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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Quantifying potential sources of surface water contamination with Campylobacter jejuni and Campylobacter coli
Mughini-Gras, Lapo ; Penny, Christian ; Ragimbeau, Catherine ; Schets, Franciska M. ; Blaak, Hetty ; Duim, Birgitta ; Wagenaar, Jaap A. ; Boer, Albert de; Cauchie, Henry-Michel ; Mossong, Joel ; Pelt, Wilfrid Van - \ 2016
Water Research 101 (2016). - ISSN 0043-1354 - p. 36 - 45.
campylobacter - surface water - water quality - pollution - water pollution - microbiology - wild birds - poultry - campylobacter jejuni - campylobacter coli - netherlands - luxembourg - oppervlaktewater - waterkwaliteit - verontreiniging - waterverontreiniging - microbiologie - wilde vogels - pluimvee - nederland - luxemburg
Campylobacter is the most common causative agent of human bacterial gastroenteritis and is frequently found in surface water, where it indicates recent contamination with animal faeces, sewage effluent, and agricultural run-off. The contribution of different animal reservoirs to surface water contamination with Campylobacter is largely unknown. In the Netherlands, the massive poultry culling to control the 2003 avian influenza epidemic coincided with a 44–50% reduction in human campylobacteriosis cases in the culling areas, suggesting substantial environment-mediated spread of poultry-borne Campylobacter. We inferred the origin of surface water Campylobacter jejuni and Campylobacter coli strains in Luxembourg and the Netherlands, as defined by multilocus sequence typing, by comparison to strains from poultry, pigs, ruminants, and wild birds, using the asymmetric island model for source attribution. Most Luxembourgish water strains were attributed to wild birds (61.0%), followed by poultry (18.8%), ruminants (15.9%), and pigs (4.3%); whereas the Dutch water strains were mainly attributed to poultry (51.7%), wild birds (37.3%), ruminants (9.8%), and pigs (1.2%). Attributions varied over seasons and surface water types, and geographical variation in the relative contribution of poultry correlated with the magnitude of poultry production at either the national or provincial level, suggesting that environmental dissemination of Campylobacter from poultry farms and slaughterhouses can be substantial in poultry-rich regions.
Thermococcus kodakarensis : the key to affordable biohydrogen production
Spaans, S.K. - \ 2016
University. Promotor(en): John van der Oost, co-promotor(en): Servé Kengen. - Wageningen : Wageningen University - ISBN 9789462577725 - 245 p.
thermococcus - thermococcus kodakarensis - hydrogen - bioenergy - canonical analysis - biosynthesis - nadph - archaea - microbiology - waterstof - bio-energie - canonische analyse - biosynthese - microbiologie
Substraatloos telen bemoeilijkt door gebrek aan kennis microbiologie : heeft de praktijk voldoende geduld?
Streminska, Marta ; Vermeulen, Tycho - \ 2016
horticulture - greenhouse horticulture - cropping systems - agricultural research - soilless culture - water - substrates - microbiology - water temperature - chrysanthemum - lettuces - ornamental herbaceous plants - summer flowers - vegetables - cut flowers - plant protection

De laatste jaren groeien de inzichten in het bodemleven, zowel bij de teelt in de grond als op substraat. Maar die kennis blijkt niet één op één bruikbaar bij een switch naar teelt op water. Telers van chrysant, sla, kruiden en zomerbloemen op water kampen met hardnekkige onbegrepen problemen. “Misschien heb je bij waterteelt wel heel andere nuttige micro-organismen nodig dan nu op de markt zijn.”

Microben maken mede de wijn : regionale verschillen in gistpopulaties beïnvloeden het aromaprofiel van wijn
Maanen, G. van; Vermeulen, T. - \ 2015
Bionieuws 2015 (2015)15. - ISSN 0924-7734 - p. 1 - 1.
wijnen - smaak - gisten - microbiologie - fermentatie - wijnbouw - wijngaarden - wines - taste - yeasts - microbiology - fermentation - viticulture - vineyards
Wijn dankt zijn karakter niet alleen aan lokale omstandigheden in klimaat, bodem en teelt, maar ook aan aanwezige gisten, claimen Nieuw-Zeelandse microbiologen.
Shrimp quality and safety management along the supply chain in Benin
Dabade, D.S. - \ 2015
University. Promotor(en): Marcel Zwietering; D.J. Hounhouigan, co-promotor(en): Heidy den Besten. - Wageningen : Wageningen University - ISBN 9789462574205 - 158
garnalen - penaeus - penaeus monodon - voedselkwaliteit - voedselveiligheid - bacteriëntelling - kwaliteitscontroles - kwaliteitszorg - benin - microbiologie - risicobeheersing - risicoanalyse - kwantitatieve methoden - shrimps - food quality - food safety - bacterial counting - quality controls - quality management - microbiology - risk management - risk analysis - quantitative methods

Abstract

This thesis focuses on quality and safety management of tropical shrimp (Penaeus spp.) using Benin (West Africa) as an example of a shrimp exporting country. The entire supply chain, from fishing areas (brackish waters) to shrimp processing plants, was investigated. The steps of the chain prior to shrimp processing at the freezer plants were critical for shrimp quality and safety because of prevailing temperature abuse and inappropriate hygienic conditions. Combining culture-dependent (plate counts) and culture independent (DGGE, clone libraries analysis) approaches, it was found that bacterial concentration in shrimps was higher than that of their surrounding water and sediment. Conversely, bacterial diversity was higher in water or sediment than in shrimps. At species level, distinct bacterial communities were associated with sediment, water or shrimp samples. Spoilage evaluation of shrimps showed that during storage at 0ºC, Pseudomonas spp. were dominant, whereas at 7ºC and 28ºC, H2S-producing bacteria were the dominant group of microorganisms. An empirical model predicting shrimp shelf-life as a function of constant storage temperature was developed. Isolates producing strong off-odor were identified by 16S rRNA sequencing as mainly lactic acid bacteria (LAB) and Enterobacteriaceae at 28ºC or 7ºC and Pseudomonas spp. and LAB (Carnobacterium maltaromaticum) at 0ºC. The fastest growing isolates namely, Pseudomonas psychrophila and C. maltaromaticum were selected for their spoilage activity and for modeling studies. P. psychrophila had a higher growth rate and a higher spoilage activity at 0 to 15ºC, while at 28ºC, C. maltaromaticum had a higher growth rate. Models predicting the growth of pseudomonads in shrimps as a function of temperature were constructed. These models were validated under dynamic storage temperatures simulating actual temperature fluctuation in the supply chain. Using different risk classification approaches, the main foodborne pathogen risks identified were Vibrio parahaemolyticus and Salmonella. The management of the risks posed by the main pathogens was addressed using different scenarios to meet the set food safety objectives. Based on quantitative and ecological studies, this thesis developed tools that can be used in decision-making regarding tropical shrimp quality and safety management.

Allemaal beestjes : hoe bacteriën ons gezond houden
Puylaert, P.G.B. ; Fuentes, S. ; Belzer, C. ; Vos, W.M. de - \ 2014
Nederland : Maven Publishing - ISBN 9789491845130 - 334
microbiologie - bacteriologie - bacteriën - mens - gezondheid - microbiology - bacteriology - bacteria - man - health
Dit boek gaat op safari langs de miljarden bacteriën van het menselijk lichaam. Op heldere wijze wordt beschreven hoe lichaam en micro-organismen vanaf de geboorte met elkaar samenwerken en hoezeer onze gezondheid van deze samenwerking afhangt. Het onderzoek op dit gebied bevindt zich in een stroomversnelling: er zijn opzienbarende wetenschappelijke ontdekkingen gedaan over hoe voeding, sport, medicijnen, leefomgeving en probiotica de gezondheid van ons microbioom beïnvloeden. Dit boek brengt deze nieuwe ontwikkelingen in beeld en vertaalt ze naar inzichten voor het dagelijks leven.
Discovery of inhibitors of bacterial histidine kinases
Velikova, N.R. - \ 2014
University. Promotor(en): Jerry Wells, co-promotor(en): A. Marina. - Wageningen : Wageningen University - ISBN 9789462571112 - 225
gastheer-pathogeen interacties - bacteriën - kinasen - histidine - geneesmiddelresistentie - antibiotica - microbiologie - host pathogen interactions - bacteria - kinases - drug resistance - antibiotics - microbiology
Discovery of Inhibitors of Bacterial Histidine Kinases Summary

The thesis is on novel antibacterial drug discovery (http://youtu.be/NRMWOGgeysM). Using structure-based and fragment-based drug discovery approach, we have identified small-molecule histidine-kinase inhibitors with antibacterial effect against multi-drug resistant strains, including clinical isolates of multi-drug resistant bacteria such as MRSA. Furthermore, we have shown broadening of the antibacterial spectrum and lowering the toxicity of the histidine-kinase inhibitors using nanoparticles. The results open up exciting possibilities for development of novel antibacterial(nano)medicines.

Microbial (per)chlorate reduction in hot subsurface environments
Liebensteiner, M. - \ 2014
University. Promotor(en): Fons Stams, co-promotor(en): Bart Lomans. - Wageningen : Wageningen University - ISBN 9789462571259 - 172
perchloraten - chloraten - reductie - microbiologie - micro-organismen - ondergrondse lagen - perchlorates - chlorates - reduction - microbiology - microorganisms - subsurface layers

The microbial reduction of chlorate and perchlorate has been known for long as a respiratory process of mesophilic bacteria that thrive in diverse environments such as soils, marine and freshwater sediments. Chlorate and perchlorate are found in nature deriving from anthropogenic and natural sources and can, in the absence of oxygen, be reduced by respective microorganisms to chloride coupled to energy conservation and growth. These classical chlorate- and perchlorate-reducing microorganisms employ enzymes that reduce perchlorate (or chlorate) to the intermediate chlorite, followed by the disproportionation of chlorite to chloride and dioxygen. The latter has been regarded as key reaction for complete (per)chlorate reduction, catalyzed by the enzyme chlorite dismutase, which forms oxygen under anaerobic conditions. This de novo produced oxygen is reduced by terminal oxidases in the metabolism of facultative anaerobic (per)chlorate-reducing microorganisms and can be used by oxygenases for the activation of recalcitrant substrates, as was shown earlier for hydrocarbons.

The potentially stimulating effect of chlorate and perchlorate on microorganisms indigenous to petroleum reservoirs was discussed, seeking new strategies for microbial enhanced oil recovery (based on subsurface growth stimulation and partial hydrocarbon degradation) and reservoir souring control (by inhibiting sulfate-reducing prokaryotes and diminishing sulfide formation).

This thesis reports the capability of hyperthermophilic and thermophilic prokaryotes that originate from subsurface environments to grow by the reduction of chlorate and/or perchlorate. In contrast to the classical metabolism of mesophilic (per)chlorate-reducing microorganisms this study demonstrated that a chlorite-disproportionating enzyme is commonly absent in (hyper)thermophilic (per)chlorate reducers. The absence of this enzyme that was previously defined as prerequisite for (per)chlorate reduction is overcome by the chemical reactivity of reduced sulfur compounds with chlorite generated. In the here more closely investigated hyperthermophilic archaea (Archaeoglobus fulgidus and Aeropyrum pernix) and thermophilic Firmicutes (Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP) chlorite is formed by the activity of molybdopterin oxidoreductases. The respective enzymes are remotely related to perchlorate reductases of mesophilic bacteria and nitrate reductases of the bacterial Nar-type. In contrast to classical bacterial Nar-type enzymes, above-mentioned enzymes seem to have their catalytic subunits outside of the cell. As a consequence the reduction of (per)chlorate forms chlorite extracellularly where it reacts with reduced sulfur species present in the medium/environment (e.g. sulfide), forming chloride anions and oxidized sulfur species (SxOyz-).

The hyperthermophilic archaeon Archaeoglobus fulgidus reduces these chemically formed sulfur species concomitantly to (per)chlorate reduction, which regenerates sulfide for the continuous reduction of (per)chlorate. This interaction of biotic and abiotic reactions during (per)chlorate reduction establishes an intraspecies “sulfur loop” that enables complete reduction of perchlorate to chloride.

Whereas A. pernix also relies on the chemical reactivity of chlorite with thiosulfate, this archaeon does not employ systems for regenerating the reducing agents biologically; which is reflected by the accumulation of sulfate during perchlorate reduction. The Crenarchaeon A. pernix, formerly known as a strictly aerobic microorganism, expands the trait of microbial (per)chlorate reduction up to 100°C.

In addition to the intraspecies “sulfur loop” of A. fulgidus, there were indications that the reduction of perchlorate may also proceed syntrophically, as indicated by a thermophilic bacterial consortium. In the respective culture, it seems that one microorganism reduces perchlorate, forming chlorite, which is chemically reduced by sulfide to chloride anions and oxidized sulfur compounds. Another group of microorganisms uses the respective sulfur compounds as electron acceptors and regenerates sulfide. Sulfur (of different redox states) depicts the mediating agent in this interspecies “sulfur loop”, but may possibly be substituted in nature by other compounds such as ferrous/ferric iron.

Here presented (per)chlorate reduction sensu lato, which lacks the action of a chlorite-disproportionating enzyme may be widely spread among prokaryotes. For example enzymes closely resembling the designated (per)chlorate-reducing enzyme in Archaeoglobus fulgidus are also found in other strictly anaerobic thermophiles, of which C. hydrogenoformans and M. glycerini NMP were already confirmed to grow by the reduction of (per)chlorate as well.

The substrate ambiguity of particular periplasmic DMSO enzymes may enable a broader group of microorganisms of (per)chlorate reduction sensu lato, in case sulfide is present in the environment. A broadened substrate spectrum of respective enzymes (beyond their canonical function) may possibly have had evolutionary advantages. Chlorine oxyanions are naturally formed and have been introduced on Earth for ages already. The reduction of (per)chlorate and formation of chlorite in ancient anaerobic microorganisms may even have contributed to the evolution of proteins adapted to oxidizing conditions on early Earth and preceded the evolution of oxygenic photosynthesis.

It is shown that subsurface-inhabiting (hyper)thermophiles are able to grow by the reduction of (per)chlorate, which is also of interest for applications in the field of oil recovery. The finding that (per)chlorate reduction is interfering with the sulfur metabolism of a major contributor to reservoir souring in hot oil fields, A. fulgidus, draws promising scenarios for future attempts in developing novel souring control strategies.

(Per)chlorate reduction by A. fulgidus was also coupled to the oxidation of butyrate, a volatile fatty acid commonly present in petroleum reservoirs. For sustainable applications in the oil recovery business, it is desirable to rely, as little as possible, on external substrates. In this respect the fact that A. fulgidus couples (per)chlorate reduction to the oxidation of butyrate is advantageous. Possibly the microorganism can also degrade long-chain alkanes and alkenes coupled to (per)chlorate reduction, a feature that was shown earlier coupled to sulfate reduction.

All together a shift of A. fulgidus from sulfate reduction to (per)chlorate reduction in oil fields would not only diminish souring, but maintain/stimulate in-situ growth of the microorganism (based on intrinsic carbon sources) which has additionally advantageous effects for improved sweeping efficiencies during water flooding.

Ecologie van bodemmicro-organismen: de basis voor een gezonde bodem
Boer, W. de - \ 2014
Gewasbescherming 45 (2014)1. - ISSN 0166-6495 - p. 4 - 6.
bodemecologie - terrestrische ecosystemen - microbiologie - openbare redes - gewasbescherming - bodemweerbaarheid - bodembiologie - soil ecology - terrestrial ecosystems - microbiology - public speeches - plant protection - soil suppressiveness - soil biology
Dit is de titel van de inaugurele rede die op 14 februari 2013 heb gehouden in de aula van Wageningen University bij de aanvaarding van het ambt als buitengewoon hoogleraar Microbiële Bodemecologie. Onlangs is de gedrukte versie verschenen. In de rede wordt ingegaan op het belang van interacties tussen bodemmicro-organismen voor het functioneren van het bodemecosysteem en met name op de natuurlijk regulerende werking die microbiële interacties kunnen hebben op ziekteverwekkers in de bodem.
Development of gut microbiota in pigs and the effect of diet, antibiotics and other environmental factors
Zhang, J. - \ 2014
University. Promotor(en): Hauke Smidt; Willem de Vos. - Wageningen : Wageningen University - ISBN 9789462570924 - 245
varkens - darmmicro-organismen - microbiota van het spijsverteringskanaal - antibiotica - dieet - microbiologie - pigs - intestinal microorganisms - gastrointestinal microbiota - antibiotics - diet - microbiology

The intestinal tract of humans and animals is colonized by trillions of microorganisms that constitute a community or ecosystem known as the gut microbiota. The gut microbiota undergoes remarkable alterations during early age, reaches a relative stable state in adulthood, and is driven by internal and external factors such as genotype of the host, diet and antibiotics. The objective of this research was to determine the effects of antibiotic treatment, microbial exposure and diet on the development of intestinal microbiota, focusing on the pig as an important production animal as well as a model for human. To achieve this objective, a series of intervention experiments were performed both in piglets and adult pigs.

To determine the impact of antibiotic treatment on the development of intestinal microbiota of piglets, two experiments were performed. The first experiment aimed to determine the effect of perinatal maternal antibiotic treatment on the intestinal microbiota of piglets. In this experiment, the sows received amoxicillin orally around parturition, and their offspring was serially sacrificed up to 42 days of age for analysis of ileal and colonic microbiota. It was observed that amoxicillin treatment drastically impacted the sows’ faecal microbiota, and furthermore influenced specific microbial groups in the ileum and colon of the piglets before and after weaning. These findings indicated that maternal amoxicillin treatment may indirectly affect the gut microbiota of offspring through disturbing the maternal microbiota and the transfer of maternal microbiota to the offspring. In a second experiment, we determined the effect of early antibiotic treatment on intestinal microbial colonization and immune development of piglets. Additionally, the effect of stress factors associated with routine farm practice was investigated. Antibiotic treatment affected the composition and diversity of jejunal microbiota, and reduced the expression of a large number of genes involved in immune-related processes. The cumulative effect of management procedures on top of the use of an antibiotic was limited. This study reinforced the notion that the early phase of life is critical for intestinal immune development, also under regular production circumstances.

Apart from antibiotic treatment, the effect of early microbial association on the development of intestinal microbiota and immune system of piglets was also studied in this thesis. One group of caesarean derived piglets was inoculated with a mixture of three microbial species (Lactobacillus amylovorus, Clostridium glycolicum, and Parabacteroides sp. ASF519) at day 1 and 2 after birth (the simple microbial association group), whereas a second group of piglets was inoculated with the above mixture at day 1 and 2 after birth as well as diluted adult sow faeces at day 3 and 4 after birth as the complex microbial association (CA) group. CA caused an increase of faecal microbial diversity and accelerated the faecal microbiota to develop into a stable and diverse microbiota. CA significantly affected luminal microbial composition and gene expression in jejunal and ileal mucosa, albeit in different ways. In the pig ileum, CA led to an increased relative abundance of microbial groups known to have beneficial effects, whereas it reduced the relative contribution of potential pathobionts. CA also induced the enrichment of immune-related gene sets in the ileal mucosa.

Another research goal of this thesis was to determine the influence of diet on the microbiota in the large intestine of adult pigs. To this end, the effect of resistance starch (RS) was evaluated in two studies. In the first study, pigs were either assigned to an RS diet or a digestible starch (DS) diet for two weeks. Samples from along the intestine were collected for measuring luminal microbiota composition, short chain fatty acid (SCFA) concentrations and the expression of host genes involved in SCFA uptake, SCFA signalling, and satiety regulation in mucosal tissue. In both the caecum and colon, differences in microbiota composition and SCFA concentrations were observed between DS- and RS-fed pigs. Caecal tissue expression of genes encoding monocarboxylate transporter 1 and glucagon was induced by RS. Based on these results, an additional experiment was performed. In this study, ten pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsies and luminal content, were fed a DS diet, or a diet high in RS (34%) for two consecutive periods of 14 days in a crossover design. RS increased the relative abundance of several butyrate-producing microbial groups and reduced that of potentially pathogenic members of the genus Leptospira and the phylum of Proteobacteria. Concentrations of acetate, propionate and butyrate in carotid plasma were significantly higher after RS consumption. Upon RS feeding, oxidative metabolic pathways, such as TCA cycle and beta-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor PPARG was identified as a potential key upstream regulator.

In conclusion, this thesis provides direct evidence that maternal antibiotic treatment, early antibiotic admistration and microbial exposure affect the development of intestinal microbiota of the piglets. Moreover, both early antibiotic admistration and microbial exposure affected piglet mucosal tissue gene expression. These findings reinforce the notion that the early phase of life is critical for the development of intestinal microbiota and immune system. Furthermore, it is proposed that manipulation of the microbial association at early age may be a way of supporting functional gut development. In addition to the above discussed early life envents, a diet with RS can also affect the microbiota in the large intestine of adult pigs. This thesis provides an enhanced understanding of the interaction between diet, microbiota and host in a number of complementary pig models and revealed the impact of antibiotics in early life microbial colonization. The gained insight is expected to be instrumental in improving sustainable pig management. Moreover, it may also be useful in understanding similar processes in the human gut.

Microbiological and geochemical dynamics of the subsurface: chemical oxidation and bioremediation of organic contaminants
Sutton, N.B. - \ 2014
University. Promotor(en): Huub Rijnaarts, co-promotor(en): Tim Grotenhuis. - Wageningen : Wageningen University - ISBN 9789462570269 - 295
bodemverontreiniging - biologische processen - geochemie - bioremediëring - microbiologie - ecotoxicologie - oxidatie - biodegradatie - microbiologie van de ondergrond - soil pollution - biological processes - geochemistry - bioremediation - microbiology - ecotoxicology - oxidation - biodegradation - subsurface microbiology
Verontreiniging van de ondergrond als gevolg van stedelijke en industriële activiteiten vormt een ernstig milieurisico. Om deze locaties te zuiveren en in hun oorspronkelijke staat te herstellen is het noodzakelijk dat efficiënte saneringstechnologieën ontwikkeld worden. Echter, de aanwezigheid en de behandeling van deze verontreinigingen biedt ook mogelijkheden voor wetenschappelijk onderzoek naar fundamentele onderwerpen op het gebied van de microbiële ecologie en bodemgeochemie. Dit proefschrift beschrijft in situ chemische oxidatie (ISCO) en in situ bioremediatie (ISB) van organische verontreinigingen
Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor
Oosterkamp, M.J. - \ 2013
University. Promotor(en): Fons Stams, co-promotor(en): Caroline Plugge; Peter Schaap. - Wageningen : Wageningen University - ISBN 9789461737779 - 191
bacteriën - aromatische koolwaterstoffen - fysiologie - biochemie - elektronen - genomen - nitraten - chloraten - microbiologie - bacteria - aromatic hydrocarbons - physiology - biochemistry - electrons - genomes - nitrates - chlorates - microbiology
Darmbacteriën vormen de mens
Vos, Willem de - \ 2013
intestinal microorganisms - gastrointestinal microbiota - microbiology - health - bacteria - babies
RegIII proteins as gatekeepers of the intestinal epithelium
Loonen, L.M.P. - \ 2013
University. Promotor(en): Jerry Wells, co-promotor(en): Peter van Baarlen. - S.l. : s.n. - ISBN 9789461736727 - 205
eiwitten - darmen - darmslijmvlies - darmziekten - colitis - bacterieziekten - immuunsysteem - verdedigingsmechanismen - muizen - diermodellen - microbiologie - immuniteit - geneeskunde - proteins - intestines - intestinal mucosa - intestinal diseases - bacterial diseases - immune system - defence mechanisms - mice - animal models - microbiology - immunity - medicine

Mammalian RegIII proteins are expressed in the intestine and in the pancreas in response to inflammation or infection. In the mouse intestine, expression of RegIIIβ and RegIIIγ is increased by microbial colonization, inflammation and infection. At the outset of this thesis human PAP and mouse RegIIIγ were reported to be bactericidal for Gram-positive bacteria. Additionally, human PAP had been shown to attenuate NF-κbsignallingin human monocytes and epithelial cells and administration of anti-PAP antibodies increased inflammation in an experimental rat model of acute pancreatitis. The overarching goals of this thesis were to find out more about the protective role of mouse RegIIIβ and RegIIIγ in the intestine and explore their protective role in colitis and bacterial infection.

In Chapter 2 we investigated expression of RegIIIβ and RegIIIγ in intestine of Muc2 knockout (-/-) mice, which develop colitis after about 4 weeks, due to the absence of a secreted mucus layer in the small intestine or colon. RegIII proteins were expressed in Paneth cells, enterocytes and goblet cells pointing to a new function for goblet cells in innate immunity. Ang4 expression was confined to Paneth cells and goblet cells. Absence of Muc2 increased expression levels of RegIIIβ, RegIIIγ, and Ang4 and colitis appeared first in the distal colon where the RegIII expression is lowest.

In Chapter 3 we investigated the distinct phases of colitis development in Muc2-/- mice from before weaning to 4 and 8 weeks of age, also taking into account the effect that mucin deficiency has in the ileum. Gene set enrichment approaches showed increased expression of innate and adaptive immune pathways associated with colitis over time, whereas in the ileum many immune signalling pathways were down-regulated. Nevertheless, RegIIIβ and RegIIIγ were significantly upregulated, suggesting their proposed antimicrobial and/or anti-inflammatory activities might be related to the suppression of immune pathways and avoidance of immune-mediated damage. Furthermore, we showed that RegIIIβ could specifically bind to mucin and fucosylated glycans in vitro, which may serve to inhibit bacterial binding to membrane bound mucins on the epithelium, and also enable RegIIIβ to be retained in the secreted mucin.

An in vitro approach was used in Chapter 4, where we investigated the activities of RegIIIγ and RegIIIβby expressing and purifying recombinant proteins. Both proteins were insoluble when expressed in E. coli but RegIIIβ could be expressed and secreted in baculovirus as a soluble protein. As previous work reported that RegIII proteins were bactericidal even when produced as inclusion bodies in E. coli and refolded, we followed similar procedures to obtain soluble RegIII proteins. In our hands both the E. coli and baculovirus produced proteins bound strongly to both Gram-positive and Gram-negative bacteria after processing of an N-terminal pro-peptide by trypsin, but lacked any appreciable bactericidal activity. Furthermore these proteins did not influence the growth of Salmonella enteritidis andListeria monocytogenes. Attempts to crystallize the proteins were unsuccessful but structural models of the protein were generated based on the crystal structure of human PAP. These models were used to dock known ligands of RegIIIγ or RegIIIβ. Only one ligand is known for RegIIIγ, which is peptidoglycan, but for RegIIIβ the ligands include peptidoglycan, lipid A and the fucose-containing glycans identified in chapter 3. RegIIIβ was predicted to have two different binding sites which would allow it to bind to mucins and bacteria simultaneously, thereby preventing penetrating of the mucus.

In Chapter 5 a RegIIIβ-/- mouse was used to study the role of the protein during infection with Gram-negative Salmonella enteritidis or Gram-positive Listeria monocytogenes. Whereas recovery of S. enteritidis orL. monocytogenes from faeces was similar in RegIIIβ-/- and wild type (WT) mice, significantly higher numbers of viable S. enteritidis, but not L. monocytogenes, were recovered from the colon, mesenteric lymph nodes, spleen, and liver of the RegIIIβ-/- than the WT mice. The results suggest that mouse RegIIIβ plays a protective role against intestinal translocation of the Gram-negative bacterium S. enteritidis but not against the Gram-positive bacterium L. monocytogenes.

In Chapter 6, the generation of a RegIIIγ-/- mouse is described. One of the main phenotypic differences between the RegIIIγ-/- and WT was an altered distribution of the ileal mucus and increased bacterial contact with the epithelium. Additionally, measurement of innate immune markers in the mucosa suggested heightened inflammation in the RegIIIγ-/- mice. Compared to WT mice, RegIIIγ-/- mice infected with S. enteritidis and L. monocytogenes showed an increase of mucosal inflammatory markers indicating protective, anti-microbial roles of RegIIIγ in defense against both Gram-positive and Gram-negative bacteria.

Chapter 7summarizes and discusses the key results of the thesis in the context of the wider literature and possible directions for future research

Waar zitten de hoofdschakelaars voor de knopvorming in champignons? : rapportage van PRI voor ondersteuning STW project aan afdeling Microbiologie, Universiteit Utrecht
Sonnenberg, A.S.M. ; Baars, J.J.P. - \ 2011
Wageningen : Plant Research International (Rapport / Plant Research International 2011-1) - 11
paddestoelen - agaricus - genen - milieufactoren - knoppen - onderzoek - microbiologie - mushrooms - genes - environmental factors - buds - research - microbiology
In de afgelopen vier jaar is bij het Laboratorium voor Biologie van de Universiteit Utrecht onderzoek gedaan naar genen die een belangrijke rol spelen bij de vorming van paddenstoelen. Het opsporen van dergelijke genen en het achterhalen van hun werking is erg belangrijk om te begrijpen hoe de knopvorming tot stand komt en welke omgevingsfactoren daarbij een rol spelen.
Microcanon : wat je beslist moet weten over microbiologie
Smit, H. ; Doorn, J. van; Oost, J. van der; Reijnders, W. ; Willemsen, P.T.J. - \ 2011
Diemen : Veen Magazines (Wetenschappelijke Bibliotheek van Natuurwetenschap&Techniek 109) - ISBN 9789085713272 - 246
microbiologie - bacteriën - virussen - biotechnologie - bacterieziekten - microbiology - bacteria - viruses - biotechnology - bacterial diseases
Micro-organismen zijn onmisbaar voor het leven op aarde. De organismen zijn zo klein dat we ze niet zien, maar ze zijn des te belangrijk. Deze kleine organismen kunnen een positieve of negatieve invloed hebben. Soms klein, soms groot. De Microcanon geeft daarvan een goed beeld in zo'n zestig voorbeelden. Een team van auteurs beschrijft op begrijpelijke wijze de belangrijkste feiten uit de microbiologie. De micro-organismen zijn niet alleen onmisbaar bij grote geologische processen zoals de koolstof- en stikstofkringloop, maar ook in het dagelijks leven en natuurlijk ook binnen de land- en tuinbouw. Het kennen van deze organismen en hun processen is van groot belang
Biotechnological aspects of anaerobic oxidation of methane coupled to sulfate reduction
Meulepas, R.J.W. - \ 2009
University. Promotor(en): Cees Buisman, co-promotor(en): Piet Lens; Fons Stams. - [S.l. : S.n. - ISBN 9789085853978 - 173
anaërobe omstandigheden - oxidatie - methaan - microbiologie - biotechnologie - anaërobe microbiologie - sulfaatreductie - anaerobic conditions - oxidation - methane - microbiology - biotechnology - anaerobic microbiology - sulfate reduction
Sulfate reduction (SR) can be used for the removal and recovery of metals and oxidized sulfur compounds from waste streams. Sulfate-reducing bacteria reduce oxidized sulfur compounds to sulfide. Subsequently, sulfide can precipitate dissolved metals or can be oxidized to elemental sulfur. Both metal sulfides and elemental sulfur can be reused in various applications. SR with hydrogen or ethanol as electron donor is an established biotechnological process. However, the costs of these electron donors limit the application possibilities. Methane would be a cheaper and more attractive electron donor. SR coupled to the anaerobic oxidation of methane (AOM) occurs in marine sediments. Uncultured archaea, distantly related to methanogens, and bacteria are involved in this process. The in vitro demonstration of SR coupled to AOM gave rise to this research, which aims to develop a biotechnological process in which methane is used as electron donor for SR.
Three types of anaerobic granular sludge were screened for the ability to reduce sulfate with methane as electron donor. To do so, incubations were done with 13C-labeled methane. All three sludge types anaerobically oxidized 13C-labeled methane to 13C-labeled carbon dioxide. Moreover, the presence of methane enhanced the SR rate. However, AOM by sludge was not coupled to SR, but coincides with net methanogenesis. The methane-dependent SR was caused by the inhibitory effect of methane on methanogens competing (possibly in syntrophic consortia with acetogenic bacteria) with sulfate reducers for the same endogenous substrate. Therefore, anaerobic granular sludge does not form a suitable inoculum for sulfate-reducing bioreactors fed with methane.
Well-mixed ambient-pressure submersed-membrane bioreactors, fed with sulfate and methane, were inoculated with sediment from Eckernförde Bay (Baltic Sea). Initially AOM rates were extremely low (0.004 mmol L-1 day-1), but at 15ºC AOM and SR rates increased over the course of 884 days to 0.60 mmol L-1 day-1 or 1.0 mmol gVSS-1 day-1. The AOM rate doubled approximately every 3.8 months. Molecular analyses revealed that the archaea in the obtained enrichment belonged predominately to the anaerobic methanotroph ANME-2a. Both bacteria and archaea incorporated carbon derived from 13C-labeled methane into their lipids, indicating that both were involved in AOM coupled to SR. To investigate which kind of waste streams can be treated by the methane-oxidizing sulfate-reducing enrichment, the effect of environmental conditions and alternative substrates on AOM and SR was assessed. The optimum pH, salinity and temperature for SR with methane by the enrichment were 7.5, 30‰ and 20°C, respectively. The biomass had a good affinity for sulfate (Km  1.0 mM), a low affinity for methane (Km > 75 kPa) and AOM was completely inhibited by 2.4 (±0.1) mM sulfide. The enrichment utilized sulfate, thiosulfate and sulfite as electron acceptors for methane oxidation, and methane, formate, acetate and hydrogen as electron donors for SR.
This study shows that methane can be used as electron donor for sulfate reduction in bioreactors. However, the low growth rate of the responsible microorganisms still forms a major bottleneck for biotechnological applications.

A practical and low cost microbiotest to assess the phytotoxic potential of growing media and soil
Blok, C. ; Persoone, G. ; Wever, G. - \ 2006
fytotoxiciteit - biotesten - biologische technieken - groeimedia - microbiologie - phytotoxicity - bioassays - biological techniques - growing media - microbiology
A good biotest should provide the possibility to grow plants in close contact with the material to test but without interference of the physical characteristics of the latter. To achieve optimal implementation the biotest should be simple and cheap. A new microbiotest (called Phytotoxkit) has been developed to meet these demands and has been compared with a more traditional biotest
Microbiological methods for assessing soil quality
Bloem, J. ; Hopkins, D.W. ; Benedetti, A. - \ 2006
Wallingford (UK) : CABI - ISBN 0851990983 - 307
bodem - micro-organismen - bodembiologie - microbiële flora - microbiologie - methodologie - monitoring - interacties - biodiversiteit - bodemkwaliteit - soil - microorganisms - soil biology - microbial flora - microbiology - methodology - interactions - biodiversity - soil quality
This book provides a selection of microbiological methods that are already applied in regional or national soil quality monitoring programs. It is split into two parts: part one gives an overview of approaches to monitoring, evaluating and managing soil quality. Part two provides a selection of methods, which are described in sufficient detail to use the book as a practical handbook in the laboratory. The methods are described in chapters on soil microbial biomass and numbers, soil microbial activity, soil microbial diversity and community composition, and plant-microbe interactions and soil quality.
Microbiologische bestrijders: waar staan we over tien jaar
Boogert, P.H.J.F. van den; Postma, J. ; Speksnijder, A.G.C.L. - \ 2004
Gewasbescherming 35 (2004)1. - ISSN 0166-6495 - p. 30 - 33.
biologische bestrijding - pesticiden - microbiologie - duurzaamheid (sustainability) - geïntegreerde bestrijding - innovaties - kosten - marketing - onderzoek - toekomst - biological control - pesticides - microbiology - sustainability - integrated control - innovations - costs - research - future
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