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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Voedselbewerking : De balans tussen veiligheid en gezondheid
Peters, S. ; Gerritsen, J. ; Huppertz, Thom - \ 2019
VoedingsMagazine 32 (2019)2. - ISSN 0922-8012 - p. 18 - 21.
Volgens een recent onderzoek hangt de consumptie van ultra-bewerkt voedsel samen met een toename van overgewicht en welvaartsziekten. Kan een classificatie van producten op hun bewerkingsgraad - zoals NOVA - consumenten helpen om gezondere keuzes te maken?
Genome sequence of Romboutsia lituseburensis
Gerritsen, J. ; Umanetc, Alexander ; Leeuwen-Staneva, I.N. van; Hornung, B.V.H. ; Ritari, J. ; Paulin, L. ; Rijkers, Ger T. ; Vos, W.M. de; Smidt, H. - \ 2018
Wageningen University
Romboutsia lituseburensis - PRJEB7306 - Romboutsia lituseburensis - PRJEB7306 - ERP007013
The genome of Romboutsia lituseburensis has been sequenced for comparative purposes within the new genus Romboutsia.
Genome sequence of Romboutsia str. Frifi
Gerritsen, J. ; Umanetc, Alexander ; Leeuwen-Staneva, I.N. van; Hornung, B.V.H. ; Ritari, J. ; Paulin, L. ; Rijkers, Ger T. ; Vos, W.M. de; Smidt, H. - \ 2018
Wageningen University
Romboutsia sp. Frifi - PRJEB7106 - Romboutsia sp. Frifi - PRJEB7106 - ERP006791
Genome sequence of Romboutsia str. Frifi
Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent
Gerritsen, Jacoline ; Umanets, Alexander ; Staneva, Ivelina ; Hornung, Bastian ; Ritari, Jarmo ; Paulin, Lars ; Rijkers, Ger T. ; Vos, Willem M. de; Smidt, Hauke - \ 2018
International Journal of Systematic and Evolutionary Microbiology 68 (2018)11. - ISSN 1466-5026 - p. 3479 - 3486.
Clostridium - human intestine - ileostoma effluent - Peptostreptococcaceae - Romboutsia

A Gram-stain-positive, motile, rod-shaped, obligately anaerobic bacterium, designated FRIFIT, was isolated from human ileostoma effluent and characterized. On the basis of 16S rRNA gene sequence similarity, strain FRIFIT was most closely related to the species Romboutsia ilealis CRIBT (97.7 %), Romboutsia lituseburensis DSM 797T (97.6 %) and Romboutsia sedimentorum LAM201T (96.6 %). The level of DNA-DNA relatedness between strain FRIFIT and R. ilealis CRIBT was 13.9±3.3 % based on DNA-DNA hybridization. Whole genome sequence-based average nucleotide identity between strain FRIFIT and closely related Romboutsia strains ranged from 78.4-79.1 %. The genomic DNA G+C content of strain FRIFIT was 27.8 mol%. The major cellular fatty acids of strain FRIFIT were saturated and unsaturated straight-chain C12-C19 fatty acids as well as cyclopropane fatty acids, with C16 : 0 being the predominant fatty acid. The polar lipid profile comprised five phospholipids and six glycolipids. These results, together with differences in phenotypic features, support the proposal that strain FRIFIT represents a novel species within the genus Romboutsia, for which the name Romboutsiahominis sp. nov. is proposed. The type strain is FRIFIT (=DSM 28814T=KCTC 15553T).

Genome sequence of the rat gut bacterium Romboutsia ilealis CRIB
Gerritsen, J. ; Timmerman, H.M. ; Fuentes, S. ; Minnen, L.P. van; Panneman, H. ; Konstantinov, S.R. ; Rombouts, F.M. ; Gooszen, H.G. ; Akkermans, L.M.A. ; Smidt, H. ; Rijkers, G.T. - \ 2017
Romboutsia ilealis - PRJEB4727 - ERP004037
The rat illeum bacterium Romboutsia ilealis CRIB was sequenced and assembled, using a hybrid approach, consisting out of different data types (Illumina paired end, mate pair, PacBio), as well as a custom assembly workflow.
Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia
Wang, Yanwei ; Song, Jinlong ; Zhai, Yi ; Zhang, Chi ; Gerritsen, Coline ; Wang, Huimin ; Chen, Xiaorong ; Li, Yanting ; Zhao, Bingqiang ; Zhao, Bin ; Ruan, Zhiyong - \ 2015
International Journal of Systematic and Evolutionary Microbiology 65 (2015). - ISSN 1466-5026 - p. 1193 - 1198.

A Gram-stain-positive, spore-forming, obligately anaerobic bacterium, designated LAM201T, was isolated from sediment samples from an alkaline-saline lake located in Daqing oilfield, Daqing City, PR China. Cells of strain LAM201T were non-motile and straight or spiral rod-shapes. Strain LAM201T was able to utilize glucose, fructose, maltose, trehalose and sorbitol as the sole carbon source. Acetic acid, ethanol, iso-butanoic acid and iso-valeric acid were the main products of glucose fermentation. The major fatty acids of LAM201T were C16:0 (26.7%) and C18:0 (11.2%). The main polar lipids were four unknown glycolipids and five unknown phospholipids. The predominant cell-wall sugars were ribose and galactose. The cell-wall peptidoglycan of strain LAM201T contained alanine, glycine, glutamic acid and aspartic acid. Sodium sulfite was used as the electron acceptor. The G+C content of the genomic DNA was 32±0.8 mol%, as determined by the Tm method. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Romboutsia and was most closely related to Romboutsia lituseburensis DSM 797T and Romboutsia ilealis CRIBT with 97.3% and 97.2% similarities, respectively. The DNA–DNA hybridization values between strain LAM201T and the two reference strains were 37% and 31%, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM201T is suggested to represent a novel species within the genus Romboutsia, for which the name Romboutsia sedimentorum sp. nov. is proposed. The type strain is LAM201T (=ACCC 00717T=JCM 19607T).

The genus Romboutsia : genomic and functional characterization of novel bacteria dedicated to life in the intestinal tract
Gerritsen, J. - \ 2015
Wageningen University. Promotor(en): Hauke Smidt; Willem de Vos, co-promotor(en): G.T. Rijkers. - Wageningen : Wageningen University - ISBN 9789462572423 - 280
darmmicro-organismen - voeding en gezondheid - microbiota van het spijsverteringskanaal - darmziekten - moleculaire technieken - probiotica - intestinal microorganisms - nutrition and health - gastrointestinal microbiota - intestinal diseases - molecular techniques - probiotics
The genus Romboutsia: genomic and functional characterization of novel bacteria dedicated to life in the intestinal tract

PhD thesis Jacoline Gerritsen, 2015

Abstract

Humans, like other mammals, are not single-species organisms, but they constitute in fact very complex ecosystems. The extensive network of host-microbe and microbe-microbe interactions is tremendously important for our health, and we are just starting to unravel the mechanisms by which microbes contribute to host health and disease.

Especially the intestinal tract of both humans and mammals contains an enormous diversity of microbial species of which many still remain to be cultured and characterized. There are numerous diseases for which aberrations in composition and diversity of the intestinal microbiota have been reported. Probiotic microorganism defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” have the potential to modulate the intestinal microbiota and thereby contribute to health and well-being. To this end, the relative abundance of a specific bacterial phylotype, named CRIB, was found to be associated with probiotic-induced changes in gut microbiota and decreased severity of pancreatitis and associated sepsis in an experimental rat model for acute pancreatitis studies. Later, a representative of this phylotype (strain CRIB) was isolated, and characterized using a polyphasic taxonomic approach. The taxonomy of several closely related members of the family Peptostreptococcaceae was revised in order to provide a valid systematic name to the isolate, for which Romboutsia ilealis was chosen. It was found that the majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, however, the specific roles that Romboutsia species play in the intestinal tract are largely unknown. To gain more insight in metabolic and functional capabilities of members of the genus Romboutsia, efforts towards the isolation of additional representatives were undertaken. This ultimately led to the isolation of a human small intestine-derived representative (strain FRIFI) of another novel Romboutsia species which was given the name R. hominis. Characterization of both novel species of intestinal origin, i.e. R. ilealis and R. hominis, belonging to the genus Romboutsia at the genomic and functional level provided first insights into the genetic diversity within the genus Romboutsia and their adaptation to a life in the (upper) intestinal tract. To this end, Romboutsia species are flexible anaerobes that are adapted to a nutrient-rich environment in which carbohydrates and exogenous sources of amino acids and vitamins are abundantly available.

Microbiomic approaches such as those employed in this study can be used to pinpoint specific commensal microbes that might have a beneficial effect on the health of the host. In addition, the combination of genomic and functional analyses with single organisms and complex communities can be used to identify microbial functionalities that are related to health and disease, which in turn can be used to select potential probiotic strains based on specific functional properties. Ultimately, these approaches will lead to the characterization of (new) beneficial commensal microbes that exert health-promoting effects, with the ultimate possibility for them to be exploited as next-generation probiotics.

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.
Gerritsen, J. ; Fuentes Enriquez de Salamanca, S. ; Grievink, W. ; Niftrik, L. van; Tindall, B.J. ; Timmerman, H.M. ; Rijkers, G.T. ; Smidt, H. - \ 2014
International Journal of Systematic and Evolutionary Microbiology 64 (2014)Pt. 5. - ISSN 1466-5026 - p. 1600 - 1616.
ribosomal-rna genes - acid methyl-esters - lipid-composition - deoxyribonucleic-acid - electron microscopy - renaturation rates - dna hybridization - polar lipids - bacteria - chromatography
A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1d lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol %. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of Clostridium species, including C. lituseburense (97.2 %), C. glycolicum (96.2 %), C. mayombei (96.2 %), C. bartlettii (96.0 %) and C. irregulare (95.5 %). All these species show very low 16S rRNA gene sequence similarity (
The effects of probiotics on barrier function and mucosal pouch microbiota during maintenance treatment for severe pouchitis in patients with ulcerative colitis
Persborn, M. ; Gerritsen, J. ; Wallon, C. ; Carlsson, A. ; Akkermans, L.M.A. ; Soderholm, J.D. - \ 2013
Alimentary Pharmacology and Therapeutics 38 (2013)7. - ISSN 0269-2813 - p. 772 - 783.
placebo-controlled trial - familial adenomatous polyposis - follicle-associated epithelium - lactobacillus-rhamnosus gg - bacterial-infection rates - double-blind trial - anal-anastomosis - macromolecular permeability - maintaining remission - escherichia-coli
Background A total of 10-15% of patients with an ileoanal pouch develop severe pouchitis necessitating long-term use of antibiotics or pouch excision. Probiotics reduce the risk of recurrence of pouchitis, but mechanisms behind these effects are not fully understood. Aim To examine mucosal barrier function in pouchitis, before and after probiotic supplementation and to assess composition of mucosal pouch microbiota. Methods Sixteen patients with severe pouchitis underwent endoscopy with biopsies of the pouch on three occasions: during active pouchitis; clinical remission by 4 weeks of antibiotics; after 8 weeks of subsequent probiotic supplementation (Ecologic 825, Winclove, Amsterdam, the Netherlands). Thirteen individuals with a healthy ileoanal pouch were sampled once as controls. Ussing chambers were used to assess transmucosal passage of Escherichia coli K12, permeability to horseradish peroxidase (HRP) and Cr-51-EDTA. Composition and diversity of the microbiota was analysed using Human Intestinal Tract Chip. Results Pouchitis Disease Activity Index (PDAI) was significantly improved after antibiotic and probiotic supplementation. Escherichia coli K12 passage during active pouchitis [3.7 (3.4-8.5); median (IQR)] was significantly higher than in controls [1.7 (1.0-2.4); P <0.01], did not change after antibiotic treatment [5.0 (3.3-7.1); P = ns], but was significantly reduced after subsequent probiotic supplementation [2.2 (1.7-3.3); P <0.05]. No significant effects of antibiotics or probiotics were observed on composition of mucosal pouch microbiota; however, E. coli passage correlated with bacterial diversity (r = -0.40; P = 0.018). Microbial groups belonging to Bacteroidetes and Clostridium clusters IX, XI and XIVa were associated with healthy pouches. Conclusions Probiotics restored the mucosal barrier to E. coli and HRP in patients with pouchitis, a feasible factor in prevention of recurrence during maintenance treatment. Restored barrier function did not translate into significant changes in mucosal microbiota composition, but bacterial diversity correlated with barrier function.
Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype
Gerritsen, J. ; Timmerman, H.M. ; Fuentes, S. ; Minnen, L.P. van; Panneman, H. ; Konstantinov, S.R. ; Rombouts, F.M. ; Gooszen, H.G. ; Akkermans, L.M.A. ; Smidt, H. ; Rijkers, G.T. - \ 2011
Applied and Environmental Microbiology 77 (2011)21. - ISSN 0099-2240 - p. 7749 - 7756.
severe acute-pancreatitis - ribosomal-rna - necrotizing pancreatitis - clinical-course - sequence data - overgrowth - gut - translocation - microbiota - cirrhosis
Prophylactic probiotic therapy has shown beneficial effects in an experimental rat model for acute pancreatitis on the health status of the animals. Mechanisms by which probiotic therapy interferes with severity of acute pancreatitis and associated sepsis, however, are poorly understood. The aims of this study were to identify the probiotic-induced changes in the gut microbiota and to correlate these changes to disease outcome. Duodenum and ileum samples were obtained from healthy and diseased rats subjected to pancreatitis for 7 days and prophylactically treated with either a multispecies probiotic mixture or a placebo. Intestinal microbiota was characterized by terminal-restriction fragment length polymorphism (T-RFLP) analyses of PCR-amplified 16S rRNA gene fragments. These analyses showed that during acute pancreatitis the host-specific ileal microbiota was replaced by an “acute pancreatitis-associated microbiota.” This replacement was not reversed by administration of the probiotic mixture. An increase, however, was observed in the relative abundance of a novel bacterial phylotype most closely related to Clostridium lituseburense and referred to as commensal rat ileum bacterium (CRIB). Specific primers targeting the CRIB 16S rRNA gene sequence were developed to detect this phylotype by quantitative PCR. An ileal abundance of CRIB 16S rRNA genes of more than 7.5% of the total bacterial 16S rRNA gene pool was correlated with reduced duodenal bacterial overgrowth, reduced bacterial translocation to remote organs, improved pancreas pathology, and reduced proinflammatory cytokine levels in plasma. Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy.
Genome sequences of Alicycliphilus denitrificans strains BC and K601T
Oosterkamp, M.J. ; Veuskens, T. ; Plugge, C.M. ; Langenhoff, A.A.M. ; Gerritsen, J. ; Berkel, W.J.H. van; Junca, H. ; Smidt, H. ; Stams, A.J.M. - \ 2011
Journal of Bacteriology 193 (2011)18. - ISSN 0021-9193 - p. 5028 - 5029.
chlorate
Alicycliphilus denitrificans strain BC and A. denitrificans strain K601(T) degrade cyclic hydrocarbons. These strains have been isolated from a mixture of wastewater treatment plant material and benzene-polluted soil and from a wastewater treatment plant, respectively, suggesting their role in bioremediation of soil and water. Although the strains are phylogenetically closely related, there are some clear physiological differences. The hydrocarbon cyclohexanol, for example, can be degraded by strain K601(T) but not by strain BC. Furthermore, both strains can use nitrate and oxygen as an electron acceptor, but only strain BC can use chlorate as electron acceptor. To better understand the nitrate and chlorate reduction mechanisms coupled to the oxidation of cyclic compounds, the genomes of A. denitrificans strains BC and K601(T) were sequenced. Here, we report the complete genome sequences of A. denitrificans strains BC and K601(T)
Intestinal microbiota in human health and disease: the impact of probiotics
Gerritsen, J. ; Smidt, H. ; Rijkers, G.T. ; Vos, W.M. de - \ 2011
Genes & Nutrition 6 (2011)3. - ISSN 1555-8932 - p. 209 - 240.
irritable-bowel-syndrome - 16s ribosomal-rna - gradient gel-electrophoresis - mucosa-associated microbiota - invasive escherichia-coli - polymerase-chain-reaction - human gut microbiota - formula-fed infants - real-time pcr - gastrointestinal-tract microbiota
The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis
Increased serum IL-10/IL-12 ratio in wheezing infants
Koopman, L.P. ; Savelkoul, H.F.J. ; Benten, I.J. van; Gerritsen, J. ; Brunekreef, B. ; Neijens, H.J. - \ 2003
Pediatric Allergy and Immunology 14 (2003). - ISSN 0905-6157 - p. 112 - 119.
soluble e-selectin - atopic-dermatitis - interleukin-2 receptor - adhesion molecules - allergic diseases - il-10 production - t-cells - asthma - children - ige
To investigate the association between various serum markers and atopic symptoms in the first year of life, and to evaluate the prognostic value of these markers for the development of wheezing and skin rash in the second year of life. Data of 86 children on the development of wheezing and skin rash in the first 2 years of life were collected prospectively, making use of parental completed questionnaires, weekly symptom cards, structured interview and physical examination. Serum markers (IL-10, IL-12, IL-13, eotaxin, sE-selectin, sICAM-1, sIL-2R) and total and specific IgE were determined at age 1. Children who developed wheezing in the first year of life had lower serum levels of IL-12 than children without symptoms (median 40.3 pg/ml vs. 49.0 pg/ml, p = 0.01) and a higher serum IL-10/IL-12 ratio (0.41 vs. 0.31, p = 0.001) at age 1. The IL-10/IL-12 ratio increased with an increasing number of wheezing episodes. Levels of sE-selectin in children with wheezing and in children with itchy skin rash in the first year of life were higher than in symptom free children (6.1 ng/ml and 5.9 ng/ml vs. 4.9 ng/ml, p = 0.01 and p = 0.03, respectively). Children who developed wheezing in the second year of life already had increased sICAM-1 levels at age 1. Children who developed wheezing in the first year of life showed a serum cytokine response that is skewed towards a T-helper 2 profile, with lower IL-12 levels and an increased IL-10/IL-12 ratio. Children who developed wheezing in the second year of life had elevated sICAM-1 levels at age 1. Follow-up of the children is needed to evaluate the prognostic value of various serum markers for the development of allergic disease in later childhood.
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