Papers by Dirkjan Schokker
<p>Overview of the time-line, birth (day 0), administration of the treatments (day 4), meas... more <p>Overview of the time-line, birth (day 0), administration of the treatments (day 4), measurements days 8, 55, and 176, as well as the hypothetical interpretation of all results from the whole experiment, results from the previous paper about day 8 are included too [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116523#pone.0116523.ref016" target="_blank">16</a>]. On the left we categorized the gut system in three different ‘blocks’, immune programming which occurs in early life, followed by an instable period which includes weaning and later in life a stable period (homeostasis). Note that the treatments, antibiotic and/or stress, were at day 4 during the immune programming period. Next to this the significant findings of microbiota or gene expression data between treatments per time-point are depicted by “+”, and no differences between treatments with a “-”. On the right a metaphorical landscape of the gut system in time is depicted, where the top is day 0 (birth) and bottom is day 176 (slaughter). Spheres depict the current state of the system for day 8, 55, and 176, and colours correspond to the different treatments (T1; red, T2; blue, and T3; green).</p
Advances in Animal Biosciences, Jul 1, 2022
Journal of Animal Science
Probiotics are known to stabilize the microbiome especially in monogastric animals. Limited infor... more Probiotics are known to stabilize the microbiome especially in monogastric animals. Limited information is available on the potential effect on the rumen microbiome. Feedlot cattle are fed high concentrate diets which may result in subclinical and clinical acidosis due to dysbiosis. This can negatively affect the production and lead to morbidities and death. The alpha diversity of a microbiome population and the ratio of Proteobacteria towards Firmicutes and Bacteroidetes have been known to indicate potential dysbiosis. The aim of this study was to investigate the effect of probiotics on the alpha diversity and Proteobacteria ratio of the rumen microbiome of feedlot cattle during the finisher phase. Thirty-six Bonsmara bulls were randomly divided into three groups and fed for 120 days; a basal diet commonly fed in South African feedlots (CTR: control), the basal diet supplemented with monensin (30 mg/animal/day; MON) or a Bacillus-based probiotic (B. licheniformis and B. subtilis; B...
Journal of Animal Science
The threat of the development of an antibiotic resistant bacterium necessitates investigation for... more The threat of the development of an antibiotic resistant bacterium necessitates investigation for alternative feed additives. Probiotics are known to confer a health benefit to the animal and affect the production of the animal through increased nutrient digestibility. The aim of this study was to investigate the bacterial composition of the rumen of South African feedlot cattle when supplemented with a Bacillus probiotic. Twenty-four Bonsmara cattle were randomly divided into two groups: a basal diet (control, CTR) and the basal diet supplemented with Bacillus-based probiotic (B. licheniformis and B. subtilis; Bovacillus, Chr. Hansen A/S; BOV). The animals were fed for 120-days divided by starter, grower, and finisher diets. Four animals from each group were selected for rumen content collection via stomach tube during each phase. DNA extraction was performed and submitted for 16S rRNA sequencing (V3-V4). Approximately 41 300 ASVs were identified from 87 genera using DADA2, phylose...
Wageningen Academic Publishers, Aug 30, 2021
BMC Genomics, 2019
Background The mammalian intestine is a complex biological system that exhibits functional plasti... more Background The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we performed a high-level data integration of 14 whole-genome transcriptomics datasets from samples of intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information from the Reactome database. Results The results show an integrated response of the mouse intestinal mucosa to challenges with agents introduced orally that were expected to perturb homeostasis. We observed that a common set of pathways respond to different stimuli, of which the most reactive was the Regulation of Complement Cascade pathway. Altered expression of the Regulation of Complement Cascade pathway was verified in mouse organoids challenged with different stimuli in vitro. Conclusions Results of the integrated transcriptomics analysis and data driven experiment ...
This research was conducted by Wageningen Livestock Research, commissioned and funded by the Mini... more This research was conducted by Wageningen Livestock Research, commissioned and funded by the Ministry of Agriculture, Nature and Food Quality, within the framework of the Public Private Partnership 'Breed&Feed4Food' (TKI-AF-14215; project number BO-47-001-008) and supported by "Vereniging Diervoederonderzoek Nederland" (VDN).
This work is embedded within the Big Data project of Breed4Food. The selected use case was an exp... more This work is embedded within the Big Data project of Breed4Food. The selected use case was an experiment in which the gait score of turkeys was determined, here 3 animals can be used for educational purposes. This gait scoring is traditionally performed by an expert. In this experiment different type of sensors were used to explore to what extent these sensors can describe or mirror the gait score of the expert. Data & Sensors Gait score (visually by expert) Force Plate (Kistler) Accelerometers / inertial measurement units {IMUs} (Xsense MTw awinda) 3D Video camera (Intel Realsense D415)
British Poultry Science, 2018
1. An experiment was conducted to evaluate the effects of technical feed ingredients between 14 a... more 1. An experiment was conducted to evaluate the effects of technical feed ingredients between 14 and 28 d of age on performance and health status of broilers (d 14-35) fed diets with a high inclusion rate of rapeseed meal as a nutritional challenge. It was hypothesized that the feed ingredients would improve health status related parameters. 2. A total of 1008 one-day-old male Ross 308 chicks were distributed over 36 floor pens and allocated to one of six iso-caloric (AME N 13 MJ/kg) growing diets (d 15-28): a control and five test diets supplemented with quercetin (400 mg/kg), oat hulls (50 g/kg), β-glucan (100 mg/kg), lysozyme (40 mg/kg) or fish oil ω-3 fatty acids (40 g/kg), with six replicate pens per treatment. 3. Dietary inclusion of oat hulls and lysozyme resulted in a reduction in broiler performance during the first week after providing the experimental diets. 4. No effect of interventions on the microbiota diversity in the jejunum and ileum was observed. Ileal microbiota composition of birds fed oat hulls differed from the other groups, as shown by a higher abundance of the genus Enterococcus, mainly at the expense of the genus Lactobacillus. 5. In the jejunum, villus height and crypt depth of lysozyme-fed birds at d 28 were decreased compared to the control group. Higher total surface area of villi occupied by goblet cells and total villi surface area in jejunum (d 21 and 28) were observed in chickens fed oat hulls compared to other groups. 6. Genes related to the growth-factor-activity pathway were more highly expressed in birds fed β-glucan compared to the control group, while the genes related to anion-transmembrane-transporter-activity pathway in the quercetin-and oat hull-fed birds were less expressed. The genes differently expressed between dietary interventions did not seem to be directly involved in immune related processes. 7. It was concluded that the tested nutritional interventions in the current experiment only marginally effected health status related parameters.
Metabolites
The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrastin... more The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (1H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and ky...
The objective of this study was to use non-invasive fecal metabolomics to evaluate the effects of... more The objective of this study was to use non-invasive fecal metabolomics to evaluate the effects of contrasting sanitary conditions and associated subclinical health status of pigs. We analyzed fecal metabolite profiles using nuclear magnetic resonance (<sup>1</sup>H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions (LSC and HSC, respectively) differed in fecal metabolites related to degradation of dietary starch, metabolism of the intestinal microbiome, and degradation of constituents of animal (host) endogenous origin. The metabolites that differed significantly originated from metabolic processes involved in either maintaining nutrient digestion capacity, including metabolism of purines, energy metabolism, bile acid degradation and recycling, or in immune system metabolism. The results showed that the fecal metabolite profiles reflect sanitary conditions under which the pigs are kept. The fecal metabolic profiles strongly resembled pr...
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Additional file 1. Tab. S1. Antibody panels used to identify immune cells in blood and broncho-al... more Additional file 1. Tab. S1. Antibody panels used to identify immune cells in blood and broncho-alveolar lavage fluid. Fig. S1. The effect of housing condition on growth performance, T helper cells and memory T helper cells in blood, as well as memory Thelper cells in broncho-alveolar lavage fluid. Fig. S2. The effect of time on faecal microbial beta-diversity and alphadiversity. Fig. S3. The effect of gut location on luminal microbial beta-diversity and alpha-diversity. Fig. S4. The effect of housing condition on faecal microbial variation on day 12 and day 26. Fig. S5. The effect of housing condition on faecal microbial alpha-diversity over time. Fig. S6. The genera that were differentially abundant between both housing conditions. Fig. S7. Distance-based redundancy analysis (db-RDA) triplot showing the association between fecal microbiota variation and environmental variables based on weighted uniFrac distance. Fig. S8. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) plot o...
Additional file 1: Schematic representation of the study. 3-dimensional organoids were generated ... more Additional file 1: Schematic representation of the study. 3-dimensional organoids were generated from mouse duodenum (1). The organoids were subsequently dissociated into single cells (2) and grown as 2-dimensional polarised monolayers (3). Polarized monolayers of organoid cells were exposed to different protein sources [CAS, SBM, SDPP, YMW, or medium control (MC)] for 6 h (4) and further processed for imaging (5) gene expression (6), and biochemical assays (7), to investigate the effects of undigested protein sources on the duodenal epithelium.
The dataset contains an experiment that was conducted to investigate the effects of dietary inclu... more The dataset contains an experiment that was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 d of age on immune competence-related parameters and performance of broilers. A total of 960 day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to 1 of 3 experimental diets including graded levels, 0%, 5%, and 10% of rye. Here, the microbiota of jejunal digesta samples is reported, i.e. the raw fastq data, as well as the metadata. The accompanying (peer-reviewed) scientific article can be found here: PMID: 28854752 DOI: 10.3382/ps/pex152
Additional file 5: Figure S2. Network of Reactome root pathway. The nodes in this network represe... more Additional file 5: Figure S2. Network of Reactome root pathway. The nodes in this network represent the 27 root pathways as present in Reactome v51 and the edges indicate the 'leaf' pathways shared by connected root pathways. The thickness of the edges indicates the number of leaf pathways shared by the nodes. The nodes are labelled with the names of the root pathways and the number of enclosed leaf pathways is given between brackets. The inset shows a simplified example of root and leaf pathways, where the cartoon has one root pathway with three leaf pathways.
Full analysis of functional annotation clustering. The Additional File (presented as.xlsx) contai... more Full analysis of functional annotation clustering. The Additional File (presented as.xlsx) contains multiple worksheets, where the first worksheet describes the data present in the other five worksheets. Worksheets 2–5 contain the full DAVID functional annotation clustering results for the contrast A5-WA5 (up- and down-regulated genes) and A14-WA14 (up- and down-regulated genes). Whereas worksheets 4 contains the gene names (p
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Papers by Dirkjan Schokker