue - double-blind - weight-loss - akkermansia-muciniphila
    The current obesity and type 2 diabetes pandemics have causes beyond changes in eating and exercise habits against a susceptible genetic background. Gut bacteria seem to additionally contribute to the differences in body weight, fat distribution, insulin sensitivity and glucose- and lipid-metabolism. Data, mostly derived from preclinical studies, suggest that gut microbiota play an important role in conditions such as obesity, diabetes, metabolic syndrome and non-alcoholic fatty liver disease. Regulation of energy uptake from the gut, by digesting otherwise indigestible common polysaccharides in our diet, production or activation of signalling molecules involved in host metabolism, modification of gut permeability, the release of gut hormones and inflammation, are among the mechanisms by which gut microbiota may influence the host cardiometabolic phenotype. Recent evidence suggests that quantitative and qualitative differences in gut microbiota exist between lean and obese, and between diabetic and non-diabetic individuals. Modification of the gut microbiota composition and/or its biochemical capacity by specific dietary or pharmacological interventions may favourably affect host metabolism. Large-scale intervention trials, investigating the potential benefit of prebiotics and probiotics in improving cardiometabolic health in high-risk populations, are eagerly awaited
    Exploring high-end scenarios for local sea level rise to develop flood protection strategies for a lowlying delta-the Netherlands as an example
    Katsman, C.A. ; Sterl, A. ; Beersma, H.W. ; Brink, H.W. van den; Church, J.A. ; Hazeleger, W. ; Kopp, R.E. ; Kroon, D. ; Kwadijk, J. ; Lammersen, R. ; Lowe, J. ; Oppenheimer, M. ; Plag, H.P. ; Ridley, J. ; Storch, H. von; Vaughan, D.G. ; Vellinga, P. ; Vermeersen, L.L.A. ; Wal, R.S.W. ; Weise, R. - \ 2011
    Climatic Change 109 (2011)3-4. - ISSN 0165-0009 - p. 617 - 645.
    hoogwaterbeheersing - zeespiegelschommelingen - kustbeheer - flood control - sea level fluctuations - coastal management - greenland ice-sheet - last interglacial period - pine island glacier - climate-change - mass-balance - thermohaline circulation - antarctic peninsula - northeast atlantic - west antarctica - acceleration
    Sea level rise, especially combined with possible changes in storm surges and increased river discharge resulting from climate change, poses a major threat in low-lying river deltas. In this study we focus on a specific example of such a delta: the Netherlands. To evaluate whether the country’s flood protection strategy is capable of coping with future climate conditions, an assessment of low-probability/high-impact scenarios is conducted, focusing mainly on sea level rise. We develop a plausible high-end scenario of 0.55 to 1.15 m global mean sea level rise, and 0.40 to 1.05 m rise on the coast of the Netherlands by 2100 (excluding land subsidence), and more than three times these local values by 2200. Together with projections for changes in storm surge height and peak river discharge, these scenarios depict a complex, enhanced flood risk for the Dutch delta.
    Human GI tract samples of Lactobacillus plantarum 299v
    Marco, M.L. ; Vries, M.C. de; Wels, M. ; Molenaar, D. ; Mangell, P. ; Ahrne, S. ; Vos, W.M. de; Vaughan, E.E. ; Kleerebezem, M. - \ 2010
    NIZO
    GSE17634 - Lactobacillus plantarum - PRJNA118513
    Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice
    Marco, M. ; Vries, M.C. de; Wels, M.W.W. ; Molenaar, D. ; Mangell, P. ; Ahrne, S. ; Vos, W.M. de; Vaughan, E.E. ; Kleerebezem, M. - \ 2010
    ISME Journal 4 (2010)11. - ISSN 1751-7362 - p. 1481 - 1484.
    gastrointestinal-tract - plantarum wcfs1 - genes
    Probiotic bacteria provide unique opportunities to study the global responses and molecular mechanisms underlying the effects of gut-associated microorganisms in the human digestive tract. In this study, we show by comparative transcriptome analysis using DNA microarrays that the established probiotic Lactobacillus plantarum 299v specifically adapts its metabolic capacity in the human intestine for carbohydrate acquisition and expression of exopolysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a commensal microorganism in the human gut. A core L. plantarum transcriptome expressed in the mammalian intestine was also determined through comparisons of L. plantarum 299v activities in humans to those found for L. plantarum WCFS1 in germ-free mice. These results identify the niche-specific adaptations of a dietary microorganism to the intestinal ecosystem and provide novel targets for molecular analysis of microbial-host interactions which affect human health
    Exploring high-end climate change scenarios for flood protection of the Netherlands
    Vellinga, P. ; Katsman, C. ; Sterl, A. ; Beersma, J.J. ; Hazeleger, W. ; Church, J. ; Kopp, R. ; Kroon, D. ; Oppenheimer, M. ; Plag, H.P. ; Rahmstorf, S. ; Lowe, J. ; Ridley, J. ; Storch, H. von; Vaughan, D. ; Wal, R. van der; Weisse, R. ; Kwadijk, J. ; Lammersen, R. ; Marinova, N.A. - \ 2009
    De Bilt : KNMI (KNMI scientific report / Royal Netherlands Meteorological Institute WR 2009-05)
    zeespiegelschommelingen - klimaatverandering - kustgebieden - sea level fluctuations - climatic change - coastal areas
    This international scientific assessment has been carried out at the request of the Dutch Delta Committee. The "Deltacommissie" requested that the assessment explore the high-end climate change scenarios for flood protection of the Netherlands. It is a state-of–the art scientific assessment of the upper bound values and longer term projections (for sea level rise up to 2200) of climate induced sea level rise, changing storm surge conditions and peak discharge of river Rhine. It comprises a review of recent studies, model projections and expert opinions of more than 20 leading climate scientists from different countries around the North Sea, Australia and the USA
    Probiotic and Gut Lactobacilli and Bifidobacteria: Molecular Approaches to Study Diversity and Activity
    Kleerebezem, M. ; Vaughan, E.E. - \ 2009
    Annual Review of Microbiology 63 (2009). - ISSN 0066-4227 - p. 269 - 290.
    lactic-acid bacteria - diet-induced obesity - gastrointestinal-tract microbiota - gradient gel-electrophoresis - intestinal epithelial-cells - johnsonii strain ncc533 - gram-positive bacteria - alanyl ester depletion - bile-salt hydrolase - formula-fed infants
    Lactobacilli and bifidobacteria have traditionally been recognized as potential health-promoting microbes in the human gastrointestinal tract, which is clearly reflected by the pre- and probiotic supplements on the market. Bacterial genomics of lactobacilli and bifidobacteria is initiating the identification and validation of specific effector molecules that mediate host health effects. Combined with advanced postgenomic mammalian host response analyses, elucidations of the molecular interactions and mechanisms that underlie the host-health effects observed are beginning to be gathered. These developments should be seen in the complexity of the microbiota-host relationships in the intestine, which through the new metagenomic era has regained momentum and will undoubtedly progress to functional microbiomics and host response analyses within the next decade. Taken together, these developments are anticipated to dramatically alter the scope and impact of the probiotic field, offering tremendous new opportunities with accompanying challenges for research and industrial application
    Mixed-Species Genomic Microarray Analysis of Fecal Samples Reveals Differential Transcriptional Response of Bifidobacteria in Breast- and Formula-Fed Infants
    Klaassens, E.S. ; Boesten, R.J. ; Haarman, M.E. ; Knol, J. ; Schuren, F.H. ; Vaughan, E.E. ; Vos, W.M. de - \ 2009
    Applied and Environmental Microbiology 75 (2009)9. - ISSN 0099-2240 - p. 2668 - 2676.
    human gastrointestinal-tract - gradient gel-electrophoresis - human-milk oligosaccharides - alpha-l-arabinofuranosidase - 1st 6 months - lactobacillus-plantarum - intestinal microflora - bacterial samples - human feces - rna-seq
    Although their exact function remains enigmatic, bifidobacteria are among the first colonizers of the newborn infant gut, and further develop to abundant communities, notably in response to diet. Therefore, the transcriptional response of bifidobacteria was studied in rapidly processed fecal samples of young infants that were either fed with breast-milk or a formula, containing a mixture of galacto- and fructoligosaccharides. The presence and diversity of the bifidobacterial fecal communities was determined using PCR-denaturing gradient gel electrophoresis and quantitative real time PCR for specific species. Changes in total number of bifidobacteria as well as in species diversity were observed indicating their metabolic activity within the infant gut. In addition, total RNA isolated from feces of the infants was labeled and hybridized to a bifidobacterial-specific microarray, comprising approximately 6000 clones of the major bifidobacterial species of the human gut. Approximately 270 clones, that showed the most prominent hybridization with the samples, were sequenced. Less than 10% of the hybridizing clones contained ribosomal RNA genes, whereas the vast majority of the inserts showed matches with protein-encoding genes predicted to originate from bifidobacteria. Although a wide range of functional groups was covered by the obtained sequences, most (14 %) of the transcribed genes were predicted to be involved in carbohydrate metabolism while also some were implied in exopolysaccharide production or folate production. A total of 3 of these were selected for qPCR and sequence analysis that confirmed the expression of the corresponding gene and expected nucleotide sequence. In conclusion, this study shows the feasibility of obtaining insight in the transcriptional response of intestinal bifidobacteria by analyzing fecal RNA and highlights the in vivo expression of bifidobacterial genes implied in host-related functions
    Biosafety assessment of probiotics used for human consumption: recommendations from the EU-PROSAFE project
    Vankerckhoven, V. ; Huys, G. ; Vancanneyt, M. ; Vael, C. ; Klare, I. ; Romond, M.B. ; Entenza, J.M. ; Moreillon, P. ; Wind, R.D. ; Knol, J. ; Wiertz, E. ; Pot, B. ; Vaughan, E.E. ; Kahlmeter, G. ; Goossens, H. - \ 2008
    Trends in Food Science and Technology 19 (2008)2. - ISSN 0924-2244 - p. 102 - 114.
    lactic-acid bacteria - urinary-tract infection - enterococcus-faecalis - in-vitro - bile-acids - experimental endocarditis - lactobacillus-plantarum - surface protein - gastrointestinal-tract - aggregation substance
    On June 26-27, 2006, 60 academic and industry scientists gathered during the PROSAFE workshop to discuss recommendations on taxonomy, antibiotic resistance, in vitro assessment of virulence and in vivo assessment of safety of probiotics used for human consumption. For identification of lactic acid bacteria (LAB) intended for probiotic use, it was recommended that conventional biochemical methods should be complemented with molecular methods and that these should be performed by an expert lab. Using the newly developed LAB Susceptibility test Medium (LSM), tentative epidemiological cut-off values were proposed. It was recommended that potentially probiotic strains not belonging to the wildtype distributions of relevant antimicrobials should not be developed as future products for human or animal consumption. Furthermore, it was recommended that the use of strains harbouring known and confirmed virulence genes should be avoided. Finally, for in vivo assessment of safety by investigating strain pathogenicity in animal models, the rat endocarditis model appeared to be the most reliable model tested in the PROSAFE project. Moreover, consensus was reached for approving the necessity of a human colonisation study in a randomised placebo-controlled double-blind design; however, further discussions are needed on the details of such as study.
    Two homologous Agr-like quorum-sensing systems cooperatively control adherence, cell morphology, and cell viability properties in Lactobacillus plantarum WCFS1
    Fujii, T. ; Ingham, C.J. ; Nakayama, J. ; Beerthuyzen, M.M. ; Kunuki, R. ; Molenaar, D. ; Sturme, M.H.J. ; Vaughan, E.E. ; Kleerebezem, M. ; Vos, W.M. de - \ 2008
    Journal of Bacteriology 190 (2008)23. - ISSN 0021-9193 - p. 7655 - 7665.
    gram-positive bacteria - staphylococcus-aureus - bacillus-subtilis - biofilm formation - escherichia-coli - transcriptional regulators - enterococcus-faecalis - streptococcus-mutans - signal-transduction - lactococcus-lactis
    A two-component regulatory system of Lactobacillus plantarum, encoded by genes designated lamK and lamR (hpk10 and rrp10), was studied. The lamK and lamR genes encode proteins which are highly homologous to the quorum-sensing histidine kinase LamC and the response regulator LamA, respectively. Transcription analysis of the lamKR operon and the lamBDCA operon and liquid chromatography-mass spectrometry analysis of production of the LamD558 autoinducing peptide were performed for DeltalamA, DeltalamR, DeltalamA DeltalamR deletion mutants and a wild-type strain. The results suggested that lamA and lamR are cooperating genes. In addition, typical phenotypes of the DeltalamA mutant, such as reduced adherence to glass surfaces and filamentous cell morphology, were enhanced in the DeltalamA DeltalamR mutant. Microarray analysis suggested that the same cell wall polysaccharide synthesis genes, stress response-related genes, and cell wall protein-encoding genes were affected in the DeltalamA and DeltalamA DeltalamR mutants. However, the regulation ratio was more significant for the DeltalamA DeltalamR mutant, indicating the cooperative effect of LamA and LamR
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