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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    Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice
    Szklany, Kirsten ; Wopereis, Harm ; Waard, Cindy de; Wageningen, Thecla van; An, Ran ; Limpt, Kees van; Knol, Jan ; Garssen, Johan ; Knippels, Leon M.J. ; Belzer, Clara ; Kraneveld, Aletta D. - \ 2019
    Nutritional Neuroscience (2019). - ISSN 1028-415X
    Behaviour - dietary supplementation from birth - early life - fructo-oligosaccharide - galacto-oligosaccharide - healthy mice - intestinal microbiota - prebiotics - SCFA - serotonergic system

    Objective: The intestinal microbiota is acknowledged to be essential in brain development and behaviour. Their composition can be modulated by prebiotics such as short-chain galacto-oligosaccharides (scGOS) and long-chain fructo-oligosaccharide (lcFOS). Several studies reported potential health benefit of prebiotics on behaviour. As the prebiotic mixture of scGOS and lcFOS is included in infant formula, we investigated the effects of dietary supplementation with this specific mixture from the day of birth onwards on behaviour and intestinal microbiota development in mice. Method: Healthy male BALB/cByJ mice received, from day of birth, a dietary supplement with or without 3% scGOS:lcFOS (9:1). Behavioural tests were performed pre-weaning, in adolescence, early adulthood and adulthood. We assessed faecal microbiota compositions over time, caecal short-chain fatty acids as well as brain mRNA expression of Htr1a, Htr1b and Tph2 and monoamine levels. Results: Compared to control fed mice, scGOS:lcFOS fed mice showed reduced anxiety-like and repetitive behaviour over time and improved social behaviour in adulthood. The serotonergic system in the prefrontal cortex (PFC) and somatosensory cortex (SSC) was affected by the scGOS:lcFOS. In the PFC, mRNA expression of brain-derived neurotrophic factor (Bdnf) was enhanced in scGOS:lcFOS fed mice. Although the bacterial diversity of the intestinal microbiota was unaffected by the scGOS:lcFOS diet, microbiota composition differed between the scGOS:lcFOS and the control fed mice over time. Moreover, an increased saccharolytic and decreased proteolytic fermentation activity were observed in caecum content. Discussion: Supplementing the diet with scGOS:lcFOS from the day of birth is associated with reduced anxiety-like and improved social behaviour during the developmental period and later in life, and modulates the composition and activity of the intestinal microbiota in healthy male BALB/c mice. These data provide further evidence of the potential impact of scGOS:lcFOS on behaviour at several developmental stages throughout life and strengthen the insights in the interplay between the developing intestine and brain.

    The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut
    Elzinga, Janneke ; Oost, John van der; Vos, Willem M. de; Smidt, Hauke - \ 2019
    Microbiology and Molecular Biology Reviews 83 (2019)2. - ISSN 1092-2172 - p. 1 - 40.
    animal model - gut-on-a-chip - in vitro model - intestinal microbiota - minimal microbiota

    The human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticated in vitro cell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied to in vivo models that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accurate in vitro models of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut "core microbiota" are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.

    Data from: Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals
    Korpela, K. ; Flint, H.J. ; Johnstone, A.M. ; Lappi, J. ; Poutanen, K. ; Dewulf, E. ; Delzenne, N. ; Vos, Willem de; Salonen, A. - \ 2015
    University of Helsinki
    CRP - Eubacterium ruminantium - 16S rRNA - obesity - dietary intervention - Clostridium sphenoides - insulin - intestinal microbiota - prediction - bacteria - cholesterol - Clostridium felsineum
    Background: Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host. Methodology: Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set – test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters. Principal Findings: Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC = 0.77–1; predicted vs. observed correlation = 0.67–0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health. Conclusion: This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.
    Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
    Benis, N. ; Schokker, D. ; Suarez Diez, M. ; Martins dos Santos, V.A.P. ; Smidt, H. ; Smits, M.A. - \ 2015
    BMC Genomics 16 (2015). - ISSN 1471-2164
    protein-interaction network - intestinal microbiota - early-life - gastrointestinal-tract - immune-system - antibiotic exposure - adaptive immunity - resistant starch - microarray experiments - ruminococcus-bromii
    Background Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to identify biological processes involved in these long lasting effects and the (molecular) factors that regulate them. We used an antibiotic and the same antibiotic in combination with stress on piglets as an early life perturbation. Then we used host gene expression data from the gut (jejunum) tissue and community-scale analysis of gut microbiota from the same location of the gut, at three different time-points to gauge the reaction to the perturbation. We analysed the data by a new combination of existing tools. First, we analysed the data in two dimensions, treatment and time, with quadratic regression analysis. Then we applied network-based data integration approaches to find correlations between host gene expression and the resident microbial species. Results The use of a new combination of data analysis tools allowed us to identify significant long-lasting differences in jejunal gene expression patterns resulting from the early life perturbations. In addition, we were able to identify potential key gene regulators (hubs) for these long-lasting effects. Furthermore, data integration also showed that there are a handful of bacterial groups that were associated with temporal changes in gene expression. Conclusion The applied systems-biology approach allowed us to take the first steps in unravelling biological processes involved in long lasting effects in the gut due to early life perturbations. The observed data are consistent with the hypothesis that these long lasting effects are due to differences in the programming of the gut immune system as induced by the temporary early life changes in the composition and/or diversity of microbiota in the gut.
    Long-lasting effects of Early-life Antibiotic Treatment and routine Animal Handling on Gut Microbiota Composition and Immune System in Pigs
    Schokker, D. ; Zhang, J. ; Vastenhouw, S.A. ; Heilig, G.H.J. ; Smidt, H. ; Rebel, J.M.J. ; Smits, M.A. - \ 2015
    PLoS ONE 10 (2015)2. - ISSN 1932-6203
    large gene lists - intestinal microbiota - bacterial - extraction - expression - disease - health - asthma - young - diet
    Background In intensive pig husbandry systems, antibiotics are frequently administrated during early life stages to prevent respiratory and gastro-intestinal tract infections, often in combination with stressful handlings. The immediate effects of these treatments on microbial colonization and immune development have been described recently. Here we studied whether the early life administration of antibiotics has long-lasting effects on the pig’s intestinal microbial community and on gut functionality. Methodology/Principal Findings To investigate the long-lasting effect of early-life treatment, piglets were divided into three different groups receiving the following treatments: 1) no antibiotics and no stress, 2) antibiotics and no stress, and 3) antibiotics and stress. All treatments were applied at day four after birth. Sampling of jejunal content for community scale microbiota analysis, and jejunal and ileal tissue for genome-wide transcription profiling, was performed at day 55 (~8 weeks) and day 176 (~25 weeks) after birth. Antibiotic treatment in combination with or without exposure to stress was found to have long-lasting effects on host intestinal gene expression involved in a multitude of processes, including immune related processes. Conclusions/Significance The results obtained in this study indicate that early life (day 4 after birth) perturbations have long-lasting effects on the gut system, both in gene expression (day 55) as well as on microbiota composition (day 176). At day 55 high variance was observed in the microbiota data, but no significant differences between treatment groups, which is most probably due to the newly acquired microbiota during and right after weaning (day 28). Based on the observed difference in gene expression at day 55, it is hypothesized that due to the difference in immune programming during early life, the systems respond differently to the post-weaning newly acquired microbiota. As a consequence, the gut systems of the treatment groups develop into different homeostasis.
    Impact of a novel protein meal on the gastrointesinal microbiota and host transciptome of larval zebrafish Danio rerio
    Rurangwa, E. ; Sipkema, D. ; Kals, J. ; Veld, M. ter; Forlenza, M. ; Bacanu, G.M. ; Smidt, H. ; Palstra, A.P. - \ 2015
    Frontiers in Physiology 6 (2015). - ISSN 1664-042X - 27 p.
    large gene lists - intestinal microbiota - gut microbiota - digestive physiology - solea-senegalensis - metal uptake - sp-nov - fish - expression - iron
    Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilisation (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM
    Early Methanogenic Colonisation in the Faeces of Meishan and Yorkshire Piglets as Determined by Pyrosequencing Analysis
    Su, Y. ; Bian, G.R. ; Zhu, Z.G. ; Smidt, H. ; Zhu, W.Y. - \ 2014
    Archaea : an international microbiological journal 2014 (2014). - ISSN 1472-3646
    gut microbiota - methanobrevibacter-smithii - intestinal microbiota - postnatal-development - sequence-analysis - bacterial - lactobacillus - community - archaeal - methane
    Gut methanogenic archaea of monogastric animals are considered to be related to energy metabolism and adipose deposition of the host; however, information on their development in young piglets is limited. Thus, to investigate early methanogenic colonisation in the faeces of Meishan and Yorkshire piglets, faecal samples were collected from piglets at 1, 3, 7, and 14 days after birth and used to analyse the methanogenic community with 16S rRNA gene pyrosequencing. Results showed that the diversity of the methanogenic community in the faeces of neonatal piglets decreased from one to 14 days of age, as the total methanogen populations increased. The age of piglets, but not the breed, significantly affected the diversity of the methanogenic community which was dominated by the genus Methanobrevibacter. From the ages of one to 14 days, the abundance of M. smithii-related operational taxonomic units (OTUs) increased significantly, while the abundances of M. thaueri- and M. millerae-related OTUs decreased significantly. The substitution of M. smithii for M. thaueri/M. millerae was faster in Yorkshire piglets than in Meishan piglets. These results suggest that the early establishment of microbiota in neonatal piglets is accompanied by dramatic changes in the methanogenic community, and that the changes vary among pigs of different genotypes.
    Gut Microbiota Signatures Predict Host and Microbiota Responses to Dietary Interventions in Obese Individuals
    Korpela, K. ; Flint, H.J. ; Johnstone, A.M. ; Lappi, J. ; Poutanen, K. ; Dewulf, E. ; Delzenne, N. ; Vos, W.M. de; Salonen, A. - \ 2014
    PLoS ONE 9 (2014)3. - ISSN 1932-6203
    dna-extraction methods - intestinal microbiota - metabolic syndrome - species response - resistant starch - healthy humans - double-blind - weight-loss - human colon - differentiate
    Background Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host. Methodology Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set – test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters. Principal Findings Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC = 0.77–1; predicted vs. observed correlation = 0.67–0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health. Conclusion This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.
    Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids.
    Lukovac, S. ; Belzer, C. ; Pellis, L. ; Keijser, B.J. ; Vos, W.M. de; Montijn, R.C. ; Roeselers, G. - \ 2014
    mBio 5 (2014)4. - ISSN 2150-7511 - 10 p.
    chain fatty-acids - diet-induced obesity - intestinal microbiota - cholesterol-synthesis - adipose factor - gen. nov. - in-vitro - colon - cell - expression
    The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids. We have explored the transcriptional response of organoids upon exposure to short-chain fatty acids (SCFAs) and products generated by two abundant microbiota constituents, Akkermansia muciniphila and Faecalibacterium prausnitzii. We observed that A. muciniphila metabolites affect various transcription factors and genes involved in cellular lipid metabolism and growth, supporting previous in vivo findings. Contrastingly, F. prausnitzii products exerted only weak effects on host transcription. Additionally, A. muciniphila and its metabolite propionate modulated expression of Fiaf, Gpr43, histone deacetylases (HDACs), and peroxisome proliferator-activated receptor gamma (Ppar¿), important regulators of transcription factor regulation, cell cycle control, lipolysis, and satiety. This work illustrates that specific bacteria and their metabolites differentially modulate epithelial transcription in mouse organoids. We demonstrate that intestinal organoids provide a novel and powerful ex vivo model for host-microbiome interaction studies.
    Aberrant gut microbiota composition at the onset of type 1 diabetes in young children
    Goffau, M.C. de; Fuentes, S. ; Bogert, B. van den; Honkanen, H. ; Vos, W.M. de; Welling, G.W. ; Hyöty, H. ; Harmsen, H.J. - \ 2014
    Diabetologia 57 (2014)8. - ISSN 0012-186X - p. 1569 - 1577.
    intestinal microbiota - storage-conditions - disease - butyrate - age - community - immunity - health - bacteria - differs
    Aims/hypothesis Recent studies indicate that an aberrant gut microbiota is associated with the development of type 1 diabetes, yet little is known about the microbiota in children who have diabetes at an early age. To this end, the microbiota of children aged 1–5 years with new-onset type 1 diabetes was compared with the microbiota of age-matched healthy controls. Methods A deep global analysis of the gut microbiota composition was established by phylogenetic microarray analysis using a Human Intestinal Tract Chip (HITChip). Results Principal component analyses highlighted the importance of age when comparing age-matched pairs. In pairs younger than 2.9 years, the combined abundance of the class Bacilli (notably streptococci) and the phylum Bacteroidetes was higher in diabetic children, whereas the combined abundance of members of Clostridium clusters IV and XIVa was higher in the healthy controls. Controls older than 2.9 years were characterised by a higher fraction of butyrate-producing species within Clostridium clusters IV and XIVa than was seen in the corresponding diabetic children or in children from the younger age groups, while the diabetic children older than 2.9 years could be differentiated by having an increased microbial diversity. Conclusions/interpretation The results from both age groups suggest that non-diabetic children have a more balanced microbiota in which butyrate-producing species appear to hold a pivotal position.
    Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status
    Wacklin, P. ; Tuimala, J. ; Nikkilä, J. ; Tims, S. ; Mäkivuokko, H. ; Alakulppi, N. ; Laine, P. ; Rajilic-Stojanovic, M. ; Paulin, L. ; Vos, W.M. de; Mättö, J. - \ 2014
    PLoS ONE 9 (2014)4. - ISSN 1932-6203
    inflammatory-bowel-disease - human gut microbiome - blood-group antigens - intestinal microbiota - crohns-disease - celiac-disease - mucosa - twins - galactosidase - enterotypes
    The human intestine is colonised with highly diverse and individually defined microbiota, which likely has an impact on the host well-being. Drivers of the individual variation in the microbiota compositions are multifactorial and include environmental, host and dietary factors. We studied the impact of the host secretor status, encoded by fucosyltransferase 2 (FUT2) -gene, on the intestinal microbiota composition. Secretor status determines the expression of the ABH and Lewis histo-blood group antigens in the intestinal mucosa. The study population was comprised of 14 non-secretor (FUT2 rs601338 genotype AA) and 57 secretor (genotypes GG and AG) adult individuals of western European descent. Intestinal microbiota was analyzed by PCR-DGGE and for a subset of 12 non-secretor subjects and 12 secretor subjects additionally by the 16S rRNA gene pyrosequencing and the HITChip phylogenetic microarray analysis. All three methods showed distinct clustering of the intestinal microbiota and significant differences in abundances of several taxa representing dominant microbiota between the non-secretors and the secretors as well as between the FUT2 genotypes. In addition, the non-secretors had lower species richness than the secretors. The soft clustering of microbiota into enterotypes (ET) 1 and 3 showed that the non-secretors had a higher probability of belonging to ET1 and the secretors to ET3. Our study shows that secretor status and FUT2 polymorphism are associated with the composition of human intestinal microbiota, and appears thus to be one of the key drivers affecting the individual variation of human intestinal microbiota.
    Development of ileal cytokine and immunoglobulin expression levels in response to early feeding in broilers and layers
    Simon, K. ; Vries Reilingh, G. de; Kemp, B. ; Lammers, A. - \ 2014
    Poultry Science 93 (2014)12. - ISSN 0032-5791 - p. 3017 - 3027.
    immune-responses - gut microbiota - intestinal microbiota - natural antibodies - innate immunity - delayed access - axenic mice - performance - chickens - system
    Provision of feed in the immediate posthatch period may influence interaction between intestinal microbiota and immune system, and consequently immunological development of the chick. This study addressed ileal immune development in response to early feeding in 2 chicken breeds selected for different production traits: broilers and layers. Chicks of both breeds either received feed and water immediately posthatch or were subjected to a 72-h feed and water delay. Ileal cytokine and immunoglobulin mRNA expression levels were determined at different time points. Effects of early feeding were limited, but breeds differed strikingly regarding cytokine and immunoglobulin expression levels. Cytokine expression levels in broilers were low compared with layers and showed a transient drop in the second to third week of life. In contrast, broilers showed considerably higher expression levels of IgA, IgM, and IgY. These findings indicate that the 2 breeds use different immune strategies, at least on the ileal level.
    Effects of ß-Lactam Antibiotics and Fluoroquinolones on Human Gut Microbiota in Relation to Clostridium difficile Associated Diarrhea
    Knecht, H. ; Neulinger, S.C. ; Heinsen, F.A. ; Knecht, C. ; Schilhabel, A. ; Schmitz, R.A. ; Zimmermann, A. ; Martins dos Santos, V.A.P. ; Ferrer, R. ; Rosenstiel, P.C. ; Schreiber, S. ; Friedrichs, A.K. ; Ott, S.J. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203
    irritable-bowel-syndrome - ribosomal-rna - colonization resistance - intestinal microbiota - fecal microbiota - fatty-acids - disease - diversity - differs - risk
    Clostridium difficile infections are an emerging health problem in the modern hospital environment. Severe alterations of the gut microbiome with loss of resistance to colonization against C. difficile are thought to be the major trigger, but there is no clear concept of how C. difficile infection evolves and which microbiological factors are involved. We sequenced 16S rRNA amplicons generated from DNA and RNA/cDNA of fecal samples from three groups of individuals by FLX technology: (i) healthy controls (no antibiotic therapy); (ii) individuals receiving antibiotic therapy (Ampicillin/Sulbactam, cephalosporins, and fluoroquinolones with subsequent development of C. difficile infection or (iii) individuals receiving antibiotic therapy without C. difficile infection. We compared the effects of the three different antibiotic classes on the intestinal microbiome and the effects of alterations of the gut microbiome on C. difficile infection at the DNA (total microbiota) and rRNA (potentially active) levels. A comparison of antibiotic classes showed significant differences at DNA level, but not at RNA level. Among individuals that developed or did not develop a C. difficile infection under antibiotics we found no significant differences. We identified single species that were up- or down regulated in individuals receiving antibiotics who developed the infection compared to non-infected individuals. We found no significant differences in the global composition of the transcriptionally active gut microbiome associated with C. difficile infections. We suggest that up- and down regulation of specific bacterial species may be involved in colonization resistance against C. difficile providing a potential therapeutic approach through specific manipulation of the intestinal microbiome.
    Eicosapentaenoic acid free fatty acid prevents and suppresses colonic neoplasia in colitis-associated colorectal cancer acting on Notch signaling and gut microbiota
    Piazzi, G. ; Argenio, G. D'; Prossomariti, A. ; Lembo, V. ; Mazzone, G. ; Candela, M. ; Biagi, E. ; Brigidi, P. ; Vitaglione, P. ; Fogliano, V. ; Angelo and others, L. D' - \ 2014
    International Journal of Cancer 135 (2014)9. - ISSN 0020-7136 - p. 2004 - 2013.
    inflammatory-bowel-disease - dietary fish-oil - intestinal microbiota - mouse model - docosahexaenoic acid - mice - sodium - cells - differentiation - chemoprevention
    Inflammatory bowel diseases are associated with increased risk of developing colitis-associated colorectal cancer (CAC). Epidemiological data show that the consumption of ¿-3 polyunsaturated fatty acids (¿-3 PUFAs) decreases the risk of sporadic colorectal cancer (CRC). Importantly, recent data have shown that eicosapentaenoic acid-free fatty acid (EPA-FFA) reduces polyp formation and growth in models of familial adenomatous polyposis. However, the effects of dietary EPA-FFA are unknown in CAC. We tested the effectiveness of substituting EPA-FFA, for other dietary fats, in preventing inflammation and cancer in the AOM-DSS model of CAC. The AOM-DSS protocols were designed to evaluate the effect of EPA-FFA on both initiation and promotion of carcinogenesis. We found that EPA-FFA diet strongly decreased tumor multiplicity, incidence and maximum tumor size in the promotion and initiation arms. Moreover EPA–FFA, in particular in the initiation arm, led to reduced cell proliferation and nuclear ß-catenin expression, whilst it increased apoptosis. In both arms, EPA-FFA treatment led to increased membrane switch from ¿-6 to ¿-3 PUFAs and a concomitant reduction in PGE2 production. We observed no significant changes in intestinal inflammation between EPA-FFA treated arms and AOM-DSS controls. Importantly, we found that EPA-FFA treatment restored the loss of Notch signaling found in the AOM-DSS control and resulted in the enrichment of Lactobacillus species in the gut microbiota. Taken together, our data suggest that EPA-FFA is an excellent candidate for CRC chemoprevention in CAC.
    Impact of galacto-oligosaccharides on the gut microbiota composition and metabolic activity upon antibiotic treatment during in vitro fermentation
    Ladirat, S.E. ; Schuren, F.H.J. ; Schoterman, M.H.C. ; Nauta, A. ; Gruppen, H. ; Schols, H.A. - \ 2014
    FEMS microbiology ecology 87 (2014)1. - ISSN 0168-6496 - p. 41 - 51.
    intestinal microbiota - dietary modulation - prebiotics - oligofructose - diarrhea - health - resistance - disease - tract
    Prebiotics are considered to have potential to reduce disturbances in the gut microbiota induced by antibiotics. Results in literature are, however, not consistent. The current in vitro study conducted in a fermentation screening platform allowed to unambiguously compare the impact of galacto-oligosaccharides (GOS) on adult gut microbiota composition and activity upon treatment with four antibiotics at two doses. The changes in relative abundance of bacteria upon antibiotic treatment and the growth of Bifidobacterium and Lactobacillus upon GOS addition were antibiotic and dose dependant. This conclusion explains discrepancies in literature and indicates that particular combinations of GOS antibiotic should be studied. The combination GOS–Amoxicillin was especially of interest as, after decrease in Bifidobacterium levels, a recovery of mainly Bifidobacterium longum was observed and could be correlated with specific degradation patterns of GOS. Next to different degradation profiles of individual GOS, an accumulation of monosaccharides and intermediate organic acids was observed in antibiotic-treated microbiota as compared to nontreated microbiota. This showed that although GOS were utilized and beneficial bacteria could grow in 3 of 4 antibiotics tested, the metabolic activity of an antibiotic-treated microbiota was still disturbed as compared to the nontreated microbiota.
    Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection
    Fuentes Enriquez de Salamanca, S. ; Nood, E. van; Tims, S. ; Heikamp-de Jong, I. ; Braak, C.J.F. ter; Keller, J.J. ; Zoetendal, E.G. ; Vos, W.M. de - \ 2014
    ISME Journal 8 (2014). - ISSN 1751-7362 - p. 1621 - 1633.
    intestinal microbiota - gut microbiota - bacterial - disease - bacteriotherapy - enterotypes - diversity - diarrhea - therapy - article
    Recurrent Clostridium difficile infection (CDI) can be effectively treated by infusion of a healthy donor faeces suspension. However, it is unclear what factors determine treatment efficacy. By using a phylogenetic microarray platform, we assessed composition, diversity and dynamics of faecal microbiota before, after and during follow-up of the transplantation from a healthy donor to different patients, to elucidate the mechanism of action of faecal infusion. Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. All patients successfully recovered. Their intestinal microbiota changed from a low-diversity diseased state, dominated by Proteobacteria and Bacilli, to a more diverse ecosystem resembling that of healthy donors, dominated by Bacteroidetes and Clostridium groups, including butyrate-producing bacteria. We identified specific multi-species networks and signature microbial groups that were either depleted or restored as a result of the treatment. The changes persisted over time. Comprehensive and deep analyses of the microbiota of patients before and after treatment exposed a therapeutic reset from a diseased state towards a healthy profile. The identification of microbial groups that constitute a niche for C. difficile overgrowth, as well as those driving the reinstallation of a healthy intestinal microbiota, could contribute to the development of biomarkers predicting recurrence and treatment outcome, identifying an optimal microbiota composition that could lead to targeted treatment strategies.
    Altered gut microbiota and activity in a murine model of autism spectrum disorders
    Theije, C.G. de; Wopereis, H.J. ; Ramadan, M. ; Eijndthoven, T. van; Lambert, J. ; Knol, J. ; Garssen, J. ; Kraneveld, A.D. ; Oozeer, R. - \ 2014
    Brain, Behavior, and Immunity 37 (2014). - ISSN 0889-1591 - p. 197 - 206.
    valproic acid - intestinal microbiota - maternal separation - host interactions - propionic-acid - onset autism - children - brain - microflora - exposure
    Autism spectrum disorder (ASD) is a heterogeneous group of complex neurodevelopmental disorders with evidence of genetic predisposition. Intestinal disturbances are reported in ASD patients and compositional changes in gut microbiota are described. However, the role of microbiota in brain disorders is poorly documented. Here, we used a murine model of ASD to investigate the relation between gut microbiota and autism-like behaviour. Using next generation sequencing technology, microbiota composition was investigated in mice in utero exposed to valproic acid (VPA). Moreover, levels of short chain fatty acids (SCFA) and lactic acid in caecal content were determined. Our data demonstrate a transgenerational impact of in utero VPA exposure on gut microbiota in the offspring. Prenatal VPA exposure affected operational taxonomic units (OTUs) assigned to genera within the main phyla of Bacteroidetes and Firmicutes and the order of Desulfovibrionales, corroborating human ASD studies. In addition, OTUs assigned to genera of Alistipes, Enterorhabdus, Mollicutes and Erysipelotrichalis were especially associated with male VPA-exposed offspring. The microbial differences of VPA in utero-exposed males deviated from those observed in females and was (i) positively associated with increased levels of caecal butyrate as well as ileal neutrophil infiltration and (ii) inversely associated with intestinal levels of serotonin and social behaviour scores. These findings show that autism-like behaviour and its intestinal phenotype is associated with altered microbial colonization and activity in a murine model for ASD, with preponderance in male offspring. These results open new avenues in the scientific trajectory of managing neurodevelopmental disorders by gut microbiome modulation
    Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity
    Vrieze, A. ; Out, C. ; Fuentes Enriquez de Salamanca, S. ; Jonker, L. ; Reuling, I. ; Kootte, R.S. ; Nood, E. van; Holleman, F. ; Knaapen, M. ; Romijn, J.A. ; Soeters, M.R. ; Blaak, E.E. ; Dallinga-Thie, G.M. ; Reijnders, D. ; Ackermans, M.T. ; Serlie, M.J. ; Knop, F.K. ; Holst, J.J. ; Ley, C.V. ; Kema, I.P. ; Zoetendal, E.G. ; Vos, W.M. de; Hoekstra, J.B. ; Stroes, E.S. ; Groen, A.K. ; Nieuwdorp, M. - \ 2014
    Journal of Hepatology 60 (2014)4. - ISSN 0168-8278 - p. 824 - 831.
    salt hydrolase activity - diet-induced obesity - intestinal microbiota - energy-expenditure - mice - resistance - adiposity - glucagon - capacity - humans
    BACKGROUND: Obesity has been associated with changes in the composition and function of the intestinal microbiota. Modulation of the microbiota by antibiotics also alters bile acid and glucose metabolism in mice. Hence, we hypothesized that short term administration of oral antibiotics in humans would affect fecal microbiota composition and subsequently bile acid and glucose metabolism. METHODS: In this single blinded randomized controlled trial, 20 male obese subjects with metabolic syndrome were randomized to 7 days of amoxicillin 500mg t.i.d. or 7 days of vancomycin 500mg t.i.d. At baseline and after 1 week of therapy, fecal microbiota composition (Human Intestinal Tract Chip phylogenetic microarray), fecal and plasma bile acid concentrations as well as insulin sensitivity (hyperinsulinemic euglycemic clamp using [6,6-2H2]-glucose tracer) were measured. RESULTS: Vancomycin reduced fecal microbial diversity with a decrease of gram-positive bacteria (mainly Firmicutes) and a compensatory increase in gram-negative bacteria (mainly Proteobacteria). Concomitantly, vancomycin decreased fecal secondary bile acids with a simultaneous postprandial increase in primary bile acids in plasma (p
    Hydrolysates of glycated and heat treated peanut 7S globulin (Ara h 1) modulate human gut microbiota proliferation, survival and adhesion
    Teodorowicz, M. ; Swiatecka, D. ; Savelkoul, H.F.J. ; Wichers, H.J. ; Kostyra, E. - \ 2014
    Journal of Applied Microbiology 116 (2014)2. - ISSN 1364-5072 - p. 424 - 434.
    maillard reaction-products - intestinal microbiota - in-vitro - proteins - health - allergen - differentiation - prevalence - chemistry - barrier
    Aims - Evaluation of an effect of glycation of Ara h 1 on proliferation and survival rate and adhesion of intestinal Enterococcus faecalis, Escherichia coli and Lactobacillus acidophilus. Methods and Results - Pure Ara h 1 heated at three different temperature conditions (G37°C, G60°C and C145°C) in the presence or absence of glucose was subjected to enzymatic hydrolysis. Impacts of Ara h 1 hydrolysates on the bacterial proliferation, survival rate and adhesion to Caco-2 cells in mono and heterogeneous cultures were studied with fluorescent techniques: DAPI, LIVE/DEAD staining and FISH. Examined hydrolysates hindered proliferation of E. coli and E. faecalis with simultaneous decrease in their survival. Maillard reaction (MR, glycation) of Ara h 1 did not alter the effect of hydrolysates on bacterial proliferation rate. Hydrolysates modified at 60°C and 145°C with glucose altered the profile of immobilized bacteria, mostly by lowering the number of adhering E. coli and promoting the adhesion of bacteria from genera Lactobacillus and Enterococcus. Conclusions - Ara h1 hydrolysates processed in various ways demonstrated their strong modulatory effect on bacterial proliferation, survival rate and adhesion. Significance and Impact of Study - Reducing the adhesion of opportunistic bacteria by hydrolysates of Ara h 1 glycated at 60°C and 145°C, together with modulation of immobilization of beneficial lactobacilli and enterococci, may be of relevance in terms of the physiological status of the intestinal barrier
    Metaproteomics of our microbiome - Developing insight in function and activity in man and model systems
    Kolmeder, C. ; Vos, W.M. de - \ 2014
    Journal of Proteomics 97 (2014). - ISSN 1874-3919 - p. 3 - 16.
    3-dimensional peptide fractionation - gastrointestinal-tract microbiota - tandem mass-spectrometry - human gut microbiome - in-vitro model - escherichia-coli - environmental proteomics - intestinal microbiota - community structure - effective recovery
    We are all colonized by a large microbiome, a complex set of microbes that have intimate associations with us. Culture-based approaches have provided insights in the complexity of the microbial communities living on surfaces inside and outside the body. However, the application of high-throughput sequencing technologies has identified large numbers of community members at both the phylogenetic and the (meta-)genome level. The latter allowed defining a reference set of several millions of mainly bacterial genes and provided the basis for developing approaches to target the activity and function of the human microbiome with proteomic techniques. Moreover, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometers have promoted the field of metaproteomics, the study of the collective proteome of microbial communities. We here review the approaches that have been developed to study the human metaproteomes, focusing on intestinal tract and body fluids. Moreover, we complement these by considering metaproteomic studies in mouse and other model systems offering the option to study single species or simple consortia. Finally, we discuss present and future avenues that may be used to advance the application of metaproteomic approaches to further improve our understanding of the microbes inside and around our body. This article is part of a Special Issue entitled: Trends in Microbial Proteomics
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