Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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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.
Matrix-derived combination effects influencing absorption, distribution, metabolism and excretion (ADME) of food-borne toxic compounds: implications for risk assessment
Rietjens, I. ; Tyrakowska, B. ; Berg, S.J.P.L. van den; Soffers, A.E.M.F. ; Punt, A. - \ 2015
Toxicology Research 4 (2015). - ISSN 2045-452X - p. 23 - 35.
st-johns-wort - dna adduct formation - polycyclic aromatic-hydrocarbons - in-vitro - aflatoxin b-1 - oral bioavailability - gastrointestinal-tract - estragole bioactivation - efflux proteins - tea polyphenols
Absorption, distribution, metabolism and excretion (ADME) of food-borne toxic compounds may be influenced by other compounds or constituents present in the food. The present review presents an overview of evidence currently available on food matrix-derived combination effects influencing the ADME characteristics of food-borne toxic compounds and the possible implications for risk assessment. The results obtained indicate that interactions may occur at all levels of ADME and that the interactions may decrease but also increase the bioavailability and/or toxicity of the compounds of interest. The overview also illustrates that food matrix-derived combination effects should be considered on a case-by-case basis, taking into account especially the mode of action underlying the interactions and the dose dependency of the effects. Especially food matrix-derived combination effects that proceed by a reversible mode of action, such as for example binding to biotransformation enzymes or transport proteins, may be detected at concentrations used in in vitro assays and at dose levels used in animal bioassays but may be absent at dose levels representing realistic human intake. It is concluded that although food matrix-derived combination effects may exist, their detection in in vitro assays or in animal bioassays at high dose levels may not improve risk assessment practice because interactions observed may not be maintained at low realistic levels of intake. Insight in the mode of action underlying the interactions combined with physiologically based kinetic (PBK) modelling may prove a way to obtain better insight in whether interactions detected at high dose levels will still be relevant at more realistic lower intake levels, and thus to what extent these effects should be taken into account in the risk assessment for human exposure
Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines
Schokker, D. ; Veninga, G. ; Vastenhouw, S.A. ; Bossers, A. ; Bree, F.M. de; Kaal-Lansbergen, L.M.T.E. ; Rebel, J.M.J. ; Smits, M.A. - \ 2015
BMC Genomics 16 (2015). - ISSN 1471-2164
salmonella-enteritidis colonization - innate immune responsiveness - pro-inflammatory cytokine - barrier function - gastrointestinal-tract - epithelial-cells - host genotype - double-blind - chickens - resistance
Host genetic makeup plays a role in early gut microbial colonization and immune programming. Interactions between gut microbiota and host cells of the mucosal layer are of paramount importance for a proper development of host defence mechanisms. For different livestock species, it has already been shown that particular genotypes have increased susceptibilities towards disease causing pathogens. The objective of this study was to investigate the impact of genotypic variation on both early microbial colonization of the gut and functional development of intestinal tissue. From two genetically diverse chicken lines intestinal content samples were taken for microbiota analyses and intestinal tissue samples were extracted for gene expression analyses, both at three subsequent time-points (days 0, 4, and 16).
Early Changes in Microbial Colonization Selectively Modulate Intestinal Enzymes, but Not Inducible Heat Shock Proteins in Young Adult Swine
Arnal, M.E. ; Zhang, J. ; Messori, S. ; Bosi, P. ; Smidt, H. ; Lallès, J.P. - \ 2014
PLoS One 9 (2014)5. - ISSN 1932-6203 - 14 p.
alkaline-phosphatase - epithelial-cells - gut microbiota - gastrointestinal-tract - gene-expression - messenger-rna - piglets - growth - diet - rat
Metabolic diseases and obesity are developing worldwide in a context of plethoric intake of high energy diets. The intestine may play a pivotal role due to diet-induced alterations in microbiota composition and increased permeability to bacterial lipopolysaccharide inducing metabolic inflammation. Early programming of metabolic disorders appearing in later life is also suspected, but data on the intestine are lacking. Therefore, we hypothesized that early disturbances in microbial colonization have short- and long-lasting consequences on selected intestinal components including key digestive enzymes and protective inducible heat shock proteins (HSP). The hypothesis was tested in swine offspring born to control mothers (n = 12) or mothers treated with the antibiotic amoxicillin around parturition (n = 11), and slaughtered serially at 14, 28 and 42 days of age to assess short-term effects. To evaluate long-term consequences, young adult offspring from the same litters were offered a normal or a fat-enriched diet for 4 weeks between 140 and 169 days of age and were then slaughtered. Amoxicillin treatment transiently modified both mother and offspring microbiota. This was associated with early but transient reduction in ileal alkaline phosphatase, HSP70 (but not HSP27) and crypt depth, suggesting a milder or delayed intestinal response to bacteria in offspring born to antibiotic-treated mothers. More importantly, we disclosed long-term consequences of this treatment on jejunal alkaline phosphatase (reduced) and jejunal and ileal dipeptidylpeptidase IV (increased and decreased, respectively) of offspring born to antibiotic-treated dams. Significant interactions between early antibiotic treatment and later diet were observed for jejunal alkaline phosphatase and sucrase. By contrast, inducible HSPs were not affected. In conclusion, our data suggest that early changes in bacterial colonization not only modulate intestinal architecture and function transiently, but also exert site- and sometimes diet-specific long-term effects on key components of intestinal homeostasis.
Effects of acid-extrusion on the degradability of maize distillers dried grain with solubles in pigs
Vries, S. de; Pustjens, A.M. ; Rooijen, C. van; Kabel, M.A. ; Hendriks, W.H. ; Gerrits, W.J.J. - \ 2014
Journal of Animal Science 92 (2014)12. - ISSN 0021-8812 - p. 5496 - 5506.
dietary fiber - growing pigs - amino-acid - reactive lysine - nonstarch polysaccharides - nutritional implications - gastrointestinal-tract - ethanol-production - large-intestine - wheat bran
Commonly used feed processing technologies are not sufficient to affect recalcitrant non-starch polysaccharides (NSP) such as arabinoxylans present in maize distillers dried grain with solubles (DDGS). Instead, hydrothermal treatments combined with acid catalysts might be more effective to modify these NSP. The objective of this experiment was to investigate the effects of hydrothermal maleic acid treatment (acid-extrusion) on the degradability of maize DDGS in growing pigs. It was hypothesized that acid-extrusion modifies DDGS cell wall architecture and, thereby, increases fermentability of NSP. Two diets, containing either 40% (wt/wt) unprocessed or acid-extruded DDGS, were restrictedly fed to groups of gilts (n = 11, with 4 pigs per group; initial mean BW: 20.8 ± 0.2 kg) for 18 d and performance and digestibility were analyzed. Acid-extrusion tended to decrease apparent ileal digestibility (AID) of CP (~3 percentage units, P = 0.063) and starch (~1 percentage unit, P = 0.096). Apparent digestibility of CP and starch measured at the mid colon (2 percentage units, P = 0.030 for CP and 0.3 percentage units, P <0.01 for starch) and total tract (ATTD; 3 percentage units, P <0.01 for CP and 0.2 percentage units, P = 0.024 for starch) were lower for the acid-extruded diet compared with the control diet. Hindgut disappearance was, however, not different between diets indicating that reduced CP and starch digestibility were mainly due to decreased AID. Acid-extrusion tended to increase AID of NSP (6 percentage units, P = 0.092) and increased digestibility of NSP measured at the mid colon (6 percentage units, P <0.01), whereas, hindgut disappearance and ATTD of NSP did not differ between diets. Greater NSP digestibility was mainly due to greater digestibility of arabinosyl, xylosyl, and glucosyl residues, indicating that both arabinoxylan and cellulose degradability were affected by acid-extrusion. In conclusion, these results show that acid-extrusion did not improve degradation of DDGS for growing pigs. Although acid-extrusion seemed to facilitate more rapid degradation of NSP and shifted fermentation to more proximal gastrointestinal segments, total extent of NSP degradation was not affected. More than 35% of the NSP from DDGS remained undegraded, independent of technological processing. Enzyme technologies that specifically target ester-linked acetyl, feroloyl, or coumaroyl groups were identified to be of interest for future research.
Evaluation of free water and water activity measurements as functional alternatives to total moisture content in broiler excreta and litter samples
Hoeven-Hangoor, E. van der; Rademaker, C. ; Paton, N.D. ; Verstegen, M.W.A. ; Hendriks, W.H. - \ 2014
Poultry Science 93 (2014)7. - ISSN 0032-5791 - p. 1782 - 1792.
sugar-beet pulp - gastrointestinal-tract - oat hulls - nonstarch polysaccharides - growth-performance - poultry houses - low-viscosity - chickens - ammonia - diets
Litter moisture contents vary greatly between and within practical poultry barns. The current experiment was designed to measure the effects of 8 different dietary characteristics on litter and excreta moisture content. Additionally, free water content and water activity of the excreta and litter were evaluated as additional quality measures. The dietary treatments consisted of nonstarch polysaccharide content (NSP; corn vs. wheat), particle size of insoluble fiber (coarse vs. finely ground oat hulls), viscosity of a nonfermentable fiber (low- and high-viscosity carboxymethyl cellulose), inclusion of a clay mineral (sepiolite), and inclusion of a laxative electrolyte (MgSO4). The 8 treatments were randomly assigned to cages within blocks, resulting in 12 replicates per treatment with 6 birds per replicate. Limited effects of the dietary treatments were noted on excreta and litter water activity, and indications were observed that this measurement is limited in high-moisture samples. Increasing dietary NSP content by feeding a corn-based diet (low NSP) compared with a wheat-based diet (high NSP) increased water intake, excreta moisture and free water, and litter moisture content. Adding insoluble fibers to the wheat-based diet reduced excreta and litter moisture content, as well as litter water activity. Fine grinding of the oat hulls diminished the effect on litter moisture and water activity. However, excreta moisture and free water content were similar when fed finely or coarsely ground oat hulls. The effects of changing viscosity and adding a clay mineral or laxative deviated from results observed in previous studies. Findings of the current experiment indicate a potential for excreta free water measurement as an additional parameter to assess excreta quality besides total moisture. The exact implication of this parameter warrants further investigation.
Stable isotope-labelled feed nutrients to assess nutrient-specific feed passage kinetics in ruminants
Warner, D. ; Dijkstra, J. ; Hendriks, W.H. ; Pellikaan, W.F. - \ 2014
Journal of the Science of Food and Agriculture 94 (2014)5. - ISSN 0022-5142 - p. 819 - 824.
functional specific-gravity - small-particle kinetics - dairy-cows - grass silages - gastrointestinal-tract - mechanistic model - digestive-tract - milk-production - organic-matter - stem fractions
Knowledge of digesta passage kinetics in ruminants is essential to predict nutrient supply to the animal in relation to optimal animal performance, environmental pollution and animal health. Fractional passage rates (FPR) of feed are widely used in modern feed evaluation systems and mechanistic rumen models, but data on nutrient-specific FPR are scarce. Such models generally rely on conventional externalmarker techniques, which do not always describe digesta passage kinetics in a satisfactorymanner.Heretheuse of stable isotope-labelled dietary nutrients as apromising novel tool to assess nutrient-specific passage kinetics is discussed. Some major limitations of this technique include a potential marker migration, a poor isotope distribution in the labelled feed and a differential disappearance rate of isotopes upon microbial fermentation in non-steady state conditions. Such limitations can often be circumvented by using intrinsically stable isotope-labelled plant material. Data are limited but indicate that external particulate markers overestimate rumen FPR of plant fibre compared with the internal stable isotope markers. Stable isotopes undergo the same digestive mechanism as the labelled feed components and are thus of particular interest to specifically measure passage kinetics of digestible dietary nutrients.
In vitro selection and characterization of putative probiotics isolated from the gut of Acipenser baerii (Brandt, 1869)
Geraylou, Z. ; Vanhove, M.P.M. ; Souffreau, C. ; Rurangwa, E. ; Buyse, J. ; Ollevier, F. - \ 2014
Aquaculture Research 45 (2014)2. - ISSN 1355-557X - p. 341 - 352.
lactic-acid bacteria - gastrointestinal-tract - fish pathogens - intestinal microbiota - growth-performance - aquaculture - marine - lactobacillus - prevention - tolerance
To select and characterize potential probiotic bacteria from the gut microbiota of Siberian sturgeon (Acipenser baerii), 129 strains isolated from the hindgut were screened for antagonistic activity against five fish pathogens. Ten isolates showed antagonism towards three or more pathogens. Nine of these isolates were Gram-positive, belonging to Lactococcus (seven) and Bacillus (two), and a single strain belonging to the Gram-negative Citrobacter. These inhibitory isolates were identified using genetic, phentotypic and biochemical traits, and further characterized by in vitro tests assessing the adhesion and growth in mucus and resistance to gastric and intestinal fluids. The candidate probiotics were determined to be non-pathogenic through an in vivo study. Based on these assays, Lactococcus lactis ssp. lactis STG45 and STG81 showed the broadest inhibitory potential, a high viability in simulated gastrointestinal juice and the highest adhesion capacity to mucus. They were therefore selected as the most promising candidate probiotics. This is the first study screening probiotics among the gut microflora of Siberian sturgeon.
Microbiome Analysis of Stool Samples from African Americans with Colon Polyps
Brim, H. ; Yooseph, S. ; Zoetendal, E.G. ; Lee, E. ; Torralbo, M. ; Laiyemo, A.O. ; Shokrani, B. ; Nelson, K. ; Ashktorab, H. - \ 2013
PLoS One 8 (2013)12. - ISSN 1932-6203
bacteroides-fragilis enterotoxin - human gut microbiome - colorectal-cancer - gastrointestinal-tract - ribosomal-rna - flora - bacteria - prevalence - diversity - carcinoma
Background: Colonic polyps are common tumors occurring in similar to 50% of Western populations with similar to 10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation. Aim: To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions. Materials & Methods: We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing. Results: Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes. Conclusion: This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size.
Faecalibacterium prausnitzii and human intestinal health
Miquel, S. ; Martin, R. ; Rossi, O. ; Bermudez-Humaran, L.G. ; Chatel, J.M. ; Sokol, H. ; Thomas, M. ; Wells, J.M. ; Langella, P. - \ 2013
Current Opinion in Microbiology 16 (2013)3. - ISSN 1369-5274 - p. 255 - 261.
16s ribosomal-rna - irritable-bowel-syndrome - mucosa-associated microbiota - butyrate-producing bacteria - active crohns-disease - gut microbiota - ulcerative-colitis - fecal microbiota - fusobacterium-prausnitzii - gastrointestinal-tract
Faecalibacterium prausnitzii is the most abundant bacterium in the human intestinal microbiota of healthy adults, representing more than 5% of the total bacterial population. Over the past five years, an increasing number of studies have clearly described the importance of this highly metabolically active commensal bacterium as a component of the healthy human microbiota. Changes in the abundance of F. prausnitzii have been linked to dysbiosis in several human disorders. Administration of F. prausnitzii strain A2-165 and its culture supernatant have been shown to protect against 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis in mice. Here, we discuss the role of F. prausnitzii in balancing immunity in the intestine and the mechanisms involved.
Alterations in mucosal neuropeptides in patients with irritable bowel syndrome and ulcerative colitis in remission: A role in pain symptom generation?
Keszthelyi, D. ; Troost, F.J. ; Jonkers, D.M. ; Helyes, Z. ; Hamer, H.M. ; Ludidi, S. ; Vanhoutvin, S. ; Venema, K. ; Dekker, J. ; Szolcsanyi, J. ; Masclee, A.A. - \ 2013
European Journal of Pain 17 (2013)9. - ISSN 1090-3801 - p. 1299 - 1306.
vanilloid receptor vr1 - gastrointestinal-tract - abdominal-pain - substance-p - axonal-transport - trpv1 receptor - messenger-rna - rectal mucosa - expression - disease
Background Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by chronic abdominal pain. The transient receptor potential vanilloid 1 (TRPV1) channel, which is involved in visceral pain signalling, has been shown to be up-regulated in IBS. Activation of TRPV1 leads to the release of neuropeptides, such as somatostatin and substance P (SP). We hypothesized that increased pain perception in IBS could be explained by increased transcription in TRPV1 and/or altered levels of neuropeptides. We therefore assessed the transcription of TRPV1 and the mucosal concentration of somatostatin and SP in IBS in comparison to healthy volunteers and patients with ulcerative colitis (UC) in remission as disease controls, and to ascertain their relationship to pain symptoms. Method Sigmoid colonic mucosal samples were collected from 12 patients with IBS, 34 patients with UC in remission and 9 healthy volunteers, in which groups TRPV1 mRNA levels were determined using quantitative polymerase chain reaction and neuropeptide concentrations by radioimmunoassay. Pain symptom intensity was determined by questionnaires. Results Transcription of TRPV1 as well as the concentration of neuropeptides were significantly higher in IBS, but only the former correlated with pain symptom severity. Conclusion Increased transcription of TRPV1 may provide a possible explanation for pain generation in IBS. While the neuropeptides SP and somatostatin were both found to be increased in IBS, these changes are not sufficient to explain pain generation. Pain generation in IBS is probably explained by a complex redundancy in the regulation of local nociceptive mechanisms, which remains a subject of intensive investigation.
Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract
Bokhorst-van de Veen, H. van; Smelt, M.J. ; Wels, M. ; Hijum, S.A.F.T. van; Vos, P. de; Kleerebezem, M. ; Bron, P.A. - \ 2013
Biotechnology Journal 8 (2013)8. - ISSN 1860-6768 - p. 895 - 904.
gastrointestinal-tract - rhamnosus gg - human flora - mice - host - strains - protein - genome - genes - identification
Probiotic bacteria harbor effector molecules that confer health benefits, but also adaptation factors that enable them to persist in the gastrointestinal tract of the consumer. To study these adaptation factors, an antibiotic-resistant derivative of the probiotic model organism Lactobacillus plantarum WCFS1 was repeatedly exposed to the mouse digestive tract by three consecutive rounds of (re)feeding of the longest persisting colonies. This exposure to the murine intestine allowed the isolation of intestine-adapted derivatives of the original strain that displayed prolonged digestive tract residence time. Re-sequencing of the genomes of these adapted derivatives revealed single nucleotide polymorphisms as well as a single nucleotide insertion in comparison with the genome of the original WCFS1 strain. Detailed in silico analysis of the identified genomic modifications pinpointed that alterations in the coding regions of genes encoding cell envelope associated functions and energy metabolism appeared to be beneficial for the gastrointestinal tract survival of L. plantarum WCFS1. This work demonstrates the feasibility of experimental evolution for the enhancement of the gastrointestinal residence time of probiotic strains, while full-genome re-sequencing of the adapted isolates provided clues towards the bacterial functions involved. Enhanced gastrointestinal residence is industrially relevant because it enhances the efficacy of the delivery of viable probiotics in situ.
Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG
Douillard, F.P. ; Ribbera, A. ; Kant, R. ; Pietilä, T.E. ; Järvinen, H.M. ; Messing, M. ; Randazzo, C.L. ; Paulin, L. ; Laine, P.K. ; Ritari, J. ; Caggia, C. ; Lähteinen, T. ; Brouns, S.J.J. ; Satokari, R.M. ; Ossowski, I. von; Reunanen, J. ; Palva, A. ; Vos, W.M. de - \ 2013
Plos Genetics 9 (2013)8. - ISSN 1553-7404
lactic-acid bacteria - intestinal epithelial-cells - placebo-controlled trial - streptococcus-thermophilus - species identification - salmonella-typhimurium - gastrointestinal-tract - adaptive immunity - atopic disease - in-vitro
Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects
Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation
Bokhorst-van de Veen, H. van; Bongers, R.S. ; Wels, M. ; Bron, P.A. ; Kleerebezem, M. - \ 2013
Microbial Cell Factories 12 (2013)1. - ISSN 1475-2859 - 15 p.
gram-positive bacteria - heat-shock response - lactic-acid bacteria - bacillus-subtilis - listeria-monocytogenes - gastrointestinal-tract - low gc - streptococcus-pneumoniae - comparative genomics - helicobacter-pylori
Background - To cope with environmental challenges bacteria possess sophisticated defense mechanisms that involve stress-induced adaptive responses. The canonical stress regulators CtsR and HrcA play a central role in the adaptations to a plethora of stresses in a variety of organisms. Here, we determined the CtsR and HrcA regulons of the lactic acid bacterium Lactobacillus plantarum WCFS1 grown under reference (28°C) and elevated (40°C) temperatures, using ctsR, hrcA, and ctsR-hrcA deletion mutants. Results - While the maximum specific growth rates of the mutants and the parental strain were similar at both temperatures (0.33¿±¿0.02 h-1 and 0.34¿±¿0.03 h-1, respectively), DNA microarray analyses revealed that the CtsR or HrcA deficient strains displayed altered transcription patterns of genes encoding functions involved in transport and binding of sugars and other compounds, primary metabolism, transcription regulation, capsular polysaccharide biosynthesis, as well as fatty acid metabolism. These transcriptional signatures enabled the refinement of the gene repertoire that is directly or indirectly controlled by CtsR and HrcA of L. plantarum. Deletion of both regulators, elicited transcriptional changes of a large variety of additional genes in a temperature-dependent manner, including genes encoding functions involved in cell-envelope remodeling. Moreover, phenotypic assays revealed that both transcription regulators contribute to regulation of resistance to hydrogen peroxide stress. The integration of these results allowed the reconstruction of CtsR and HrcA regulatory networks in L. plantarum, highlighting the significant intertwinement of class I and III stress regulons. Conclusions - Taken together, our results enabled the refinement of the CtsR and HrcA regulatory networks in L. plantarum, illustrating the complex nature of adaptive stress responses in this bacterium
Resistant Starch Induces Catabolic but Suppresses Immune and Cell Division Pathways and Changes the Microbiome in Proximal Colon of Male Pigs
Haenen, D. ; Souza Da Silva, C. ; Zhang, J. ; Koopmans, S.J. ; Bosch, G. ; Vervoort, J.J.M. ; Gerrits, W.J.J. ; Kemp, B. ; Smidt, H. ; Müller, M.R. ; Hooiveld, G.J.E.J. - \ 2013
The Journal of Nutrition 143 (2013)12. - ISSN 0022-3166 - p. 1889 - 1898.
chain fatty-acids - inflammatory-bowel-disease - endoplasmic-reticulum stress - butyrate-producing bacteria - activated receptor-gamma - human large-intestine - gene-expression - gastrointestinal-tract - transcription factors - gut microbiota
Consumption of resistant starch (RS) has been associated with various intestinal health benefits, but knowledge on its effects on global gene expression in the colon is limited. The main objective of the current study was to identify genes affected by RS in the proximal colon to infer which biologic pathways were modulated. Ten 17-wk-old male pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsy samples and luminal content, were fed a digestible starch (DS) diet or a diet high in RS (34%) for 2 consecutive periods of 14 d in a crossover design. Analysis of the colonic transcriptome profiles revealed that, upon RS feeding, oxidative metabolic pathways, such as the tricarboxylic acid cycle and ß-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor peroxisome proliferator-activated receptor ¿ (PPARG) was identified as a potential key upstream regulator. RS significantly (P <0.05) increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdenii, and reduced the abundance of potentially pathogenic members of the genus Leptospira and the phylum Proteobacteria. Concentrations in carotid plasma of the 3 main short-chain fatty acids acetate, propionate, and butyrate were significantly higher with RS consumption compared with DS consumption. Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet.
Dietary electrolyte balance affects the nutrient digestibility and maintenance energy expenditure of Nile tilapia
Subramanian, S. ; Geurden, I. ; Orozco, Z.G.A. ; Kaushik, S.J. ; Verreth, J.A.J. ; Schrama, J.W. - \ 2013
British Journal of Nutrition 110 (2013). - ISSN 0007-1145 - p. 1948 - 1957.
acid-base-balance - cation-anion difference - water rainbow-trout - juvenile african catfish - clarias-gariepinus burchell - fresh-water - alkaline tide - oreochromis-niloticus - gastrointestinal-tract - oncorhynchus-mykiss
Acid–base disturbances caused by environmental factors and physiological events including feeding have been well documented in several fish species, but little is known about the impact of dietary electrolyte balance (dEB). In the present study, we investigated the effect of feeding diets differing in dEB ( - 100, 200, 500 or 800 mEq/kg diet) on the growth, nutrient digestibility and energy balance of Nile tilapia. After 5 weeks on the test diet, the growth of the fish was linearly affected by the dEB levels (P<0·001), with the lowest growth being observed in the fish fed the 800 dEB diet. The apparent digestibility coefficient (ADC) of fat was unaffected by dEB, whereas the ADC of DM and protein were curvilinearly related to the dEB levels, being lowest and highest in the 200 and 800 dEB diets, respectively. Stomach chyme pH at 3 h after feeding was linearly related to the dEB levels (P<0·05). At the same time, blood pH of the heart (P<0·05) and caudal vein (P<0·01) was curvilinearly related to the dEB levels, suggesting the influence of dEB on postprandial metabolic alkalosis. Consequently, maintenance energy expenditure (MEm) was curvilinearly related to the dEB levels (P<0·001), being 54 % higher in the 800 dEB group (88 kJ/kg0·8 per d) than in the 200 dEB group (57 kJ/kg0·8 per d). These results suggest that varying dEB levels in a diet have both positive and negative effects on fish. On the one hand, they improve nutrient digestibility; on the other hand, they challenge the acid–base homeostasis (pH) of fish, causing an increase in MEm, and thereby reduce the energy required for growth.
Large intestinal fermentation capacity of fattening pigs on organic farms as measured in vitro using contrasting substrates
Sappok, M.A. ; Pellikaan, W.F. ; Verstegen, M.W.A. ; Bosch, G. ; Sundrum, A. ; Hendriks, W.H. - \ 2013
Journal of the Science of Food and Agriculture 93 (2013)10. - ISSN 0022-5142 - p. 2402 - 2409.
gas-production kinetics - dietary fiber - gastrointestinal-tract - growing pigs - stomached animals - digestibility - temperature - microbiota - digestion - feces
Background In accordance with the EU regulations, organic farms require pigs to be fed diets high in fibre, which may impact on the pigs' large intestinal fermentation capacity. The ability of pigs to ferment non-starch polysaccharides (NSP) depends on characteristics of the dietary NSP source and microbes present in the large intestine of pigs. Little information exists on the fibre fermentation capacity of organically raised pigs. The aim of this study was to determine the variation in fibre fermentation capacity of fattening pigs within and between organic farms using an in vitro batch culture method and three contrasting substrates: oligofructose, soy pectin and cellulose. Results Pigs from different organic farms showed varying fermentation capacities as assessed by gas production, kinetics and fermentation end-products formed (P¿
Interpreting experimental data on egg production - applications of dynamic differential equations
France, J. ; Lopez, S. ; Kebreab, E. ; Dijkstra, J. - \ 2013
Poultry Science 92 (2013)9. - ISSN 0032-5791 - p. 2498 - 2508.
drosophila-melanogaster - gastrointestinal-tract - quantitative genetics - mathematical-models - phosphorus - calcium - absorption - fertility - algorithm
This contribution focuses on applying mathematical models based on systems of ordinary first-order differential equations to synthesize and interpret data from egg production experiments. Models based on linear systems of differential equations are contrasted with those based on nonlinear systems. Regression equations arising from analytical solutions to linear compartmental schemes are considered as candidate functions for describing egg production curves, together with aspects of parameter estimation. Extant candidate functions are reviewed, a role for growth functions such as the Gompertz equation suggested, and a function based on a simple new model outlined. Structurally, the new model comprises a single pool with an inflow and an outflow. Compartmental simulation models based on nonlinear systems of differential equations, and thus requiring numerical solution, are next discussed, and aspects of parameter estimation considered. This type of model is illustrated in relation to development and evaluation of a dynamic model of calcium and phosphorus flows in layers. The model consists of 8 state variables representing calcium and phosphorus pools in the crop, stomachs, plasma, and bone. The flow equations are described by Michaelis-Menten or mass action forms. Experiments that measure Ca and P uptake in layers fed different calcium concentrations during shell-forming days are used to evaluate the model. In addition to providing a useful management tool, such a simulation model also provides a means to evaluate feeding strategies aimed at reducing excretion of potential pollutants in poultry manure to the environment.
Adhesion and Nanomechanics of Pili from the Probiotic Lactobacillus rhamnosus GG
Tripathi, P. ; Beaussart, A. ; Alsteens, D. ; Dupres, V. ; Claes, I. ; Ossowski, I. von; Vos, W.M. de; Palva, A. ; Lebeer, S. ; Vanderleyden, J. ; Dufrene, Y.F. - \ 2013
ACS Nano 7 (2013)4. - ISSN 1936-0851 - p. 3685 - 3697.
atomic-force-microscopy - coli p-pili - functional-analysis - escherichia-coli - stabilizing isopeptide - streptococcus-pyogenes - gastrointestinal-tract - mechanical force - binding-protein - antigen-i/ii
Knowledge of the mechanisms by which bacterial pili adhere to host cells and withstand external forces is critical to our understanding of their functional roles and offers exciting avenues in biomedicine for controlling the adhesion of bacterial pathogens and probiotics. While much progress has been made in the nanoscale characterization of pili from Gram-negative bacteria, the adhesive and mechanical properties of Gram-positive bacterial pili remain largely unknown. Here, we use single-molecule atomic force microscopy to unravel the binding mechanism of pili from the probiotic Gram-positive bacterium Lactobacillus rhamnosus GG (LGG). First, we show that SpaC, the key adhesion protein of the LGG pilus, is a multifunctional adhesin with broad specificity. SpaC forms homophilic trans-interactions engaged in bacterial aggregation and specifically binds mucin and collagen, two major extracellular components of host epithelial layers. Homophilic and heterophilic interactions display similar binding strengths and dissociation rates. Next, pulling experiments on living bacteria demonstrate that LGG pili exhibit two unique mechanical responses, that is, zipper-like adhesion involving multiple SpaC molecules distributed along the pilus length and nanospring properties enabling pili to resist high force. These mechanical properties may represent a generic mechanism among Gram-positive bacterial pili for strengthening adhesion and withstanding shear stresses in the natural environment. The single-molecule experiments presented here may help us to design molecules capable of promoting or inhibiting bacterial-host interactions
Using recombinant Lactococci as an approach to dissect the immunomodulating capacity of surface piliation in probiotic Lactobacillus rhamnosus GG
Ossowski, I. von; Pietilä, T.E. ; Rintahaka, J. ; Nummenmaa, E. ; Mäkinen, V.M. ; Reunanen, J. ; Satokari, R.M. ; Vos, W.M. de; Palva, I. ; Palva, A. - \ 2013
PLoS One 8 (2013)5. - ISSN 1932-6203
lactic-acid bacteria - intestinal epithelial-cells - functional-analysis - dendritic cells - gastrointestinal-tract - dependent mechanism - protein-production - oral consumption - adhesion - pili
Primarily arising from their well understood beneficial health effects, many lactobacilli strains are considered good candidates for use as probiotics in humans and animals. Lactobacillar probiosis can itself be best typified by the Lactobacillus rhamnosus GG strain, which, with its well-documented clinical benefits, has emerged as one of the most widely used probiotics in the food and health-supplement industries. Even so, many facets of its molecular mechanisms and limitations as a beneficial commensal bacterium still remain to be thoroughly explored and dissected. Because L. rhamnosus GG is one of only a few such strains exhibiting surface piliation (called SpaCBA), we sought to examine whether this particular type of cell-surface appendage has a discernible immunomodulating capacity and is able to trigger targeted responses in human immune-related cells. Thus, presented herein for this study, we recombinantly engineered Lactococcus lactis to produce native (and pilin-deleted) SpaCBA pili that were assembled in a structurally authentic form and anchored to the cell surface, and which had retained mucus-binding functionality. By using these recombinant lactococcal constructs, we were able to demonstrate that the SpaCBA pilus can be a contributory factor in the activation of Toll-like receptor 2-dependent signaling in HEK cells as well as in the modulation of pro- and anti-inflammatory cytokine (TNF-a, IL-6, IL-10, and IL-12) production in human monocyte-derived dendritic cells. From these data, we suggest that the recombinant-expressed and surface-anchored SpaCBA pilus, given its projected functioning in the gut environment, might be viewed as a new microbe-associated molecular pattern (MAMP)-like modulator of innate immunity. Accordingly, our study has brought some new insight to the molecular immunogenicity of the SpaCBA pilus, thus opening the way to a better understanding of its possible role in the multifaceted nature of L. rhamnosus GG probiosis within the human gut
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