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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Determining Key Research Areas for Healthier Diets and Sustainable Food Systems in Viet Nam
Raneri, Jessica E. ; Kennedy, Gina ; Nguyen, Trang ; Wertheim-Heck, S.C.O. ; Haan, Stef de; Do, Ha Thi Phuong ; Nguyen, Phuong Hong ; Thi, Huong Le ; Mai, Truong Tuyet ; Duong, Thi Thanh Thuy ; Hung, Nguyen ; Nguyen, Tuan ; Huynh, Tuyen ; Nodari, Gulia Rota ; Spellman, Olga ; Talsma, Elise F. ; Stoian, Dietmar ; Duong, Minh-Cam ; Tran, Lam Nguyen ; Bene, Christophe - \ 2019
IFPRI (IFPRI Discussion Paper 1872) - 127 p.
food systems - diet - nutrition - agriculture
Vietnamese food systems are undergoing rapid transformation, with important implications for human and environmental health and economic development. Poverty has decreased, and diet quality and under-nutrition have improved significantly since the end of the Doi Moi reform period (1986-1993) as a result of Viet Nam opening its economy and increasing its regional and global trade. Yet poor diet quality is still contributing the triple burden of malnutrition, with 25 percent stunting among children under age 5, 26 percent and 29 percent of women and children, respectively, anemic, and 21 percent of adults overweight. Agricultural production systems have shifted from predominantly diverse smallholder systems to larger more commercialized and specialized systems, especially for crops, while the ‘meatification’ of the Vietnamese diet is generating serious trade-offs between improved nutrition and sustainability of the Vietnamese food systems. The food processing industry has developed rapidly, together with food imports, resulting in new and processed food products penetrating the food retail outlets, trending towards an increase in the Westernized consumption patterns that are shifting nutrition-related problems towards overweight and obesity and, with it, an increase of non-communicable disease-related health risks. While regulatory policies exist across the food system, these are not systematically implemented, making food safety a major concern for consumers and policy makers alike. Where data exists, it is not easy to aggregate with data from across food system dimensions, making it difficult for Viet Nam to make an informed analysis of current and potential food system trade-offs. In our research, we reviewed existing literature and data, and applied a food systems framework to develop an initial food systems profile for Viet Nam and to identify a comprehensive set a of research questions to fill current data gaps identified through the review. Insights on these would provide the comprehensive evidence needed to inform policy makers on how to develop new food systems policies for Viet Nam, and further refine and improve existing policies to achieve better quality diets and more sustainable food systems in Viet Nam. Based on these, we then engaged with stakeholders to develop research priorities in the Viet Nam context and identified 25 priority research questions. This paper aims to stimulate such reflections by clearly outlining key areas for research, government policy, and development programs on priority investment to build the evidence base around inclusive food systems interventions that aim to result in healthier diets and more sustainable food systems for Viet Nam.
Diagnostiek Ontwikkeling en Toepassing voor het optimaliseren van uiergezondheid
Griffioen, Karien ; Velthuis, A.G.J. ; Wal, F.J. van der; Mevius, D.J. ; Achterberg, R.P. ; Cornelissen, J.B.W.J. ; Dijkman, Remco ; Heuvelink, Annet E. ; Hop, G.E. ; Holstege, Manon M.C. ; Scherpenzeel, Christian ; Lam, Theo - \ 2019
Corrigendum to “Quantification of lipoprotein profiles by nuclear magnetic resonance spectroscopy and multivariate data analysis”
Aru, Violetta ; Lam, Chloie ; Khakimov, Bekzod ; Hoefsloot, Huub C.J. ; Zwanenburg, Gooitzen ; Lind, Mads Vendelbo ; Schäfer, Hartmut ; Duynhoven, John van; Jacobs, Doris M. ; Smilde, Age K. ; Engelsen, Søren B. - \ 2019
TrAC : Trends in Analytical Chemistry 119 (2019). - ISSN 0165-9936

The authors regret that there was an error in the published Table 2. Wrong literature reference numbers were given in Table 2 making the interpretation of the table very confusing to the reader. Table 2 should be replaced with the following corrected table.

Relationship between resumption of ovarian activity, days open, energy balance and metabolic status in dairy cows with different dry period lengths in early lactation
Ma, J. ; Hoeij, R.J. van; Lam, T.J.G.M. ; Kemp, B. ; Knegsel, A.T.M. van - \ 2019
In: Proceedings of the 17th International Conference on Production Diseases in Farm Animals. - Bern, Switserland : University of Bern - ISBN 9783906813936 - p. 176 - 176.
Negative energy balance (NEB) in dairy cows results from a fast increase in milk production post calving while feed intake is limited in this period. NEB is accompanied with an altered metabolic status, which triggers metabolic disorders. Metabolic status in early lactation is related with reproductive performance, e.g. reduced concentrations of insulin and IGF-I, which contributes to reduced follicular responsiveness to gonadotrophic stimulation, and thus prevents the dominant follicle to ovulate, resulting in a delay in the resumption of cyclicity. Omitting or shortening the dry period (DP), adjusting dietary energy level or feeding different dietary energy sources is of interest because that could minimize the risk of NEB, postpartum metabolic diseases and suboptimal fertility like delayed resumption of postpartum ovarian cyclicity. The aim of this study is to investigate the effect of DP length, dietary energy level, dietary energy source and interactions among these factors on fertility (resumption of ovarian cyclicity and days open) of dairy cows postpartum. Additionally, the relation between energy balance and metabolic status of dairy cows during early lactation and resumption of ovarian cyclicity and days open will be evaluated.
Data from: Multi-variable approach pinpoints origin of oak wood with higher precision
Akhmetzyanov, L. ; Buras, Allan ; Sass-Klaassen, U.G.W. ; Ouden, J. den; Mohren, G.M.J. ; Groenendijk, Peter ; García-González, Ignacio - \ 2019
dendroprovenancing - earlywood vessels - latewood width - multi-variable approach - region-specific growth patterns - Quercus spp. - wood anatomy - Quercus robur - Quercus petraea - Quercus pyrenaica - Quercus faginea
Aim: Spatial variations of environmental conditions translate into biogeographic growth patterns of tree growth. This fact is used to identify the origin of timber by means of dendroprovenancing. Yet, dendroprovenancing attempts are based on ring-widths measurements, and neglect additional tree-ring parameters. To explore the effect of including additional variables in dendroprovenancing, we investigate whether and, if so, why the incorporation of wood-anatomical parameters can increase the precision of identifying the origin of oak wood. Since such features reflect environmental conditions of different periods – which vary between source regions – we hypothesize that their inclusion allows more precise dendroprovenancing. Location: Europe, Spain. Taxon: Quercus robur L., Quercus petraea (Matt.) Liebl., Quercus faginea Lam., Quercus pyrenaica Willd. Methods: We sampled four oak species resembling a longitudinal and an elevational/continental gradients. We measured multiple tree-ring variables to (1) extract meaningful variables, (2) represent statistical relations among variables, (3) analyse regional-specific growth patterns in individual time series and (4) determine underlying climate-growth relationships. Leave-one-out analyses were used to test whether a combination of selected variables allows dendroprovenancing of a randomly selected tree within the area. Results: A combination of latewood width and earlywood vessels size can be used to pin-point the origin of oak wood with higher precision than latewood width only. Variation in latewood widths appointed the wood to areas across the longitudinal gradient, whereas variation in vessels assigned wood to locations along a latitudinal/topographic gradient. The climatic factors behind these gradients are respectively an East-West gradient in June-July temperature, and a North-South gradient in winter/ spring temperatures. The leave-one-out analyses supported the robustness of the results. Main conclusions: Integration of multiple tree-ring variables in combination with multivariate techniques leads to higher precision in the dendroprovenancing of ring-porous oak species.
Blood and urine analyses after radioembolization of liver malignancies with [166Ho]Ho-acetylacetonate-poly(L-lactic acid) microspheres
Bakker, Robbert C. ; Roos, Remmert de; Tessa Ververs, F.F. ; Lam, Marnix G.E.H. ; Lee, Martijn K. van der; Zonnenberg, Bernard A. ; Krijger, Gerard C. - \ 2019
Nuclear medicine and biology 71 (2019). - ISSN 0969-8051 - p. 11 - 18.
Blood - Holmium - Radioisotope - SIRT - Urine

Background: [ 166 Ho]Ho-acetylacetonate-poly(L-lactic acid) microspheres were used in radioembolization of liver malignancies by intra-arterial administration. The primary aim of this study was to assess the stability and biodistribution of these microspheres. Materials and methods: Peripheral blood and urine samples were obtained from two clinical studies. Patient and in vitro experiment samples were analyzed using inductively coupled plasma mass spectrometry (ICP-MS), gamma-ray spectroscopy, light microscopy, Coulter particle counting, and high performance liquid chromatography (HPLC). Results: The median percentage holmium compared to the total amount injected into the hepatic artery was 0.19% (range 0.08–2.8%) and 0.32% (range 0.03–1.8%) in the 1 h blood plasma and 24 h urine, respectively. Both the blood plasma and urine were correlated with the neutron irradiation exposure required for [ 166 Ho]Ho-AcAc-PLLA microsphere production (ρ = 0.616, p = 0.002). After a temporary interruption of the phase 2 clinical study, the resuspension medium was replaced to precipitate [ 166 Ho]Ho 3+ pre-administration using phosphate. The in vitro near-maximum neutron irradiation experiments showed significant [ 166 Ho]Ho-AcAc-PLLA microsphere damage. Conclusion: The amount of holmium in the peripheral blood and urine samples after [ 166 Ho]Ho-AcAc-PLLA microsphere intrahepatic infusion was low. A further decrease was observed after reformulation of the resuspension solution but minimization of production damage is necessary.

Multi-variable approach pinpoints origin of oak wood with higher precision
Akhmetzyanov, Linar ; Buras, Allan ; Sass-Klaassen, Ute ; Ouden, Jan den; Mohren, Frits ; Groenendijk, Peter ; García-González, Ignacio - \ 2019
Journal of Biogeography 46 (2019)6. - ISSN 0305-0270 - p. 1163 - 1177.
dendroprovenancing - earlywood vessels - latewood width - multi-variable approach - Quercus spp. - region-specific growth patterns - wood anatomy

Aim: Spatial variations of environmental conditions translate into biogeographical patterns of tree growth. This fact is used to identify the origin of timber by means of dendroprovenancing. Yet, dendroprovenancing attempts are commonly only based on ring-width measurements, and largely neglect additional tree–ring variables. We explore the potential of using wood anatomy as a dendroprovenancing tool, and investigate whether it increases the precision of identifying the origin of oak wood. Since different tree–ring variables hold different information on environmental conditions prevailing at specific times of the growing season—which vary between source regions—we hypothesize that their inclusion allows more precise dendroprovenancing. Location: Europe, Spain. Taxon: Quercus robur L., Quercus petraea (Matt.) Liebl., Quercus faginea Lam., Quercus pyrenaica Willd. Methods: We sampled four oak species across Northern Spain, i.e. from the Basque country and Cantabria and—in the Basque country—from low to high elevation (topographic/latitudinal gradient). We measured multiple tree–ring variables to (a) extract complementary variables; (b) present statistical relations among them; (c) analyse region-specific variation in their patterns based on time–series of individual trees; and (d) determine underlying climate–growth relationships. Leave-one-out analysis was used to test whether a combination of selected variables allowed dendroprovenancing of a randomly selected tree within the area. Results: A combination of latewood width (LW) and earlywood vessel size was used to pinpoint the origin of oak wood with higher precision than ring width or LW only. Variation in LW pinpointed the wood to east and west areas, whereas variation in vessels assigned wood to locations along a latitudinal/topographic gradient. The climatic triggers behind these gradients are respectively an east–west gradient in June–July temperature and a north–south gradient in winter/spring temperatures. The leave-one-out analyses supported the robustness of these results. Main conclusions: Integration of multiple wood–xylem anatomical variables analysed with multivariate techniques leads to higher precision in the dendroprovenancing of ring-porous oak species.

Failure costs associated with mastitis in smallholder dairy farms keeping Holstein Friesian × Zebu crossbreed cows
Mekonnen, S.A. ; Koop, G. ; Getaneh, A.M. ; Lam, T.J.G.M. ; Hogeveen, H. - \ 2019
Animal 13 (2019)11. - ISSN 1751-7311 - p. 2650 - 2659.
clinical mastitis - dairy - failure cost - smallholder farms - subclinical mastitis

Mastitis is a costly disease and in many areas of the world, these costs have been quantified to support farmers in their decision making with regard to prevention of mastitis. Although for subsaharan circumstances estimates have been made for the costs of subclinical mastitis (SCM), farm-specific cost estimations comprising both clinical mastitis (CM) and SCM are lacking. In this paper, we quantified failure costs of both CM and SCM on 150 Ethiopian market-oriented dairy farms keeping Holstein Friesian × Zebu breed cows. Data about CM were collected by face-to-face interviews and the prevalence of SCM was estimated for each farm using the California mastitis test. All other relevant information needed to calculate the failure costs, such as the consequences of mastitis and price levels, was collected during the farm visits, except for the parameter for milk production losses due to SCM, which was based on literature estimates and subjected to sensitivity analyses. The average total failure costs of mastitis was estimated to be 4 765 Ethiopian Birr (ETB) (1 ETB = 0.0449 USD) per farm per year of which SCM contributed 54% of the costs. The average total failure costs per lactating cow per farm per year were 1 961 ETB, with a large variation between farms (range 0 to 35 084 ETB). This large variation in failure costs between farms was mainly driven by variation in incidence of CM and prevalence of SCM. Milk production losses made the largest contribution (80%), whereas culling contributed 13% to 17% to the total failure costs. In our estimates, costs of veterinary services, drugs, discarded milk and labour made a minor contribution to the total failure costs of mastitis. Relative to the income of dairy farmers in North Western Ethiopia; the total failure costs of mastitis are high. In general, Ethiopian farmers are aware of the negative consequences of CM, but creating awareness of the high costs of SCM and showing large variation between farmers may be instrumental in motivating farmers to also take preventive measures for SCM.

Clostridium difficile in wild rodents and insectivores in the Netherlands
Krijger, I.M. ; Meerburg, B.G. ; Harmanus, C. ; Burt, S.A. - \ 2019
Letters in Applied Microbiology (2019). - ISSN 0266-8254
animal to human - Clostridioides difficile - farms - house mouse - Mus musculus - Rattus rattus - transmission - zoonotic pathogen

With wild rodents and insectivores being present around humans and their living, working and food production environments, it is important to gain knowledge of the zoonotic pathogens present in these animals. The enteropathogen Clostridium difficile, an opportunistic anaerobic bacteria, can be carried by both animals and humans, and is distributed globally. It is known that there is genetic overlap between human and animal sources of C. difficile. In this study, the aim was to assess the presence of C. difficile in rodents and insectivores trapped on and around pig and cattle farms in the Netherlands. In total 347 rodents and insectivores (10 different species) were trapped and 39·2% tested positive for presence of C. difficile. For all positive samples the ribotype (RT) was determined, and in total there were 13 different RTs found (in descending order of frequency: 057, 010, 029, 005, 073, 078, 015, 035, 454, 014, 058, 062, 087). Six of the RTs isolated from rodents and insectivores are known to be associated with human C. difficile infection; RT005, RT010, RT014, RT015, RT078 and RT087. The presence of rodents and insectivores in and around food production buildings (e.g. farms) could contribute to the spread of C. difficile in the human environment. In order to enable on-farm management for pathogen control, it is essential to comprehend the role of wild rodents and insectivores that could potentially affect the ecology of disease agents on farms. Significance and Impact of the Study: This study shows that rodents and insectivores in and around food production buildings (e.g. farms) can carry Clostridium difficile ribotypes associated with human C. difficile infection (CDI). C. difficile spores in rodent and insectivore droppings are able to survive in the environment for prolonged periods, leading to host-to-host exposure and transmission. Therefore we can state that rodent and insectivore presence on farms is a risk for zoonotic pathogen transmission of C. difficile.

Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells
Charkoftaki, Georgia ; Thompson, David C. ; Golla, Jaya Prakash ; Garcia-Milian, Rolando ; Lam, T.T. ; Engel, Jasper ; Vasiliou, Vasilis - \ 2019
Chemico-Biological Interactions 304 (2019). - ISSN 0009-2797 - p. 88 - 96.
Farm-level risk factors for bovine mastitis in Dutch automatic milking dairy herds
Deng, Z. ; Koop, G. ; Lam, T.J.G.M. ; Lans, I.A. van der; Vernooij, J.C.M. ; Hogeveen, H. - \ 2019
Journal of Dairy Science 102 (2019)5. - ISSN 0022-0302 - p. 4522 - 4535.
automatic milking system - mastitis - nonlinear principal component analysis - principal component regression - risk factor

Automatic milking systems (AMS) are installed on a growing number of dairy farms worldwide. Management to support good udder health might be different on farms with an AMS compared with farms milking with a conventional milking system, as risk factors for mastitis on farms using an AMS may differ. The aim of this study was to identify farm level factors associated with mastitis on Dutch dairy farms using an AMS. In 2008, risk factor data were collected using a questionnaire combined with on-farm recordings of cow, stall, and AMS hygiene on 135 farms. These risk factor data were linked to 4 udder-health-associated dependent variables: average herd somatic cell count (HeSCCav), variance of the average herd somatic cell count (SCC) on test days (HeSCCvar), the average proportion of new high SCC cases (NHiSCC), and the farmer-reported annual incidence rate of clinical mastitis (IRCM). We employed regression models using multiple imputation to deal with missing values. Due to the high dimensionality of the risk factor data, we also performed nonlinear principal component analysis (NLPCA) and regressed the dependent variables on the principal components (PC). Good hygiene of cows and of AMS were found to be related to a lower HeSCCav and less NHiSCC. Effective postmilking teat disinfection was associated with a lower NHiSCC. A higher bulk tank milk SCC threshold for farmers' action was related to more NHiSCC. Larger farm size was related to lower HeSCCvar but higher NHiSCC. Negative attitude of farmers to animal health, higher frequency of checking AMS, and more time spent on viewing computer data were all positively related to higher IRCM. An NLPCA with 3 PC explained 16.3% of the variance in the risk factor variables. Only the first 2 PC were associated with mastitis. The first PC reflected older and larger farms with poor cow hygiene and AMS hygiene, and was related to higher HeSCCav and NHiSCC, whereas the second PC reflected newly built smaller farms with poor cow hygiene and low milk production, and was associated with higher HeSCCvar and NHiSCC, but lower IRCM. Our study suggests that many of the risk factors on conventional milking system farms are applicable to AMS farms, specifically concerning hygiene of the cows and the milking machine, but on large AMS farms, udder health may need more attention than on smaller AMS farms. Multiple imputation is instrumental to deal with missing values and NLPCA is a useful technique to process high dimensional data in our study.

Intramammary antimicrobial treatment of subclinical mastitis and cow performance later in lactation
Borne, Bart H.P. van den; Schaik, Gerdien van; Lam, Theo J.G.M. ; Nielen, Mirjam ; Frankena, Klaas - \ 2019
Journal of Dairy Science 102 (2019)5. - ISSN 0022-0302 - p. 4441 - 4451.
antimicrobial - clinical mastitis - dairy cow - milk yield - somatic cell count

The aim of this study was to evaluate long-term therapeutic effects of antimicrobial treatment of recently acquired subclinical mastitis (RASCM) during lactation. Quarter-level clinical mastitis (CM) follow-up, composite somatic cell counts (SCC), and cow-level milk yield later in lactation were evaluated using follow-up data from 2 previously published linked randomized field trials. The first trial randomly assigned antimicrobial treatment with any intramammary product or negative control to culture-positive quarters of cows having a first elevated composite SCC after 2 consecutive low composite SCC measurements. Untreated cows that had a second elevated composite SCC at the next measurement and were staphylococci-positive (i.e., Staphylococcus aureus or non-aureus staphylococci) were randomly assigned to treatment or control. Quarter-level CM cases were reported by the participating herd personnel, and milk yield and composite SCC data were obtained from the regular test-day recording. Frailty survival models were used to evaluate the long-term therapeutic effects of antimicrobial treatment of RASCM on quarter-level CM follow-up. Mixed linear regression models were applied to quantify the effect on milk yield and composite SCC. Data of 638 quarters from 486 cows in 38 herds were available for statistical analyses, of which 229 quarters of 175 cows received antimicrobial treatment for RASCM. Antimicrobial treatment culminated in reduced composite SCC levels later in lactation but did not result in different milk yield levels or CM follow-up compared with control cows. Antimicrobial treatment of cows with RASCM should therefore only be considered in exceptional situations given the current focus on antimicrobial usage reduction in animal husbandry.

Efficient production of N-acetylglucosamine with chitinolytic enzymes from Myceliophthorathermophila C1
Kaisler, Małgorzata - \ 2019
Wageningen University. Promotor(en): G. Eggink, co-promotor(en): C.G. Boeriu; L.A.M. van den Broek. - Wageningen : Wageningen University - ISBN 9789463435772 - 155
Development of a valid judgment bias test for dairy cattle
Kremer, L.A.M. ; Webb, L.E. ; Bokkers, Eddie ; Reenen, C.G. van - \ 2018
Development of a valid judgment bias lest for dairy cows
Kremer, L.A.M. ; Webb, L.E. ; Bokkers, Eddie ; Boer, I.J.M. de; Reenen, C.G. van - \ 2018
National approaches to reduce antimicrobial usage in dairy herds – Lessons learned in five European countries
Borne, Bart van den; Reyher, Kirsten ; Persson, Y. ; Vliegher, S. de; Farre, M. ; Scherpenzeel, C. ; Lam, T. ; Koops, W. ; Hogeveen, H. - \ 2018
- 1 p.
SyNDI : Synchronous network data integration framework
Lindfors, Erno ; Dam, Jesse C.J. van; Lam, Carolyn Ming Chi ; Zondervan, Niels A. ; Martins dos Santos, Vitor A.P. ; Suarez-Diez, Maria - \ 2018
BMC Bioinformatics 19 (2018)1. - ISSN 1471-2105
Cytoscape - Galaxy - Mycobacterium tuberculosis - Network biology - Staphylococcus aureus - Synchronous network visualization - Systems biology - Workflow

Background: Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Those resulting networks sometimes describe a wide range of aspects, for example different experiment conditions, species, tissue types, stimulating factors, mutants, or simply distinct interaction features of the same network produced by different algorithms. For these scenarios, synchronous visualization of more than one distinct network is an excellent mean to explore all the relevant networks efficiently. In addition, complementary analysis methods are needed and they should work in a workflow manner in order to gain maximal biological insights. Results: In order to address the aforementioned needs, we have developed a Synchronous Network Data Integration (SyNDI) framework. This framework contains SyncVis, a Cytoscape application for user-friendly synchronous and simultaneous visualization of multiple biological networks, and it is seamlessly integrated with other bioinformatics tools via the Galaxy platform. We demonstrated the functionality and usability of the framework with three biological examples - we analyzed the distinct connectivity of plasma metabolites in networks associated with high or low latent cardiovascular disease risk; deeper insights were obtained from a few similar inflammatory response pathways in Staphylococcus aureus infection common to human and mouse; and regulatory motifs which have not been reported associated with transcriptional adaptations of Mycobacterium tuberculosis were identified. Conclusions: Our SyNDI framework couples synchronous network visualization seamlessly with additional bioinformatics tools. The user can easily tailor the framework for his/her needs by adding new tools and datasets to the Galaxy platform.

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).

Veehouderij en gezondheid omwonenden III : Longontsteking in de nabijheid van geiten- en pluimveehouderijen; actualisering van gegevens uit huisartspraktijken 2014-2016
IJzermans, C.J. ; Smit, L.A.M. ; Heederik, D.J.J. ; Hagenaars, T.J. ; Baliatsas, C. ; Dückers, M. ; Huss, A. ; Hogerwerf, L. ; Post, P. ; Boender, G.J. ; Petie, R. - \ 2018
Utrecht : NIVEL - ISBN 9789461225153 - 52
Molecular networks affected by neonatal microbial colonization in porcine jejunum, luminally perfused with enterotoxigenic Escherichia coli, F4ac fimbria or Lactobacillus amylovorus
Trevisi, Paolo ; Priori, Davide ; Jansman, Alfons J.M. ; Luise, Diana ; Koopmans, Sietse Jan ; Hynönen, Ulla ; Palva, Airi ; Meulen, Jan van der; Bosi, Paolo - \ 2018
PLoS ONE 13 (2018)8. - ISSN 1932-6203

The development of an early complex gut microbiota may play an important role in the protection against intestinal dysbiosis later in life. The significance of the developed microbiota for gut barrier functionality upon interaction with pathogenic or beneficial bacteria is largely unknown. The transcriptome of differently perfused jejunal loops of 12 caesarian-derived pigs, neonatally associated with microbiota of different complexity, was studied. Piglets received pasteurized sow colostrum at birth (d0), a starter microbiota (Lactobacillus amylovorus (LAM), Clostridium glycolicum, and Parabacteroides) on d1-d3, and a placebo inoculant (simple association, SA) or an inoculant consisting of sow’s diluted feces (complex association, CA) on d3-d4. On d 26–37, jejunal loops were perfused for 8 h with either enterotoxigenic Escherichia coli F4 (ETEC), purified F4 fimbriae, LAM or saline control (CTRL). Gene expression of each intestinal loop was analyzed by Affymetrix Porcine Gene 1.1_ST array strips. Gene Set Enrichment Analysis was performed on expression values. Compared to CTRL, 184 and 74; 2 and 139; 2 and 48 gene sets, were up- and down-regulated by ETEC, F4 and LAM, respectively. ETEC up-regulated networks related to inflammatory and immune responses, RNA processing, and mitosis. There was a limited overlap in up-regulated gene sets between ETEC and F4 fimbriae. LAM down-regulated genes related to inflammatory and immune responses, as well as to cellular compound metabolism. In CA pigs, 57 gene sets were up-regulated by CA, while 73 were down-regulated compared to SA. CA up-regulated gene sets related to lymphocyte modulation and to cellular defense in all loop perfusions. In CA pigs, compared to SA pigs, genes for chemokine and cytokine activity and for response to external stimuli were down-regulated in ETEC-perfused loops and up-regulated in CTRL. The results highlight the importance of the nature of neonatal microbial colonization in the response to microbial stimuli later in life.

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