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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Bioremediation : An Overview on Current Practices, Advances, and New Perspectives in Environmental Pollution Treatment
Hlihor, Raluca Maria ; Gavrilescu, Maria ; Tavares, Teresa ; Favier, Lidia ; Olivieri, Giuseppe - \ 2017
BioMed Research International 2017 (2017). - ISSN 2314-6133
Detection of bacterial DNA in bile of cats with lymphocytic cholangitis
Otte, C.M.A. ; Pérez, O.N. ; Favier, R.P. ; Rothuizen, J. ; Penning, L.C. - \ 2012
Veterinary Microbiology 156 (2012)1-2. - ISSN 0378-1135 - p. 217 - 221.
16s ribosomal-rna - gradient gel-electrophoresis - polymerase-chain-reaction - helicobacter-pylori - pcr amplification - sp-nov. - jeotgalicoccus - disease - liver - populations
In this study, we have successfully used molecular methods based on the amplification of the 16S ribosomal RNA gene on feline bile samples to show that bile of cats with LC is not sterile. This is probably due to the fact that the inflammatory process in the biliary tree causes dilatations. As a result, bacteria can easily migrate from the intestines via the common bile duct. The diversity of species identified and the presence of Helicobacter spp. DNA in both patients and controls suggests that bacteriobilia is secondary to the disease and is not the cause of LC.
Naar een gedeelde agend voor infrastructuur en agrologistiek rondom Greenports : discussienota
Annevelink, E. ; Hermans, C.M.L. ; Maas, A.A. van der; Pegge, S.M. ; Ruijs, M.N.A. ; Tromp, S.O. ; Favier, M. ; Geijn, W. van de; Bleumink, P. ; Roelofs, B. - \ 2006
Wageningen : Agrotechnology & Food Sciences Group - 43
landbouwproducten - concentratie van de productie - ruimtelijke ordening - stedelijke planning - landinrichting - overheidsbeleid - tuinbouw - economische ontwikkeling - economische situatie - infrastructuur - innovaties - agro-industriële ketens - logistiek - agricultural products - concentration of production - physical planning - urban planning - land development - government policy - horticulture - economic development - economic situation - infrastructure - innovations - agro-industrial chains - logistics
Naar een gedeelde agenda voor infrastructuur en agrologistiek rondom Greenports : achtergrond rapport
Annevelink, E. ; Hermans, C.M.L. ; Maas, A.A. van der; Pegge, S.M. ; Ruijs, M.N.A. ; Tromp, S.O. ; Favier, M. ; Geijn, W. van de; Bleumink, P. ; Roelofs, B. - \ 2006
Wageningen : Agrotechnology & Food Sciences Group (Rapport / Wageningen UR, Agrotechnology & Food Sciences Group 626) - ISBN 9085850126 - 106
landbouwproducten - concentratie van de productie - ruimtelijke ordening - stedelijke planning - landinrichting - overheidsbeleid - tuinbouw - economische ontwikkeling - economische situatie - infrastructuur - logistiek - agro-industriële ketens - agricultural products - concentration of production - physical planning - urban planning - land development - government policy - horticulture - economic development - economic situation - infrastructure - logistics - agro-industrial chains
Knockout of the alanine racemase gene in Lactobacillus plantarum results in septation defects and cell wall perforation
Palumbo, E. ; Favier, C.F. ; Deghorain, M. ; Cocconcelli, P.S. ; Grangette, C. ; Mercenier, A.M.E. ; Vaughan, E.E. ; Hols, P. - \ 2004
FEMS Microbiology Letters 233 (2004)1. - ISSN 0378-1097 - p. 131 - 138.
lactic-acid bacteria - lipoteichoic acid - bacillus-subtilis - escherichia-coli - teichoic-acid - lysis - methicillin - autolysis - mutants - impact
A stable mutant of Lactobacillus plantarum deficient in alanine racemase (Alr) was constructed by two successive homologous recombination steps. When the mutant was supplemented with D-alanine, growth and viability were unaffected. Surprisingly, deprivation Of D-alanine during exponential growth did not result in a rapid and extensive lysis as observed in Alr-deficient strains of Escherichia coli or Bacillus subtilis. Rather, the starved mutant cells underwent a growth arrest and were gradually affected in viability with a decrease in colony forming units over 99% in less than 24 h. Additionally, fluorescent techniques demonstrated a loss of cell envelope integrity in the starved cells. Prolonged D-alanine starvation resulted in cells with an aberrant morphology. Scanning and transmission electron microscopy analyses revealed an increase in cell length, deficiencies in septum formation, thinning of the cell envelope and perforation of the cell wall in the septum region. We discuss the involvement of peptidoglycan hydrolases in these phenotypic defects in the context of the crucial role played by D-alanine in peptidoglycan biosynthesis and teichoic acids substitution. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Microbial diversity studies of the porcine gastrointestinal ecosystem during weaning transition
Konstantinov, S.R. ; Favier, C.F. ; Zhu Wei-Yun, ; Williams, B.A. ; Kluss, J. ; Souffrant, W.B. ; Vos, W.M. de; Akkermans, A.D.L. ; Smidt, H. - \ 2004
Animal Research 53 (2004)4. - ISSN 1627-3583 - p. 317 - 324.
gel-electrophoresis analysis - 16s ribosomal dna - bacterial communities - human intestine - ecology - pigs - antibiotics - evolution - animals - tract
At the time of weaning, major quantitative and qualitative changes occur in the composition of the intestinal microbiota of piglets, influenced by diet, environmental factors, and the host. Within a short period of time, the intestinal microbiota must ultimately develop from a simple, unstable community into a complex and stable one. Here we present data on the development of the intestinal microbiota based on 16S rRNA gene sequence diversity. In addition to a PCR-based analysis of the 16S rRNA gene by cloning and denaturing gradient gel electrophoresis (DGGE), data on fluorescent in situ hybridisation ( FISH) are presented to quantify the total bacterial communities, major Lactobacillus populations and specific Lactobacillus species. The results reported here indicate that the addition of non-digestible, fermentable carbohydrates (= prebiotics) leads to an enrichment of lactobacilli in the small intestine, and increased stability and diversity of the bacterial community in the colon. The data support the hypothesis that changes of the diet can modulate the composition of the microbiota in the intestine. These findings may have potentially major implications for the development of dietary strategies aiming to improve animal health during the weaning process.
Postnatal development of the intestinal microbiota of the pig
Akkermans, A.D.L. ; Konstantinov, S.R. ; Zhu, W.Y. ; Favier, C.F. ; Williams, B.A. - \ 2003
In: Proceedings of the 9th International Symposium on Digestive Physiology in Pigs, Banff, Canada, 14-17 May 2003. - Banff, Canada : - p. 49 - 57.
Development of bacterial and bifidobacterial communities in feces of newborn babies
Favier, C.F. ; Vos, W.M. de; Akkermans, A.D.L. - \ 2003
Anaerobe 9 (2003). - ISSN 1075-9964 - p. 219 - 229.
16s ribosomal-rna - gradient gel-electrophoresis - bottle-fed infants - human intestinal microflora - species-specific primers - formula-fed infants - fecal flora - microbial ecology - targeted probes - human-colon
Microbial 16S rDNA from babies' fecal samples were amplified by PCR, and analysed by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. PCR-DGGE profiles were used to follow in time the colonization of the intestine by bacteria. Four healthy babies, one baby who received antibiotics and their parents participated to the present study to determine the extent to which administration of antibiotics can modify the bacterial colonization of neonatal human gut and verify the influence of parental factors on the formation of the fecal bacterial community. In the healthy babies, Escherichia coli or bacteria belonging to Clostridium spp. were the initial colonizers rapidly followed by Bifidobacterium, Bacteroides, Clostridium, Streptococcus, Enterococcus and Actinomyces. Bifidobacterium species appeared already after five days in the breast-fed babies while there was a delay in the baby who received a formula based diet during only one day after birth. In each baby two or three bifidobacterial species including B. infantis were found. The observed variations in species were not associated with the feeding changes. The comparison of DGGE profiles of the babies and their parents patterns showed bands with equal migration suggesting a vertical transmission determined by genetic and environmental factors. The brief appearance of pioneer bacteria determined as being E coli and Enterococcus spp. in the profile from the. baby under antibiotic therapy, was succeeded by a small stable community consisting of Ruminococcus species. No Bifidobacterium sequences were detectable in this antibiotic-treated baby in spite of a partly breast-milk diet. (C) 2003 Elsevier Ltd. All rights reserved.
Molecular monitoring of succession of bacterial communities in human neonates
Favier, C. ; Vaughan, E.E. ; Vos, W.M. de; Akkermans, A.D.L. - \ 2002
Applied and Environmental Microbiology 68 (2002)1. - ISSN 0099-2240 - p. 219 - 226.
The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes. DGGE profiles of the dominant populations in the intestines of the infants were obtained by analyzing daily or weekly fecal samples. After delivery, the germfree infant gastrointestinal tracts were rapidly colonized, and the succession of bacteria in each ecosystem was monitored. During the first few days of life the profiles were simple, but they became more complex as the bacterial diversity increased with time in both babies. Clone libraries of amplified 16S rDNA fragments from baby feces were constructed, and these libraries allowed identification of the bacterial types by comparative DNA sequence analysis; the bacteria identified included members of the genera Bifidobacterium, Ruminococcus, Enterococcus, Clostridium, and Enterobacter. Species most closely related to the genera Bifidobacterium and Ruminococcus in particular dominated the intestinal microbiota based on the stability over time and the numbers, as estimated by the intensities of the bands. However, 19 of the 34 cloned rDNA sequences exhibited less than 97␒dentity with sequences of known bacteria or cloned sequences in databases. This study showed that using PCR-DGGE and 16S rDNA sequence analysis together resulted in a dynamic description of bacterial colonization in the infant intestinal ecosystem and allowed visualization of bacteria that are difficult to cultivate or to detect by other methods
Diversity of Bifidobacterium and Lactobacillus spp. in Breast-Fed and Formula-Fed Infants as Assessed by 16S rDNA Sequence Differences
Satokari, R.M. ; Vaughan, E.E. ; Favier, C.F. ; Doré, J. ; Edwards, C. ; Vos, W.M. de - \ 2002
Microbial Ecology in Health and Disease 14 (2002). - ISSN 0891-060X - p. 97 - 105.
A qualitative molecular monitoring approach based on PCR and denaturing gradient gel electrophoresis (DGGE) was used to study the diversity of dominant bacteria, bifidobacteria and lactobacilli in vaginally delivered full-term infants. Seven breast-fed and six formula-fed infants participated in the study. 16S rDNA targeted primers were used for the specific PCR amplification of fragments from bacteria, bifidobacteria and lactobacilli from faecal samples that were collected before and after weaning at the age of approximately 1 and 7 months, respectively. The PCR fragments were subsequently resolved in a sequence-dependent manner by DGGE. In addition, cloning and sequence analysis of the PCR fragments was used to identify the species from which they originated. Based on the number of fragments in the DGGE profiles it was estimated that breast-fed and formula-fed infants harboured bacterial communities of equal complexity. There was no conspicuous difference in the distribution of Bifidobacterium or Lactobacillus species between breast-fed and formula-fed infants. The most frequently found representatives of these genera were B. infantis and species belonging to the L. acidophilus-group in both groups of infants. The predominant Bifidobacterium and Lactobacillus populations in most infants consisted of only one or two species.
Microbial colonization of the mammalian intestine : a molecular approach
Akkermans, A.D.L. ; Zoetendal, E.G. ; Favier, C. ; Konstantinov, S. ; Vos, W.M. de; Williams, B.A. - \ 2001
In: ISME-9 Interactions in the Microbial World, Amsterdam, 2001
Culture-independent detection of bacterial populations in the human intestinal tract
Akkermans, A.D.L. ; Zoetendal, E.G. ; Konstantinov, S. ; Favier, C. ; Satokari, R. ; Vaughan, E.E. ; Heilig, G.H.J. ; Vos, W.M. de - \ 2001
International Journal of Antimicrobial Agents 17 (2001). - ISSN 0924-8579 - p. 104 - 104.
Temperature and denaturating gradient gel electrophoresis analysis of 16S rRNA from human faecal samples
Akkermans, A.D.L. ; Zoetendal, E.G. ; Favier, C.F. ; Heilig, H.G.H.J. ; Akkermans-van Vliet, W.M. ; Vos, W.M. de - \ 2000
Bioscience and Microflora 19 (2000). - ISSN 1342-1441 - p. 93 - 98.

The gastrointestinal tract (GIT) of mammals harbours a complex community of obligate and facultative anaerobic bacteria. The composition of the GIT microbiota is dependent on the physiological condition, age, genetics, and diet of the host. During the past 5 years a number of molecular fingerprinting methods have been developed to characterise complex communities based on 16S rRNA sequence diversity. This paper describes the use of temperature and denaturing gradient gel electrophoresis (T/DGGE) of bacterial 16S rRNA/DNA in faecal samples from humans, in which special attention was given to the quantification of the sequence diversity. After birth the GIT community develops into a relatively simple community consisting of 1-8 major types within three months. Adults show more complex, but remarkably constant patterns. These patterns are hardly affected by changes in diet. Significant differences were observed between different individuals, particularly between genetically unrelated persons. In general, bacterial communities of faecal samples from genetically related adults (i.e. twins, brothers, sisters) show higher similarity of DGGE banding patterns than those from genetically unrelated individuals, although occasionally all persons in one family show highly similar profiles. The DGGE banding patterns of humans are significantly different from those of other mammals, such as pigs, gorillas and cats, indicating that genetic factors of the host affect the composition of the GI-tract flora. The major bacterial groups were identified by cloning and sequencing of the dominant 16S rDNA molecules. At least three sequences with highest homology to Ruminococcus obeum and Eubacterium halii and Fusobacterium prausnitzii were present in all human subjects and are likely to play a universal role in the GI-tract. Other sequences were found in variable ratios in different individuals.
Photopyroelectric Measurement of Thermal Diffusivity of Industrial Polymers : Low Density Polyethylene and Polyvinyl Chloride Foils
Favier, J.P. ; Dadarlat, D. ; Bicanic, D. ; Riezebos, K.J. ; Berg, C. van den; Gerkema, E. - \ 1999
Instrumentation Science and Technology (1999)27. - ISSN 1073-9149 - p. 275 - 286.
Thermal diffusivity of a hard boiled candy obtained by photothermal beam deflection and standard photopyroelectric method.
Favier, J.P. ; Dadarlat, D. ; Gibkes, J. ; Berg, C. van den; Bicanic, D. - \ 1998
Instrumentation Science and Technology 26 (1998). - ISSN 1073-9149 - p. 113 - 124.
Adulteration of extra virgin oil by sunflower and safflower oils-optothermal approach.
Favier, J.P. ; Bicanic, D. - \ 1998
Journal of the American Oil Chemists Society 75 (1998). - ISSN 0003-021X - p. 359 - 362.
CO2 laser infrared optothermal spectroscopy for quantitative adulteration: studies in binary mixtures of extra-virgin olive oil.
Favier, J.P. ; Bicanic, D. ; Cozijnsen, J. ; Veldhuizen, B. van; Helander, P. - \ 1998
Journal of the American Oil Chemists Society 75 (1998). - ISSN 0003-021X - p. 359 - 362.
Novel method for determination of glucose concentration during fermentation by Saccharomyces cerevisiae.
Iersel, M. van; Favier, J.P. ; Meersman, E. - \ 1997
In: EBC Congress - p. 485 - 491.
The Optothermal Approach to a Real Time Monitoring of Glucose Content During Fermentation by Brewers Yeast.
Favier, J.P. ; Bicanic, D. ; Helander, P. ; Iersel, M. van - \ 1997
Journal of Biochemical and Biophysical Methods 34 (1997). - ISSN 0165-022X - p. 205 - 211.
Optothermal Detection of Infrared Radiation Induced Absorption in Aqueous Solution of Carbohydrates: Lactose and Starch.
Favier, J.P. ; Bicanic, D. ; Doka, O. ; Chirtoc, M. ; Helander, P. - \ 1997
Journal of Agricultural and Food Chemistry 45 (1997). - ISSN 0021-8561 - p. 777 - 780.
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