Dirkjan SchokkerWageningen University & Research | WUR · Wageningen Bioveterinary Research
Dirkjan Schokker
PhD
About
121
Publications
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Introduction
Data Integration
Intestinal Functionality and Health
Big Data; Omics
Animals; Pigs and Chicken
Additional affiliations
January 2016 - March 2022
January 2012 - December 2015
October 2007 - October 2011
Education
September 2005 - August 2007
September 2002 - September 2005
Publications
Publications (121)
Insects like the black soldier fly larvae (Hermetia illucens; BSFL) have been proposed as protein-rich feed ingredients to support the growing demand for meat. The BSFL hold also promise for use as a protein source in pet foods and, as such, it has been studied for palatability, nutritional quality and health effects in dogs and cats. This study ai...
Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can a...
We aimed to evaluate the effects of including black soldier fly larvae meal (BSFL) meal in a dry extruded food on nutritional quality and some health aspects in healthy adult cats. Two dry extruded foods with either poultry meal (control) or 37.5% BSFL meal were fed to eight (3.8-5.2 kg BW; 2.3-y.o.) cats in a cross-over design with two 28-day peri...
Endotoxins released from poultry feces have been associated with impaired human health. Because endotoxins are released from gram-negative intestinal bacteria, it was hypothesized that dietary strategies may influence endotoxin excretion via modulation of gut microbiota. We therefore tested dietary strategies that could potentially reduce cloacal e...
Goat milk is produced on mainstream and artisanal farms. It was expected that the farm management may influence the microbial population of the milk. Therefore, we investigated the bacterial content and microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus le...
Background
To improve our understanding of host and intestinal microbiome interaction, this research investigated the effects of a high-level zinc oxide in the diet as model intervention on the intestinal microbiome and small intestinal functionality in clinically healthy post-weaning piglets. In study 1, piglets received either a high concentratio...
Simple Summary
Consumer preferences are demanding the removal of antibiotic growth promoters from animal diets. To meet the demand of animal protein for the growing human population, alternative feed additives, such as probiotics and essential oils, need to be investigated to increase the overall efficiency of farm animals. The microorganisms in th...
Host genotype, early post-hatch feeding, and pre- and probiotics are factors known to modulate the gut microbiome. However, there is a knowledge gap on the effect of both chicken genotype and these dietary strategies and their interplay on fecal microbiome composition and diversity, which, in turn, can affect the release of endotoxins in the excret...
Modern broiler breeds allow for high feed efficiency and rapid growth, but come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are furthermore affected by the composition of the gut microbiota, which in turn is influenced by diet composition. In this study we therefore assessed how d...
Aneuploidy is the loss or gain of one or more chromosomes. Although it is a rare phenomenon in liveborn individuals, it is observed in livestock breeding populations. These breeding populations are often routinely genotyped and the genotype intensity data from single nucleotide polymorphism (SNP) arrays can be exploited to identify aneuploidy cases...
Background
Organoids are in vitro model systems generated from tissues. Organoids express specific physiological functions associated with their original tissue location and they express tissue-segment-specific genes. The aim of this study was to investigate the resemblance of duodenum, ileum (with or without Peyer’s Patches (PP) – PP could be reco...
Organoids are in vitro model systems generated from tissues. Organoids express specific physiological functions associated with their original tissue location and they express tissue-segment-specific genes. The aim of this study was to culture pig organoids from different areas of intestinal segments: duodenum, ileum (with or without Peyers Patches...
In precision dairy farming there is a need for continuous and real-time availability of data on cows and systems. Data collection using sensors is becoming more common and it can be difficult to connect sensor measurements to the identification of the individual cow that was measured. Cows can be identified by RFID tags, but ear tags with identific...
More and more sensor and automation data are available that enable animal breeders to define novel traits. However, sensor and automation data are often frequently measured differently (e.g., milk yield and different milk components are continuously measured during each milking). These differences are challenging animal breeders to define traits an...
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...
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...
This study aimed to identify whether early-life conditions in broiler chickens could affect their behavior and welfare, and whether or not this was associated with an altered gut microbiome composition or diversity. Broilers were tested in a 2 x 2 factorial design with hatching conditions [home pen (OH) or at the hatchery (HH)] and enrichment (dark...
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 m...
Improved understanding of the microbial populations during intensive feeding of feedlot cattle holds potential for optimizing production efficiency. Ionophores are used to increase the production and efficiency of ruminants and are commonly used in South African feedlots. Bonsmara bull calves (n=24) were subject to a four-phase feedlot diet in a gr...
Herein, we investigated to what extent molecular phenotypes of the systemic level (blood) and local (intestine) are associated with the performance of laying hens at 95 weeks of age. After the trial had run for 95 weeks, two performance groups were generated, i.e., egg production (PROD) and egg breaking strength (BS). A subset of 21 cages, 116 hens...
Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The “it’s the song, not the singer” theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns...
Providing pigs a diet that matches their nutrient requirements involves optimizing the diet based on the nutrient digestibility values of the considered feed ingredients. Feeding the same quantity of a diet to pigs with similar BW but with different requirements, however, can result in a different average daily gain (ADG) and backfat thickness (BF)...
Background
Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophylactic antibiotic use is urgent for the sustainable swine production globally. To this end, housing methodology providing effectiv...
Health and performance are important aspects in the broiler industry. Underlying complex traits like total mean weight and feed efficiency are polygenic and related to genetic background and an association of the microbiota with these traits has been identified. Whether this association is also reflected in the fecal samples of broilers is not exte...
Black soldier fly larva (BSF, Hermetia illucens L.) meal is considered as an alternative protein source with has the
potential to partially replace conventional protein source such as soybean meal (SBM) in livestock species, including
pigs. Measuring the profile of systemic amine metabolites by the ultraperformance liquid chromatography-tandem
mass...
Differences in sanitary conditions, as model to induce differences in subclinical immune stimulation, affect the growth performance and nutrient metabolism in pigs. The objective of the present study was to evaluate the colonic microbiota and the colonic and systemic metabolome of female pigs differing in health status induced by sanitary condition...
Background: Holobionts are defined as a host and its microbiota, and there is not a consensus about their status as a unit of selection. The “it’s the song, not the singer” theory proposes that functional traits, instead of taxonomical composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We...
Appetite is the desire for feed and water and the voluntary intake of feed and is an important regulator of livestock productivity and animal health. Economic traits such as growth rate and muscle development (meat deposition) in broilers are directly correlated to appetite. Factors that may influence appetite include environmental factors, such as...
With the increasing availability of large amounts of data in the livestock domain, we face the challenge to store, combine and analyse these data efficiently. With this study, we explored the use of a data lake for storing and analysing data to improve scalability and interoperability. Data originated from a 2-day animal experiment in which the gai...
The objective of this study is to investigate the effect of a maternal antibiotic administration during the last week of gestation on the early life intestinal development in neonatal piglets. Colonization of the gut with bacteria starts during birth and plays a major role in the intestinal and immunological development of the intestine. We demonst...
This chapter discusses the concepts and the approaches taken with the quantification or mathematical modelling of rumen microbiota. The consequences from the perspective of mathematical modelling of microbial functionality at the whole rumen level are discussed as it is thought that models need to cover this level to predict fermentative and digest...
Here, we describe the use of monolayers of intestinal epithelial cells derived from intestinal organoids and transcriptomics to investigate the direct effects of dietary protein sources on epithelial function. Mechanically dissociated 3D organoids of mouse duodenum were used to generate a polarized epithelium containing all cell types found in the...
Major advances in analytical techniques and genomics have transformed our understanding of rumen microbiology. This understanding is of critical importance to livestock production since rumen function affects nutritional efficiency, emissions from ruminants (such as methane and nitrous oxide) as well as animal health. This collection reviews what w...
The Dutch government has set an objective to reduce greenhouse gasses (GHG) emissions to 116 Mton CO2-equivalent in 2030. The agriculture sector aims for 11–23 Mton of GHG emission by 2050 and thus contributes to this objective. For this sector, the major contributor to the GHG emission in the Netherlands is the dairy sector. Before any mitigation...
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 t...
Microbiota play an important role in total tract nutrient digestion, especially when fibrous diets are fed to pigs. This study aimed to use metagenomics to predict faecal nutrient digestibility in grower-finisher pigs. The study design consisted of 160 three-way crossbreed grower-finisher pigs (80 female and 80 male) which were either fed a diet ba...
Background
Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcri...
Big Data is a theme that receives a lot of attention, and is often characterised as managing and analysing large datasets to reveal new valuable patterns. In the livestock domain, big data is also becoming more common and is being anchored into the mind-set of researchers, due to, for example, sensors generating ...
1. An experiment was conducted to evaluate the effects of technical feed ingredients between 14 and 28 days of age on performance and health status of broilers (d14 – 35) fed diets with a high inclusion rate of rapeseed meal as a nutritional challenge.
2. A total of 1,008 one-day-old male Ross 308 chicks was distributed over 36 floor pens and alloc...
Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely depende...
Protein sources may contain bioactive components with activities beyond their strictly nutritional properties. We have investigated the use of enteroids as a model to test the effects of different protein sources on the intestinal epithelium. Confluent 2D monolayers generated from mouse 3D enteroids from the duodenum were shown to form polarized mo...
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.2...
Design of the experiment.
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Feed intake (A) and bodyweight (B) of mice fed with different experimental diets.
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Ingredient and calculated or analyzed nutrient composition of the experimental diets for mice, as fed basis.
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Members of microbial family belonging to ‘others’ as shown in Fig 2.
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The mean number of 16S rRNA sequence reads (A) and the number of OTU (B) counts detected in the ileal samples of mice fed with different experimental diets.
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Concentrations of serum cytokines and chemokines in response to dietary treatment in mice.
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Unique significantly expressed gene-sets (FDR <0.05) in ileum of mice fed with different protein sources compared to SBM-fed diet as shown in Fig 1.
(DOCX)
Digestibility of nutrients in pig diets is an important component of overall feed efficiency. Targeted improvement of digestibility is currently mainly achieved by optimization of pig diets, based on information generated from digestibility trials that aim to establish fecal digestibility coefficients of different nutrients across a variety of ingr...
Growth in world population will inevitably leads to increased demand for protein for humans and animals. Protein from insects and blood plasma are being considered as possible alternatives, but more research on their nutritional quality and health effects is needed. Here, we studied the effect of dietary protein source on metabolism and metabolic a...
An experiment 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...
The genotype and external phenotype of organisms are linked by so-called internal phenotypes which are influenced by environmental conditions. In this study, we used five existing -omics datasets representing five different layers of internal phenotypes, which were simultaneously measured in dietarily perturbed mice. We performed 10 pair-wise corre...