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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    Ecophysiology of novel intestinal butyrate-producing bacteria
    Bui, Thi Phuong Nam - \ 2016
    Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Caroline Plugge. - Wageningen : Wageningen University - ISBN 9789462577015 - 202
    butyrates - butyric acid bacteria - intestines - microbial interactions - faecal examination - mice - man - infants - genomics - intestinal physiology - microbial physiology - biochemical pathways - lysine - sugar - butyraten - boterzuurbacteriën - darmen - microbiële interacties - fecesonderzoek - muizen - mens - zuigelingen - genomica - darmfysiologie - microbiële fysiologie - biochemische omzettingen - lysine - suiker

    The human intestinal tract harbours a trillion on microbial cells, predominantly anaerobes. The activity and physiology of these anaerobes is strongly associated with health and disease. This association has been investigated for a long time.However, this has not been fully understood. One of the reasons is the limited availability of cultured representatives. It is estimated that there may be more than 3000 species colonised in the gut of healthy individuals, however, only a bit over 1000 species have been isolated and characterised. Among the intestinal microbes, butyrate-producing bacteria are of special interest as the butyrate produced, is crucial to maintain a healthy gut. In addition, butyrate-producing bacteria have shown a reverse correlation with several intestinal diseases. In Chapter 2 we described a novel species Anaerostipes rhamnosivorans 1y2T isolated from an infant stool. This strain belonged to genus Anaerostipes within Clostridium cluster XIVa. A. rhamnosivorans had a capability of converting rhamnose into butyrate that is unique within intestinal butyrate-producing bacteria. The genomic analysis also revealed the entire rhamnose fermentation pathway as well as the acetyl-CoA pathway for butyrate production. This bacterium is able to produce butyrate from a wide range of sugars as well as lactate plus acetate. In Chapter 3, we described the microbial interactions between A. rhamnosivorans and Bacteriodes thetaiotaomicron in dietary pectins; Blautia hydrogenotrophica in lactate and small amount of acetate; Methanobrevibacter smithii in glucose. We observed that A. rhamnosivorans was able to benefit from its partners in all cocultures for butyrate production. This is likely due to its high metabolic flexibility. While the interaction between A. rhamnosivorans and B. thetaiotaomicron appeared as syntrophy, the interaction between A. rhamnosivorans and hydrogenotrohic microbes were cross-feeding type where hydrogen was transferred between two species. The latter resulted in an increase in butyrate level. In Chapter 4 we described a novel species Intestinimonas butyriciproducens SRB521T representing a novel genus Intestinimonas from a mouse caecum within Clostridium cluster IV. This bacterium produced butyrate and acetate as end products from Wilkins-Chalgren-Anaerobe broth.

    Butyrate production is assumed to derive from carbohydrate employing acetyl-CoA pathway. No gut bacterium is known to convert proteins or amino acids to butyrate although butyrogenic pathways from amino acid degradation have been detected in the human gut using metagenomic approach. In Chapter 5 we discovered a novel butyrate synthesis pathway from the amino acid lysine and the Amadori product fructoselysine in Intestinimonas butyriciproducens AF211 that was isolated from human stool. This strain appeared to grow much better in lysine as compared to sugars although lysine and acetyl-CoA pathways were both detected in its complete genome. Moreover, the strain AF211 was able to metabolise efficiently fructoselysine into butyrate, and acetate was found to affect the fructoselysine fermentation, representing the impact of the environmental conditions where acetate is abundant in the gut. While the lysine pathway was found in the gut of many individuals, the fructoselysine pathway was present in only half of those samples. The finding that strain I. butyriciproducens AF211 is capable of the butyrogenic conversion of amino acid lysine and fructoselysine, an Amadori product formed in heated foods via the Maillard reaction, indicated a missing link that coupling protein metabolism and butyrate formation. As this Amadori product has been implicated to play a role in aging process, the use of strain AF211 as fructoselysine clearance in the gut needs further investigation. In Chapter 6 we performed genomic and physiological comparison between the I. butyriciproducens strain AF211 (human isolate) and SRB521T (mouse isolate). I. butyriciproducens was the most abundant species within the Intestinimonas genus and highly prevalent in humans based on metadata analysis on 16S amplicons. We confirmed that the butyrogenesis from lysine was a shared characteristic between the two I. butyriciproducens strains. We also observed the host specific features including tolerance to bile, cellular fatty acid composition, more efficient capability of converting sugars into butyrate, especially galactose and arabinose, in the human strain AF211. In addition, genomic rearrangements as well as variations in bacteriophages differed among strains.

    Molecular mechanisms underlying the effects of dietary fiber in the large intestine
    Lange, K. - \ 2015
    Wageningen University. Promotor(en): Michael Muller, co-promotor(en): Guido Hooiveld. - Wageningen : Wageningen University - ISBN 9789462572706 - 201
    voedingsvezels - voeding en gezondheid - darmfysiologie - dikke darm - transcriptomica - microbiota van het spijsverteringskanaal - dietary fibres - nutrition and health - intestinal physiology - large intestine - transcriptomics - gastrointestinal microbiota


    Interactions between diet, microbiota and host response are important for intestinal health. Dietary fibers are known to promote intestinal health. Dietary fibers are edible plant-derived food components that encompass complex carbohydrates and lignin, resist the digestion in the small intestine of which some are degraded and fermented by gut microbiota in the large intestine, i.e. cecum and colon. The beneficial health effects of dietary fiber are suggested to be mediated by short-chain fatty acids (SCFA), which are produced by gut microbial fermentation. The underlying mechanisms of the interaction between dietary fiber, SCFA, and the host, however, are not in detail known.

    The objective of the research described in this thesis was to investigate the molecular effects and mechanisms underlying the effects of dietary fiber and its fermentation products, SCFA, in the large intestine.

    Firstly, the colonic transcriptional response to the main SCFA, acetate, propionate and butyrate, was investigated. SCFA were administered by rectal infusion in C57BL/6 mice fed a low fat/high carbohydrate (LFD) or high fat/low carbohydrate diet (HFD) and whole-genome gene expression analysis was performed on colonic scrapings by microarray technology. The analysis revealed specific and overlapping genes regulated between acetate, propionate and butyrate. In addition, gene response to SCFA was dependent on the diet, in particular for propionate. A set of propionate-regulated genes was activated on LFD while suppressed on a HFD and vice versa, indicating that diet composition is important factor in colonic response to SCFA.

    Secondly, the molecular effects of different dietary fibers and a control diet on the large intestine were investigated. Five different dietary fibers (inulin, fructo-oligosaccharide, arabinoxylan, guar gum, resistant starch) and a control diet were fed to C57BL/6 mice (10 days). The transcriptional response to the fermentable fibers was comparable in gene expression, microbiota composition, and luminal SCFA level in colon. In common for all fermented dietary fibers, the transcriptional regulator Pparg was identified as potential upstream regulator for the mucosal gene expression response. Moreover, bacteria mainly belonging to Clostridium cluster XIVa were found to correlate with mucosal genes related to metabolic, energy-generating processes.

    Next to common responses, analysis of the transcriptome revealed distinct responses of different dietary fibers. With respect to the cecal metatranscriptome, we identified distinct activities of bacterial families in the fermentation of dietary fiber. Moreover, using multivariate statistical analysis, we found correlations of the mucosal transcriptome with both the microbiota composition and metatranscriptome.

    In addition, we showed that SCFA, particularly butyrate and to a lesser extend propionate, transactivate PPARg and regulate the PPARg target gene Angptl4 in colonic cells.

    Thirdly, we tested the hypothesis that epithelial Pparg plays an important role in the fermentation of dietary fibers in the gut. Mice with an intestine-specific knock out (KO) of Pparg (cre-villin) and wild type (WT) mice were fed inulin (10 days). Whole-genome gene expression analysis of the colon revealed that diet had a larger effect than genotype on colonic, luminal microbiota composition, metabolome and mucosal transcriptome. We identified genes that were regulated by inulin in Pparg-dependent manner. In addition, we also identified genes regulated by butyrate in Pparg-dependent manner in organoids grown from colonic crypt cells derived from KO or WT mice.

    In conclusion, we identified distinct mucosal gene expression responses to the main fermentation products of dietary fiber, SCFA, on both low fat/high carbohydrate and high fat/low carbohydrate diet backgrounds. Dietary fibers induce common and specific effects in colon. Epithelial Pparg partially governs the response to fermentation of dietary fiber in colon. Next to the commonalties of dietary fiber for intestinal physiology, specific and differential effects were identified for microbial gene activity and composition as well as mucosal transcriptome response indicating that omics tools are useful in elucidating and dissecting effects of dietary fiber.

    Rumen fermentation profile and intestinal digestibility of maize and grass silages
    Ali, M. - \ 2013
    Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): John Cone; Gert van Duinkerken. - S.l. : s.n. - ISBN 9789461736581 - 157
    melkkoeien - maïskuilvoer - graskuilvoer - pensfermentatie - verteerbaarheid - darmfysiologie - chemische samenstelling - diervoeding - voedingsfysiologie - dairy cows - maize silage - grass silage - rumen fermentation - digestibility - intestinal physiology - chemical composition - animal nutrition - nutrition physiology

    Maize and grass silages are commonly used as major feed materials for dairy cows in Europe and are becoming common parts of dairy cow rations in other parts of the world. Thenutritive value of maize and grass silages varies greatly due to variation in chemical composition. A combination of different factors such as the use of various cultivars, fertilization practices, growing conditions, harvesting technology, maturity at harvest and ensiling conditions cause this variation in chemical composition. The first aim of this thesis was to investigate relationships between the chemical composition and the in situ rumen degradation characteristics and in situ mobile nylon bag digestibility of dietary nutrients of maize and grass silages. Maize and grass silages with a broad range in chemical composition and quality parameters were selected from different Dutch commercial farms. The broad range in the chemical composition of the maize and grass silages resulted in a large variation in rumen degradable fractions of dry matter (DM), organic matter (OM), crude protein (CP), neutral detergent fibre (NDF) and starch. The intestinal digestibility of CP, NDF and/or starch was affected by the concentration of these components in the maize and grass silages, by the rumen incubation time and the rumen escape content. Regression equations were developed describing relationships between the chemical composition and the in situ ruminal and postruminal degradation characteristics of dietary nutrients of maize and grass silages. A number of the developed regression equations presented in this thesis can be used for accurate and rapid estimation of the ruminal and postruminal degradation characteristics of dietary nutrients of maize and grass silages, without conducting time consuming and expensive in situ experiments. The second aim of this thesis was to determine whether three cows are sufficient to cover the variation between individual cows in in situ rumen degradation characteristics of dietary nutrients of maize and grass silages. Significant differences (P<0.05) were found between individual cows for a number of parameters of DM, OM and CP of maize silages, indicating that four or more cows should be used for nylon bag incubations of maize silages. For grass silages, no significant differences (P>0.05) between individual cows were found for all the parameters of DM, OM, CP and NDF. The results suggest that using three cows are sufficient for nylon bag incubations of grass silages and pooling of rumen incubated residues is allowed to obtain a representative sample. The third aim of this thesis was to compare two fractionation methods; the washing machine method and a modified method, for nitrogen (N) and starch fractions of maize silages and N fractions of grass silages. The N and/or starch fractions of maize and grass silages determined, using the washing machine method (washing with water for 40 min) and the modified method (shaking with buffer solution for 60 min) were compared. The different methodological approaches of both methods resulted in different values for the washout (W), the soluble (S) and the non-washout (D+U) fractions of N of maize and grass silages and for the W, the insoluble washout (W-S) and the D+U fractions of starch of maize silages. The loss of insoluble small particles of starch was less during shaking of nylon bags in buffer solution, compared to washing nylon bags in the washing machine. Therefore, large differences were found between the D+U fractions of starch determined by both methods compared to the D+U fractions of N of maize silages. The developed regression equations for W, S and D+U fractions of N in grass silages and for D+U fractions of starch in maize silages determined by both methods can be used for rapid estimation of these fractions from chemical characteristics of maize and grass silages. The information on nutrient bioavailability of maize and grass silages presented in this thesis can be used to more accurately formulate dairy ration in terms of maintenance, health and production of dairy cows.

    Digestion of dietary fat : gastrointestinal behaviour of emulsions and human physiological responses
    Helbig, A. - \ 2013
    Wageningen University. Promotor(en): Harry Gruppen; Rob Hamer, co-promotor(en): Erika Silletti. - S.l. : s.n. - ISBN 9789461735607 - 166
    voedingsvet - spijsvertering - vetemulsies - spijsverteringskanaal - darmfysiologie - verzadigdheid - dietary fat - digestion - fat emulsions - digestive tract - intestinal physiology - satiety

    Two in vitromodels were used to understand emulsion behavior and the subsequent formation of free fatty acids (FFA), monoglycerides (MG) and diglycerides (DG). Emulsions stabilized by whey protein isolate (WPI) or gum arabic (GA), varying in droplet size, were digested under intestinal conditions. Concentrations of FFA, MG and DG, assessed by gas chromatography, decreased with increasing droplet size. FFA release from gum arabic-stabilized emulsions was higher compared to WPI-stabilized emulsions showing an influence of the interface. Next, lipolysis of protein stabilized emulsions (i.e. WPI or lysozyme) and the influence of flocculation at the isoelectric point (pI) were investigated in a dynamic gastrointestinal model. The stomach properties including gradual acidification caused WPI-stabilized emulsions to cream during transition through the pI of the protein. This resulted in delayed intestinal lipolysis compared to the lysozyme-stabilized emulsion. Thus, since gastric passage affects emulsion behavior and intestinal lipolysis, the gastric passage should be part of digestion models. Next, in a human study emulsion behavior and resulting lipolytic products were related to the release of satiety hormones, satiety perception and ad libitumintake. Also, gallbladder volume and oral processing were studied. A delayed entry into the duodenum and lipolysis for the un-homogenized sample resulted in lower CCK, delayed GLP-1/PYY responses and barely gallbladder contraction compared to the homogenized emulsion. No difference was found between treatments on ghrelin, only the perception 'desire to eat´ was elevated for homogenized emulsions. Oral processing induced prolonged gallbladder contraction, but had no additive effect on other measures. A homogenous system as such is possibly not effective to induce pronounced satiety perceptions compared to phase separated or creamed systems using the same emulsifier. Moreover, the release of gastrointestinal hormones cannot directly be related to the satiating effect of food.

    Chicken intestinal development in health and disease : transcriptomic and modeling approaches
    Schokker, D.J. - \ 2012
    Wageningen University. Promotor(en): Mari Smits, co-promotor(en): Annemarie Rebel. - S.l. : s.n. - ISBN 9789462575325 - 225
    fowls - intestines - biological development - gene expression - transcriptomics - animal health - poultry diseases - intestinal physiology - immunology - mathematical models - kippen - darmen - biologische ontwikkeling - genexpressie - transcriptomica - diergezondheid - pluimveeziekten - darmfysiologie - immunologie - wiskundige modellen

    Intestinal health is an important condition for sustainable animal production. Since it is known that there is significant variation in intestinal health and functionality, there is much to gain in this respect. However, to fully exploit the biological potential of the animal’s gastro-intestinal tract, the mechanism and regulation of major intestinal processes need to be unraveled first. In addition, identification of key components and processes involved in intestinal adaptation mechanisms may help to identify internal and external factors that influence the health and functioning of the gut. Improved knowledge in this area may contribute in defining rational strategies to improve sustainable animal production.
    Traditionally research used reductionist approaches and focused on specific components or isolated processes related to intestinal functioning. However, the recent developments in the areas of genomics and computational sciences provide tools and methods that allow studying the system of the gut as a whole. In this thesis we have set first steps in the use of such Systems Biology approaches towards the identification of the key components and processes involved in intestinal functioning and health. We investigated molecular processes associated with gut development in chickens under two extreme contrasting conditions. We used an infection with Salmonella immediately after hatch and control animals to create the two contrasting phenotypic conditions. We used microarray-based genome-wide mRNA profiling to identify patterns of gene expression and cellular processes associated with each conditions. Comparisons between the two conditions and the application of modeling approaches revealed genes, groups of genes, molecular pathways, gene networks, and high level regulators of system behavior. We also used a mathematical modeling approach to describe the dynamics of cellular components of the immune system and their corresponding interactions under the same two contrasting conditions.
    We identified different temporal gene expression profiles associated with morphological, functional and immunological processes. Several of these processes differed between the two contrasting conditions, whereas others were not affected be the experimental treatments. By inferring gene association networks, we observed that an infection with Salmonella considerably changes the behavior of intestinal tissue as well as the regulation of the underlying molecular processes. For each contrasting condition, we identified a specific set of potential high-level regulator genes (hubs). We hypothesize that these hubs are steering systems behavior. Bioinformatic analysis of the hubs suggested that the disturbance with Salmonella is associated with a shift from transcriptional regulation in the non-disturbed tissue to cell-cell communication in the disturbed tissue. Furthermore, the generated mathematical model describes the dynamics of the cellular components of the immune system as well as the dynamics of the invading pathogen well. The model was able to predict the cellular immune response of the host against an invading pathogen.
    We developed basic knowledge of (molecular) processes that are associated with different physiological conditions of intestinal tissue and we acquired global views on adaptation mechanisms of the intestine, including the regulation thereof. This information can be used to formulate new hypotheses about behavioral aspects of the gut, for the discovery of new biological mechanisms, and ultimately for the development of tools and rational strategies to improve intestinal functionality and health, either via diet and/or the host genotype. Such developments are urgently required to diminish the incidence and impact of intestinal diseases in farm animal species and to reduce the use of antibiotics in animal husbandry.

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