Research Institute for Farm Animal Biology (FBN)

Understanding natural behaviour is vital for promoting good welfare of goats in human care. Observations of feral and wild populations, as well as goats in research settings, provide insight into natural behaviours. An overview is presented of the natural environments that goats thrive in, and how they interact with these environments. Goats are known to climb, hide, travel great distances, and be flexible in their foraging and social interactions; they use well-developed cognitive capacities throughout these activities. Yet, in human care, often these abilities are not promoted, potentially compromising welfare. These welfare concerns are typically system specific. For instance, indoor housed animals may face a lack of exercise opportunities, barren housing that does not promote climbing or hiding, lack of outdoor access, compromised doe-buck and doe-kid relationships, and large group sizes. Conversely, animals managed outdoors or extensively face exposure, predation, parasitic infections, teeth and toxicity issues, and potentially social isolation in the case of companion animal settings. This chapter reflects on how promoting natural behaviours can reduce these negative welfare outcomes, and importantly, how these behaviours themselves are positive welfare indicators. The discussion captures numerous systems, including those producing dairy, meat, and fibre; captured ferals, companions and working animals are also considered.

The present work investigated the effects of embryonic temperature on the responses of Atlantic salmon (Salmo salar) alevins to a bacterial challenge using Yersinia ruckeri as a model pathogen. Embryos were reared at 4 °C, 6 °C, and 8 °C from fertilization to the eyed-egg stage. Alevins, before the start of feeding, were challenged with the pathogen, and mortality and early immune responses in mucosal organs were assessed. Fish from the 4 °C and 6 °C groups exhibited higher survival probabilities than those from the 8 °C group 72 h post-infection. Mild histopathological changes were observed in the gills and skin across all temperature groups, with bacterial antigen detected in the secondary lamellae of gills and in the skin epithelial and basal layers. Gene expression profiling revealed slightly distinct immune gene expression patterns in low-temperature groups (4 °C and 6 °C) compared to the 8 °C group. Gelsolin (gsn) expression increased in the skin across all temperature groups at 72 h post-infection. Claudin (cldn4) and collagen (col1a) were only upregulated in the skin of the 4 °C group, while heat shock protein 70 (hspa1a) was downregulated in the gills of infected fish at 72 h compared to controls. Toll-like receptor 13 (tlr13) expression increased in infected fish at 24 h compared to controls. In the 6 °C and 8 °C groups, gsn expression also increased at 72 h post-infection. Cldn4 expression increased only in the gills of 8 °C infected fish. This study revealed that low embryonic temperature could influence survival and mucosal immune defences following a bacterial challenge in Atlantic salmon alevins.

Background: In broiler chickens, the efficient utilization of macro- and micronutrients is influenced by various metabolic pathways that are closely linked to feed efficiency (FE), a critical metric in poultry industry, with residual feed intake (RFI) as the preferred proxy. Feed restriction is considered an approach to address the underlying molecular mechanisms of feed conversion. We hypothesized that broiler chickens with divergent RFI subjected to quantitative feed restriction differ in their pattern of molecular pathways for efficient nutrient utilization in liver as post-absorptive tissue. Methods: Cobb 500FF broiler chickens divergent for RFI (n = 112) were feed-restricted from day 9 until market weight at day 33–37 post-hatch. Based on a previous trial, feed restriction levels were set at 92% (low-RFI birds) and 80% (high-RFI birds) relative to the control groups. Transcriptomic analyses of the liver were conducted. Results: Due to the interaction of the RFI group and feeding regimen, a total of 140 to 507 differentially expressed genes were identified for the respective contrasts, with implications for hepatic metabolism and cellular stress response. Although the broilers did not realize their full growth potential under restrictive feeding (12.4% reduced body weight vs. controls, p = 0.094), the gene expression patterns indicate a lower susceptibility to blood coagulation (KNG1, FGG, and FGB), suggesting that controlled and mild feed restriction could lead to health benefits in less feed-efficient broilers. Moreover, FE traits are shown to be linked to cellular detoxification processes (MGST3 and CYP2AC2) and triacylglycerol syntheses (MOGAT1 and LPIN1). Conclusions: Divergent transcriptional profiles between broiler groups under varied caloric conditions indicate potential for optimizing nutritional management strategies.

Migratory birds are able to navigate over great distances with remarkable accuracy. The mechanism they use to achieve this feat is thought to involve two distinct steps: locating their position (the ‘map’) and heading towards the direction determined (the ‘compass’). For decades, this map-and-compass concept has shaped our perception of navigation in animals, although the nature of the map remains debated. However, some recent studies suggest the involvement of the Earth’s magnetic field in the map step. Here, we tested whether migratory songbirds, Eurasian reed warblers (Acrocephalus scirpaceus), can determine their position based on two magnetic field components that are also associated with direction finding, i.e. magnetic inclination and magnetic declination. During a virtual magnetic displacement experiment, the birds were exposed to altered magnetic inclination and magnetic declination values that would indicate a displacement from their natural migratory corridor, but the total intensity of the field remained unchanged, creating a spatial mismatch between these components. The response was a change in the birds’ migratory direction consistent with a compensatory re-orientation. This suggests that birds can extract positional as well as directional information from these cues, even when they are in conflict with another component of the magnetic field. It remains to be seen whether birds use the total intensity of Earth’s magnetic field for navigation.

The diversification of modern aquaculture systems with high-value finfish species, includingPercidae, is hampered by various diseases or even epidemics caused by a wide range ofviruses, bacteria, fungi and parasites. The present meta-analysis revealed six viral, four fungal,and 30 bacterial families as the dominant threats to percid aquaculture, in addition to abroad and diverse list of 91 aquatic parasite families. Understanding the multi-facetedinteractions between the percid host and diverse pathogens paves the way for effectivehealth concepts in aquaculture. In the past decades, both general and percid-specific immunedefence mechanisms have been elucidated that mitigate the invasion and pathogenicity ofharmful microorganisms and parasites. Some of these immune parameters offer valuableapproaches to optimize the current farming of percid fishes, which is still dominated byconventional pharmaceuticals, whereas immunostimulatory feed additives or vaccinationstrategies remain rarely used. Another efficient and sustainable way to combat commondiseases in aquaculture is through selective breeding, but selective breeding programs forpercids are not yet in operation. This review identifies existing knowledge gaps regardingimmune modulation in percids and suggests approaches to increase their immunocompetence.The variety of criteria suggested here may be incorporated into modern healthcare conceptsfor percid fishes to ensure adaptation to societal and food production demands.

The objectives of this study were to investigate whether an increased dietary myo-inositol (MI) supply translates into changes in MI concentrations and endogenous mucosal phosphatase activities in the intestine of laying hens and whether different laying hen strains respond differently to MI supplementation. The diets were corn–soybean meal-based and supplemented without (MI0) or with 1 (MI1), 2 (MI2), or 3 (MI3) g MI/kg feed. Ten hens per strain (Lohmann Brown-classic (LB) and Lohmann LSL-classic (LSL)) and diet were sacrificed at the age of 30 wk following a 4-wk stay in a metabolic unit. The blood plasma, digesta of the duodenum+jejunum and distal ileum, mucosa of the duodenum, and eggs were collected at wk 30. The concentration of MI in the blood plasma was increased by MI supplementation (P < 0.001); however, that of MI3 did not further increase compared with MI2. The concentration of MI in the duodenum+jejunum and ileum increased steadily (P < 0.001). The MI concentration in the duodenum+jejunum was higher in LB than in LSL hens (P = 0.017). The MI concentration in egg yolk was increased by MI supplementation (P < 0.001) and was higher in LB than in LSL hens (P = 0.015). Strain or diet did not affect mucosal phosphatase activity. Myo-inositol flow at the terminal ileum and postileal disappearance increased with each increment in MI supplementation (P < 0.001) and was higher in LB than in LSL hens (P ≤ 0.041). Regression analysis indicated that, on average, 84% of supplemented MI was retained in the body or metabolized and excreted in a different form. Based on the measured MI concentrations in the blood and eggs, dietary MI was not completely absorbed in the small intestine and, to a different extent, in the two laying hen strains. A higher dietary MI supply was followed by higher intestinal absorption or metabolism by microorganisms. The fate of supplemented MI and its relevance to birds warrant further research.

The internal timekeeping system regulates the daily cycle of physiological and behavioural changes in living organisms. This rhythmic phenomenon also influences cellular responses to reactive oxygen species, such as hydrogen peroxide (H2O2). However, the interaction between H2O2 and fish mucosal cells is not well understood. This study examined the temporal variations of immunological and physiological responses to H2O2 in salmonid gill cells using the RTgill-W1 cell line. The results showed that gene expression levels varied during a 24-hour cycle but did not exhibit rhythmicity. The presence of a 12-hour light-dark cycle (12L:12D) signal increased gene expression levels compared to a 24-hour dark cycle (0L:24D). To investigate whether the time of day affects the defences in gills, cells were exposed to H2O2 at two different times (Zeitgeber time 2, ZT2, or ZT14). Although significant expression changes were observed in genes related to stress and NF-κB signalling, only a limited time-dependent pattern of response to H2O2 was observed. The intracellular metabolome of gill cells was primarily composed of organic acid and derivatives, organoheterocyclic compounds, benzoids, organic oxygen and nitrogen compounds. Exposure to H2O2 at ZT2 led to significant changes in the metabolome compared to the control group, while no such changes were observed at ZT14. Within the control groups, the concentrations of 11 metabolites significantly varied between ZT2 and ZT14, with higher levels at ZT14. These metabolites were involved in arginine biosynthesis, amino acid metabolism, and nitrogen metabolism. In contrast, the level of 26 metabolites significantly varied between ZT2 and ZT14 in H2O2-exposed groups, with lower levels at ZT14. Comparing control and H2O2-exposed groups at ZT2, 38 metabolites were affected, primarily organic acid and derivatives and organic oxygen compounds. Functional annotation revealed that these altered metabolites were involved in 15 different pathways, with valine, leucine, and isoleucine biosynthesis being the most affected. This study reveals the presence of a time-dependent response to H2O2 in salmonid gill cells, which is reflected in the intracellular metabolome. The findings provide new insights into the temporal regulation of mucosal defences in fish.

Thromboembolic complications are common in severe COVID-19 and are thought to result from excessive neutrophil-extracellular-trap (NET)-driven immunothrombosis. Glycosylation plays a vital role in the efficiency of immunoglobulin A (IgA) effector functions, with significant implications for NET formation in infectious diseases. This study represents the first comprehensive analysis of plasma IgA glycosylation during severe SARS-CoV-2 or Influenza A infection, revealing lower sialylation and higher galactosylation of IgA1 O-glycans in acute respiratory distress syndrome (ARDS), regardless of the underlying cause of the disease. Importantly, N-glycans displayed an infection-specific pattern, with N47 of IgA2 showing diminished sialylation and bisection, and N340/N327 of IgA1/2 demonstrating lower fucosylation and antennarity along with higher non-complex glycans in COVID-19 compared to Influenza. Notably, COVID-19 IgA possessed strong ability to induce NET formation and its glycosylation patterns correlated with extracellular DNA levels in plasma of critically ill COVID-19 patients. Our data underscores the necessity of further research on the role of IgA glycosylation in the modulation of pathogen-specific immune responses in COVID-19 and other infectious diseases.

The impact of nutritional modification to increase functional polyunsaturated fatty acids (PUFA), such as n-3 and n-6 fatty acids (FA) or conjugated linoleic acid (CLA), on milk proteome profile during early lactation remains largely unknown. We used an untargeted proteomics approach to investigate the impact of lactation day and PUFA supplementation on the proteome signature in skimmed milk over the course of early lactation. Sixteen Holstein dairy cows received abomasal infusion of saturated FA (CTRL) or a mixture of essential FA and CLA (EFA + CLA group) from − 63 to + 63 days relative to parturition. Using quantitative proteomics, 479 unique proteins were identified in skimmed milk at days 1, 28, and 63 postpartum. The top discriminating proteins between transition milk (day 1) and mature milk (days 28 and 63), including members of complements (i.e. C2 and C5), growth factor (TGFB2), lipoproteins (i.e. APOE and APOD), and chaperones (i.e. ST13 and CLU), are associated with calves’ immune system and gut development. The EFA + CLA supplementation moderately affected a few proteins associated with regulating mammary glands’ lipogenesis through the (re)assembly of lipoprotein particles, possibly under the PPAR signaling pathway. Collectively, skimmed milk proteome is dynamically regulated initially by cow’s metabolic and physiological changes and to a lesser extent by nutritional PUFA modifications.

The ability to discriminate quantities is crucial for humans and other animals, by allowing individuals to maximize food intake and successfully navigate in their social environment. Here, we used a comprehensive approach to compare quantity discrimination abilities (i.e. ability to compare sets with different quantities of identical items, reliance on item size and spatial distribution, existence of irrational biases) in 9 different species of ungulates and provide novel insight into the socio-ecological conditions that might favor their emergence. We tested a total of 37 captive subjects including goats (Capra aegagrus hircus), llamas (Lama glama), guanacos (Lama guanicoe), Grevy's zebras (Equus grevyi), Chapman's zebras (Equus burchelli chapmanni), rhinos (Diceros bicornis michaeli), giraffes (Giraffa camelopardalis rothschildi), bison (Bison bonasus) and buffalos (Syncerus caffer nanus). Our results revealed that subjects were able to discriminate quantities when presented with two sets of food items that could differ in number, size and partially density. When presented with sets containing a different number of identical food items, subjects successfully selected the set with more items, with performance overall decreasing when sets had higher ratios (e.g., 1:3 vs 1:5). In addition, subjects could successfully maximize their food intake when both sets had the same number of items, but items had different sizes. However, performance decreased at chance levels when varying both the number of items and their size or distribution. Giraffes performed better than other species in most conditions, and we found no evidence for an irrational bias toward sets with more, smaller items or denser distributions. Overall, our study provides a first comparative assessment of quantity discrimination skills in several ungulate species.

Diet, especially the intake of dietary fibre, and weaning practices may influence pig wellbeing. This study assessed changes in salivary stress and immune markers in sows and their offspring fed either hay (HAY) or sugar beet pulp (SBP), either fine (F) or coarse (C), during gestation and lactation. The effect of weaning age (conventional-CW, late-LW) on these markers was also evaluated. Saliva was analysed for chromogranin A (CgA), cortisol, alpha-amylase, oxytocin, immunoglobulin A (IgA) and adenosine deaminase (ADA). CgA was higher at CW vs. LW in sows fed SBP-F (P=0.038). Alpha-amylase was higher in sows fed HAY-C at CW vs. LW (P=0.005) and in sows fed SBP-C at LW vs. CW (P=0.096). CgA and oxytocin were higher in sows fed SBP-F at CW vs. LW (P =0.038 and P =0.017, respectively). ADA was higher in sows fed SBP-C vs. HAY-C (P=0.035) at LW and at LW vs. CW in sows fed SBP-C (P=0.002). Piglet salivary CgA was higher at CW vs. LW in HAY-F (P=0.002) and SBP-F (P=0.031). Oxytocin was higher at CW vs. LW in piglets fed HAY-F (P=0.006). Piglet salivary IgA was higher in HAY-C vs. HAY-F at CW (P=0.010) and at LW vs. CW in piglets fed HAY-F (P=0.021). ADA was higher in piglets fed SBP-F vs. HAY-F (P=0.053) at CW and SBP-F vs. SBP-C (P=0.042) at LW. Dietary fibre type, weaning age and to a lesser extent grinding degree affect stress and immune markers in pigs. These findings highlight the impact of diet and weaning practice on pig welfare.

Skin cancer is one of the most common malignancies worldwide. Cold atmospheric pressure Plasma (CAP) is increasingly successful in skin cancer therapy, but further research is needed to understand its selective effects on cancer cells at the molecular level. In this study, A431 (squamous cell carcinoma) and HaCaT (non-malignant) cells cultured under identical conditions revealed similar ROS levels but significantly higher antioxidant levels in unstimulated A431 cells, indicating a higher metabolic turnover typical of tumour cells. HaCaT cells, in contrast, showed increased antioxidant levels upon CAP stimulation, reflecting a robust redox adaptation. Specifically, proteins involved in antioxidant pathways, including NF-κB, IκBα, Nrf2, Keap1, IKK, and pIKK, were quantified, and their translocation level upon stimulation was evaluated. CAP treatment significantly elevated Nrf2 nuclear translocation in non-malignant HaCaT cells, indicating a strong protection against oxidative stress, while selectively inducing NF-κB activation in A431 cells, potentially leading to apoptosis. The expression of pro-inflammatory genes like IL-1B, IL-6, and CXCL8 was downregulated in A431 cells upon CAP treatment. Notably, CAP enhanced the expression of antioxidant response genes HMOX1 and GPX1 in non-malignant cells. The differential response between HaCaT and A431 cells underscores the varied antioxidative capacities, contributing to their distinct molecular responses to CAP-induced oxidative stress.

Microalgae are emerging as functional feed ingredients in aquaculture due to their immune-stimulating and stress-modulating properties. We investigated the potential of the microalgae Chlorella vulgaris as a feed supplement to improve the health and modulate microbiota and stress responses of Atlantic salmon. Triplicate groups of Atlantic salmon (~ 126 g) were reared in a recirculating aquaculture system (RAS) at 15 °C and received diets supplemented with 2% (CV2) or 14% (CV14) spray-dried C. vulgaris daily, 14% once weekly (CV14w), or a control diet (CD) for 8 weeks. Subsequently, all groups were exposed to an acute one-hour peracetic acid (CH3CO3H; PAA) treatment, a commonly used disinfectant in RAS. While CV14 increased feed conversion (FCR) significantly, feeding the diets CV2 and CV14w improved protein retention efficiency. CV14 significantly modulated beta-diversity in the intestinal digesta and mucosa, but this effect was already visible in fish fed CV2. Feeding CV14 and, to a lesser degree, CV2 increased the relative abundances of Paenarthrobacter and Trichococcus in the digesta and mucosa, which are able to metabolize complex carbohydrates. However, the same diets reduced the abundance of the lactic acid bacteria Lactobacillus and Weissella in the digesta and Floricoccus in the mucosa. Peracetic acid exposure induced systemic stress (increase in plasma glucose and cortisol) and a local immune response in the gill, with the most prominent upregulation of several immune- and stress-regulated genes (clra, cebpb, marco, tnfrsf14, ikba, c1ql2, drtp1) 18 h after exposure in fish fed the control diet. Fish receiving CV14 once a week showed a reduced transcriptional response to PAA exposure. Catalase protein abundance in the liver increased following exposure to PAA, while superoxide dismutase abundance in the gill and liver was increased in response to C. vulgaris inclusion before stress. Overall, the results highlight that a high (14%) inclusion rate of C. vulgaris in feed for Atlantic salmon impairs feed conversion and shifts the intestinal microbiota composition in digesta and mucosa. Weekly feeding of C. vulgaris proves a viable approach in improving protein retention and improving transcriptional resilience towards oxidative stress in increasingly intensive production systems. Thereby this study may motivate future studies on optimizing temporal feeding schedules for health-promoting aquafeeds.

Plasma-functionalized liquids (PFLs) are rich in chemical species, such as ozone, hydrogen peroxide, singlet oxygen, hydroxyl radical and nitrogen oxides, commonly referred to as reactive oxygen and nitrogen species (RONS). Therefore, manifold applications are being investigated for their use in medicine, agriculture, and the environment. Depending on the goal, a suitable plasma source concept for the generation of PFLs has to be determined because the plasma generation setup determines the composition of reactive species. This study investigates three PFL-generating plasma sources—two spark discharges and a flow dielectric barrier discharge (DBD) system—for their efficacy in eliminating microbial contaminants from tissue samples aiming to replace antibiotics in the rinsing process. The final goal is to use these tissues as a cell source for cell-based meat production in bioreactors and thereby completely avoid antibiotics. Initially, a physicochemical characterization was conducted to better understand the decontamination capabilities of PFLs and their potential impact on tissue viability. The results indicate that the flow DBD system demonstrated the highest antimicrobial efficacy due to its elevated reactive species output and the possibility of direct treatment of tissues while tissue integrity remained. Achieving a balance between effective large-scale decontamination and the biocompatibility of PFLs remains a critical challenge.

The objective of this study was to characterize intestinal phytate degradation and mineral utilization by 2 laying hen strains before and after the onset of egg laying using diets without or with a mineral phosphorus (P) supplement. One offspring of 10 roosters per strain (Lohmann Brown-classic [LB] and Lohmann LSL-classic [LSL]) was sacrificed before (wk 19) and after (wk 24) the onset of egg-laying activity and following 4 wk placement in a metabolic unit. Diets were corn-soybean meal-based and without supplemented P (P-) or with 1 g/kg supplemented P (P+) from monocalcium phosphate. In wk 19 and 24, the blood plasma and digesta of duodenum+jejunum and distal ileum were collected. The concentration of P in blood plasma was higher in hens fed P+ than P- (P < 0.001). In duodenum + jejunum and ileum content, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in P- than in P+ (P ≤ 0.009). In duodenum+jejunum, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in wk 24 than 19 and lower in LSL than LB hens (P < 0.001). The concentration of myo-inositol (MI) in duodenum + jejunum content was lower in wk 19 than 24 (P < 0.001). Following a 4-d total excreta collection, the retained amount of P was higher in P+ than P- (P < 0.001). Phosphorus retention was lower in LB hens fed P- than in other treatments (P × strain: P = 0.039). In the jejunal tissue, some genes related to intracellular InsP metabolism were higher expressed in LB than LSL hens. The renunciation of mineral P increased endogenous phytate degradation, but more P was retained with supplemented P. Differences in endogenous phytate degradation between the periods before and after the onset of egg laying might be attributed to different Ca concentrations in intestinal digesta caused by different Ca needs in both periods.

The current study presents the analysis of stromal cells obtained from an hyperplastic left-ovary of a Holstein cow. Cultured hyperplastic stromal cells displayed a fibroblast-like morphology and ceased proliferation after the 8th passage. The non-cancerous nature of stromal cells was confirmed by in vitro cell proliferation and migration assays. Negligible amounts of E2 were detected in the spent media of cultured stromal cells, which suggests that stromal cells were non-estradiol synthesizing cells. As revealed in immunofluorescence and gene expression analysis, the hyperplastic stromal cells explicitly expressed vimentin in their cytoskeleton. Upon hematoxylin staining, a highly dense population of stromal cells was observed in the stromal tissue of the hyperplastic ovary. To explore genome-wide alterations, mRNA microarray analysis was performed using Affymetrix Bovine Gene 1.0ST Arrays compared to normal ovarian derived stromal cells. The microarray identified 1396 differentially expressed genes, of which 733 were up- and 663 down-regulated in hyperplastic stromal cells. Importantly, asporin (ASPN) and vascular cell adhesion molecule 1 (VCAM1) were among the highly up-regulated genes. Higher expression of ASPN was also confirmed by immunohistochemistry and RT-qPCR analysis. Ingenuity pathway analysis (IPA) identified about 98 significantly enriched (-log (p value ≥ 1.3) canonical pathways, importantly of which the “Sirutin Signaling Pathway” and “Mitochondrial Dysfunction” were highly activated while “Oxidative phosphorylation” was inhibited. Additionally, higher proportion of hyperplastic stromal cells in the S-phase of cell cycle, could be attributed to higher expression levels of cell proliferation genes such as CCND2 and CDK6.

During parasite infections, the liver may prioritise immune-related pathways over its metabolic functions. Intestinal infections caused by Ascaridia galli and Heterakis gallinarum impair feed intake, nutrient absorption, and weight gain. Histomonas meleagridis, vectored by H. gallinarum , can also damage liver tissues, potentially impairing liver functions. This study examined the hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after an experimental infection ( n = 18) with both A. galli and H. gallinarum or kept as uninfected control ( n = 12). Furthermore, H. gallinarum infection led to a co-infection with H. meleagridis . The mixed infections reduced feed intake and the average daily weight gain ( P < 0.001). The infections also increased the plasma concentrations of alpha (1)-acid glycoprotein and the antibody titre against H. meleagridis ( P = 0.049), with no strain differences ( P > 0.05). For host molecular response, 1887 genes were differentially expressed in LD, while 275 and 25 genes were differentially expressed in R and LB, respectively. The up-regulated genes in R and LD were mostly related to inflammatory and adaptive immune responses, while down-regulated genes in LD were involved in metabolic pathways, including gluconeogenesis. Despite performance differences among the strains, worm burdens were similar, but hepatic molecular responses differed significantly. Moreover, there was an indication of a shift in hepatic functions towards immune-related pathways. We, therefore, conclude that the liver shifts its functions from metabolic to immune-related activities in chickens when challenged with mixed parasite species.

Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow managers such as Nextflow provide a framework to overcome respective problems. This study used Nextflow to develop a bioinformatic pipeline for detecting expression quantitative trait loci (eQTL) using a DSL2 Nextflow modular syntax, to enable sharing the huge demand for computing power as well as data access limitation across different partners often associated with eQTL studies. Based on the results from a test run with pilot data by measuring the required runtime and computational resources, the new pipeline should be suitable for eQTL studies in large scale analyses.

We investigated if feeding earthworms (EW) or vermicompost (VC) to broilers improves performance and aids in coping with dietary challenges from a soluble non-starch polysaccharide (NSP)-enriched diet (negative control diet; CON-). Newly-hatched male Cobb-500 birds (N = 480) were fed either a positive (+) control diet (CON+, n = 240) or CON+ supplemented with either 1% EW (CON+EW; n = 120) or 1% VC in DM (CON+VC; n = 120) for 8 d (Period 1; P1). At the end of P1, blood and intestinal samples were taken from half the birds in each group. Half of remaining birds on CON+ stayed on CON+ for further 8 d (P2; d9 - 16) or switched to CON-. Birds on CON+EW and CON+VC in P1 were switched to CON- in P2 (CON-EW and CON-VC, respectively). The CON+VC improved (P < 0.05) BW and ADG in P1 through an elevated feed intake (FI) (P < 0.05) with no effect on FCR. CON+EW did not differ from the CON+ in terms of growth and FI in P1. In P2 CON- did not affect growth or DMI relative to CON+. In the end of P2, 10% of CON+ birds had pasty vent (PV). CON- increased incidence of PV and CON-VC aggravated this effect (P < 0.05), whereas CON-EW did not differ from CON+. CON- diet reduced proportion of 16S rDNA in colon digesta (P = 0.049), while CON-EW and CON-VC did not differ from CON+. Compared to CON-, CON-EW tended to decrease (P = 0.072) incidence of PV. Ceca were heavier (P < 0.05) in CON-EW than in CON+ fed birds. In conclusion, the challenge diet induced PV and reduced bacterial 16S rDNA in colon digesta, likely due to soluble NSP-induced anti-nutritive effects. VC supplementation enhanced early growth by increasing feed intake. Provision of EW did not impact performance but decreased incidence of PV and increased cecal size, suggesting that potential inoculation with beneficial microorganisms may counteract NSP effects.