Improving zebrafish laboratory welfare and scientific research through understanding their natural history

Nature versus laboratory: how to optimize housing conditions for zebrafish neuroscience research

Although zebrafish (Danio rerio) neuroscience research is rapidly expanding, the fundamental question of how these fish should be maintained in research laboratories remains largely unstudied. This may explain the diverse practices and broad range of environmental parameters used in zebrafish facilities. Here, we provide examples of these parameters and practices, including housing density, tank size, and water chemistry. We discuss the principles of stochastic resonance versus homeostasis and provide hypothetical examples to explain why keeping zebrafish outside of their tolerated range of environmental parameters may increase phenotypical variance and reduce replicability. We call for systematic studies to establish the optimal maintenance conditions for zebrafish. Furthermore, we discuss why knowing more about the natural behavior and ecology of this species could be a guiding principle for these studies.

Zebrafish (Danio rerio) as a Model System to Investigate the Role of the Innate Immune Response in Human Infectious Diseases

The zebrafish (Danio rerio) has emerged as a valuable model for studying host-pathogen interactions due to its unique combination of characteristics. These include extensive sequence and functional conservation with the human genome, optical transparency in larvae that allows for high-resolution visualization of host cell-microbe interactions, a fully sequenced and annotated genome, advanced forward and reverse genetic tools, and suitability for chemical screening studies. Despite anatomical differences with humans, the zebrafish model has proven instrumental in investigating immune responses and human infectious diseases. Notably, zebrafish larvae rely exclusively on innate immune responses during the early stages of development, as the adaptive immune system becomes fully functional only after 4-6 weeks post-fertilization. This window provides a unique opportunity to isolate and examine infection and inflammation mechanisms driven by the innate immune response without the confounding effects of adaptive immunity. In this review, we highlight the strengths and limitations of using zebrafish as a powerful vertebrate model to study innate immune responses in infectious diseases. We will particularly focus on host-pathogen interactions in human infections caused by various bacteria (Clostridioides difficile, Staphylococcus aureus, and Pseudomonas aeruginosa), viruses (herpes simplex virus 1, SARS-CoV-2), and fungi (Aspergillus fumigatus and Candida albicans).

The effect of laboratory diet and feeding on growth parameters in juvenile zebrafish

Despite being one of the most used laboratory species in biomedical, behavioral and physiological research, the nutritional requirements of zebrafish (Danio rerio) are poorly understood, and no standardized laboratory diet exists. Diet and feeding regimen can substantially impact the welfare of the fish and, in turn, experimental reproducibility. Consequently, the establishment of a standardized diet and feeding protocol for laboratory zebrafish is imperative to enhance animal welfare, guarantee research reproducibility and advance the economic and environmental sustainability of laboratory dietary practices. Here the aim of this systematic review is to provide an overview of the parameters that need to be standardized in future nutritional studies to facilitate future meta-analyses for confirmation of an optimal juvenile diet for growth. A comprehensive search was conducted in PubMed and Scopus to identify relevant studies published up to August 2023, and the studies were selected on the basis of the predefined inclusion/exclusion criteria. The databases yielded a total of 1,065 articles, of which 14 were included in this review. We conducted data extraction and risk-of-bias analysis in the included studies. Statistical comparisons for specific growth rate, weight gain (%) and length gain (%) parameters were performed to determine the optimal feed for enhanced juvenile growth. We identified significant heterogeneity and caveats to our findings owing to a lack of standardization of experimental conditions in nutritional studies. Our findings highlight an urgent need for research on zebrafish nutrition. Therefore, the standardized parameters we have reported here represent a critical starting point for studies.

Zebrafish Maintenance Conditions Affect Behavioral and Biochemical Biomarkers: A Possible Interfering Factor on the Research Results

Over the years, scientific research with fish models has grown at a rapid pace, and issues such as animal welfare are becoming increasingly important in various areas of animal husbandry and experimentation. Here, we evaluated whether Danio rerio behavior is affected by long-term maintenance (75 days) in an enriched environment or a chronic stress (CS) situation. In addition, we evaluated some biochemical parameters related to redox status. We concluded that long-term maintenance of zebrafish in enriched environment might induce an anxiety-like behavior pattern when these fish are faced with an acute subsequent stressor. These anxiety results, the increased school cohesion, and the absence of oxidative damage allow us to hypothesize that the fish maintained in environmental enrichment (EE) situation is more reactive, showing a strong protective reaction to the stress. From an applicable perspective, we show that both too much stress and too little stress are not ideal for zebrafish stocks. In CS situations, fish can habituate and might not respond optimally to test conditions. In opposite, the low stress promoted by environmental enrichment also renders the fish incapable of dealing with occasional stressors optimally, because now even normal conditions appear stressful to them and may elicit fear behaviors they normally would not exhibit.

Effects of housing density on anxiety-like behavior of zebrafish in the plus maze with ramp

Population density in experimental animals is a crucial factor in maintaining the wellbeing of the organisms. Inadequate housing conditions can compromise the validity and reliability of research results, making comparisons between studies difficult. In sociable species such as zebrafish (Danio rerio), which are housed in groups, overcrowding or undercrowding represents a variable that needs to be considered. In this study, we evaluated the effects of housing at different densities for different exposure times on the anxiety response measured in the Plus Maze with Ramp test in zebrafish. The subjects (144) were divided into three large groups according to the housing time (1, 7, and 30 days). Each group was divided into six subgroups based on the density of the fish (0.25, 0.5, 1, 2, 4, 6 fish/liter, n = 8) and housed in a 4-liter aquarium. After the housing conditions, each animal was tested individually in the PMR. Time and housing density altered the exploratory behavior of zebrafish. Increased housing time reduced the time spent in the ramp arms, with groups kept for 30 days spending less time in this compartment. Density increased the time spent in the flat arms in groups with 2 and 6 fish/liter and, conversely, reduced the exploration of the ramp arms. Isolation, on the other hand, increased the exploration of the ramp arms, indicating an anxiolytic effect. In this study, we demonstrate that housing conditions can act as low-intensity chronic stressors that alter anxiety-like behavior in zebrafish when tested in the PMR protocol.

Review of Pseudoloma neurophilia (Microsporidia): A common neural parasite of laboratory zebrafish (Danio rerio)

Zebrafish (Danio rerio) is now the second most used animal model in biomedical research. As with other vertebrate models, underlying diseases and infections often impact research. Beyond mortality and morbidity, these conditions can compromise research end points by producing nonprotocol induced variation within experiments. Pseudoloma neurophilia, a microsporidium that targets the central nervous system, is the most frequently diagnosed pathogen in zebrafish facilities. The parasite undergoes direct, horizontal transmission within populations, and is also maternally transmitted with spores in ovarian fluid and occasionally within eggs. This transmission explains the wide distribution among research laboratories as new lines are generally introduced as embryos. The infection is chronic, and fish apparently never recover following the initial infection. However, most fish do not exhibit outward clinical signs. Histologically, the parasite occurs as aggregates of spores throughout the midbrain and spinal cord and extends to nerve roots. It often elicits meninxitis, myositis, and myodegeneration when it infects the muscle. There are currently no described therapies for the parasite, thus the infection is best avoided by screening with PCR-based tests and removal of infected fish from a facility. Examples of research impacts include reduced fecundity, behavioral changes, transcriptome alterations, and autofluorescent lesions.

A survey of water chemistry used in zebrafish facilities and their effects on early zebrafish development

Background

There are a variety of published standard methods and water chemistry recommendations for zebrafish ( Danio rerio) husbandry, but empirical evidence for their justification is often lacking, as is information on some variables that have important biological effects on fish. Importantly, these different recommendations could contribute to variability in results and fish welfare between or within institutions.

Methods

Here we document the current range of water chemistry used by various research institutions around the world and report initial findings on their effects on the development and growth of zebrafish. Over 40 institutes responded to a survey that revealed a large variation in water chemistry used for zebrafish husbandry including differences in the set-points and acceptable ranges for temperature, pH and conductivity. In subsequent experiments, zebrafish ( D. rerio, WIK) embryos/larvae exposed to a large range of salt concentrations (50μM to 10mM Na + or 30 - 2500 μS/cm) and CO 2 levels (400 - 8,000 μatm).

Results

Larvae exposed to the lowest salt concentration (5 μM Na + or < 30μS/cm) had a slower response to touch and their swim bladders were not inflated. Larvae exposed to 5-100 μM Na + were 5 % shorter in total body length than those exposed to higher salt concentrations (>100 μM Na +). Zebrafish embryo/larvae exposed to intermediate pCO 2 values (~2000 μatm) were 1 to 3.5% longer than those exposed to either ambient (400 μatm) or higher (4000 μatm) pCO 2, but pCO 2 did not affect developmental endpoints up to 4 dpf.

Conclusions

Overall, we highlight the magnitude of variation in water chemistry used within zebrafish research and provide some empirical evidence to show that not all of these water conditions might be optimal for developing zebrafish and reproducibility of research, although further research is necessary to determine longer-term effects of water chemistry on older larvae, juveniles and adults.

Zebrafish Models in Toxicology and Disease Studies

Danio rerio is a small tropical freshwater fish, also known as Brachydanio rerio and commonly referred to as zebrafish, described for the first time in 1822 by Francis Hamilton in the Ganges River but widespread throughout the entire Great Himalayan region of Southeast Asia [...].

Evaluation of a gel-based versus micro-pellet diet for adult zebrafish (Danio rerio)

Ad libitum feeding of laboratory zebrafish has potential benefits for colony management, but would require a new type of diet, such as a gel that remains in the tank. We hypothesized that adult zebrafish fed a gel diet would have similar body size and reproductive success compared with those fed a standard micro-pellet diet. The gel diet’s impact on water quality was determined to be safe for zebrafish prior to starting a 12-week feeding study. Two hundred adult AB zebrafish of mixed sex were randomly assigned to be fed exclusively either gel or micro-pellet diet. Fish body length and mass were measured every two weeks, and fish were bred within each feed group to assess fecundity. Zebrafish consumed less gel diet than expected. Body length, mass, and breeding success were lower in the gel diet fish than in the micro-pellet diet fish. Low consumption of the gel diet and/or nutritional differences between the two diets may have contributed to reduced growth and fecundity. Though the gel diet could reduce time personnel spend feeding and be safer for fish in static tanks, the tested formulation was not a satisfactory alternative to the control micro-pellet diet in a research zebrafish colony.

Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models

Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.

A systematic review of the impact of environmental enrichment in zebrafish

Environmental enrichment (EE) consists of a series of interventions carried out in the home environment to promote greater exposure to sensory stimuli and mimic the natural habitat of laboratory-housed animals, providing environments closer to those found in nature. Some studies have shown the positive effects of EE in zebrafish housed in a laboratory environment. However, this evidence is still recent and accompanied by contradictory results. Furthermore, there is great variability in the protocols applied and in the conditions of the tests, tanks and materials used to generate an enriched environment. This substantial variability can bring many uncertainties to the development of future studies and hinder the reproducibility and replicability of research. Here, in this context, we carried out a systematic review of the literature, aiming to provide an overview of the EE protocols used in zebrafish research. The literature search was performed in PubMed, Scopus and Web of Science and the studies were selected on the basis of predefined inclusion/exclusion criteria. A total of 901 articles were identified in the databases, and 27 of those studies were included in this review. We conducted data extraction and risk-of-bias analysis in the included studies. Among these studies, the effect of EE was evaluated in two different ways: (1) for animal welfare and (2) as an intervention to prevent behavioral, biochemical, molecular, developmental and breeding dysfunctions. Although the EE protocols in zebrafish presented a series of experimental differences, the results showed that the benefits of the EE for zebrafish were consistent. According to the results described here, the use of EE in the zebrafish home tank improves welfare and may reduce sources of bias in scientific research. However, it is still necessary to develop standardized protocols to improve the application of EE in scientific studies using zebrafish.

Substrate colour guides turquoise killifish's (Nothobranchius furzeri) choice of preferred spawning habitat

Turquoise killifish (Nothobranchius furzeri) is a promising new model species used in biomedical and ecological laboratory experiments, and should be kept under optimal conditions to ensure fish welfare and the quality of science. While the popularity of this model species is rapidly increasing, we need to improve our understanding of how the species interacts with its environment to optimize its husbandry. Specifically, turquoise killifish are substrate spawners that bury their eggs in the sediment, which can be accommodated under captive conditions, but it is not yet known whether or not turquoise killifish have a preference for a specific sediment colour. Here, we performed a laboratory experiment in which fish could choose between white, orange and black sand for spawning, colours which are relevant in both laboratory and field conditions. We assessed their preference in the context of single breeding pairs, as well as in a social group setting. Additionally, we also assessed the preference of individuals for a white versus black background in a nonmating context. Single breeding pairs deposited over 3.5 times more eggs in black compared to orange or white sand. Similarly, fish in social groups deposited over 3.5 times more eggs in black compared to orange sand, which in turn was over two times higher than that in white sand. Fish showed a slight preference for the black compared to the white zone in a nonmating context, but this did not correlate with substrate choice during the spawning tests. The results suggest that turquoise killifish select their preferred spawning location based on the colour of the substrate. These findings contribute to our understanding of the species' biology and can help to guide good welfare and scientific practice.

Housing Conditions Affect Adult Zebrafish (Danio rerio) Behavior but Not Their Physiological Status

Zebrafish is a valuable model for neuroscience research, but the housing conditions to which it is exposed daily may be impairing its welfare status. The use of environmental enrichment and the refinement of methodology for cortisol measurement could reduce stress, improving its welfare and its suitability as an animal model used in stress research. Thus, this study aimed to evaluate (I) the influence of different housing conditions on zebrafish physiology and behavior, and (II) skin mucus potential for cortisol measurement in adult zebrafish. For this, AB zebrafish were raised under barren or enriched (PVC pipes and gravel image) environmental conditions. After 6 months, their behavior was assessed by different behavioral paradigms (shoaling, white-black box test, and novel tank). The physiological response was also evaluated through cortisol levels (whole-body homogenates and skin mucus) and brain oxidative stress markers. The results revealed that enriched-housed fish had an increased nearest neighbors' distance and reduced activity. However, no effect on body length or stress biomarkers was observed; whole-body and skin mucus cortisol levels had the same profile between groups. In conclusion, this study highlights the skin mucus potential as a matrix for cortisol quantification, and how housing conditions could influence the data in future studies.

Social behaviors as welfare indicators in teleost fish

Animal welfare is a key issue not only for aquaculture industry and food production, but also for daily husbandry practices in research topics related to physiology in wild and farmed animals. In this context, teleost fish constitute interesting models to assess alternative welfare indicators because of their wide diversity in reproductive and social structures. Any framework for assessing teleost fish welfare needs to account for the physiological mechanisms involved in each species as a first step. A comprehensive approach should also take into account how these physiological and behavioral parameters can be altered by environmental enrichment considering the specific requirements in each case and identifying intrinsic biological characteristics of individual species. This review will show how cortisol and sex steroids regulate social behavior in teleost fish, and how different aspects of social behavior can be employed as welfare indicators according to specific characteristics in each case. This article will consider evidence in teleost fish, including cichlids, characids and cyprinids with different reproductive strategies and social structures (e.g., territorial social hierarchies or shoaling behavior). Neotropical species will be particularly emphasized. The main laboratory-based animal welfare indicators are cortisol, a classical stress hormone, together with sex steroids. Considering that the endocrine landscape is intrinsically related to social behavior, reproductive and agonistic behavioral traits such as aggression, anxiety and courtship are key elements to assess welfare under housing and culture conditions. This review highlights the importance of assessing physiological mechanisms and identifying behavioral characteristics in teleost fish, especially in Neotropical species, as a baseline to understand which environmental enrichment can improve animal welfare in each individual species.

A minimally invasive fin scratching protocol for fast genotyping and early selection of zebrafish embryos

Current genetic modification and phenotyping methods in teleost fish allow detailed investigation of vertebrate mechanisms of development, modeling of specific aspects of human diseases and efficient testing of drugs at an organ/organismal level in an unparalleled fast and large-scale mode. Fish-based experimental approaches have boosted the in vivo verification and implementation of scientific advances, offering the quality guaranteed by animal models that ultimately benefit human health, and are not yet fully replaceable by even the most sophisticated in vitro alternatives. Thanks to highly efficient and constantly advancing genetic engineering as well as non-invasive phenotyping methods, the small zebrafish is quickly becoming a popular alternative to large animals' experimentation. This approach is commonly associated to invasive procedures and increased burden. Here, we present a rapid and minimally invasive method to obtain sufficient genomic material from single zebrafish embryos by simple and precise tail fin scratching that can be robustly used for at least two rounds of genotyping already from embryos within 48 h of development. The described protocol betters currently available methods (such as fin clipping), by minimizing the relative animal distress associated with biopsy at later or adult stages. It allows early selection of embryos with desired genotypes for strategizing culturing or genotype-phenotype correlation experiments, resulting in a net reduction of "surplus" animals used for mutant line generation.

Exploiting animal personality to reduce chronic stress in captive fish populations

Chronic stress is a major source of welfare problems in many captive populations, including fishes. While we have long known that chronic stress effects arise from maladaptive expression of acute stress response pathways, predicting where and when problems will arise is difficult. Here we highlight how insights from animal personality research could be useful in this regard. Since behavior is the first line of organismal defense when challenged by a stressor, assays of shy-bold type personality variation can provide information about individual stress response that is expected to predict susceptibility to chronic stress. Moreover, recent demonstrations that among-individual differences in stress-related physiology and behaviors are underpinned by genetic factors means that selection on behavioral biomarkers could offer a route to genetic improvement of welfare outcomes in captive fish stocks. Here we review the evidence in support of this proposition, identify remaining empirical gaps in our understanding, and set out appropriate criteria to guide development of biomarkers. The article is largely prospective: fundamental research into fish personality shows how behavioral biomarkers could be used to achieve welfare gains in captive fish populations. However, translating potential to actual gains will require an interdisciplinary approach that integrates the expertise and viewpoints of researchers working across animal behavior, genetics, and welfare science.

Screening of Mineralogenic and Osteogenic Compounds in Zebrafish—Tools to Improve Assay Throughput and Data Accuracy

Bone disorders affect millions of people worldwide and treatments currently available often produce undesirable secondary effects or have limited efficacy. It is therefore of the utmost interest for patients to develop more efficient drugs with reduced off-target activities. In the long process of drug development, screening and preclinical validation have recently gained momentum with the increased use of zebrafish as a model organism to study pathological processes related to human bone disorders, and the development of zebrafish high-throughput screening assays to identify bone anabolic compounds. In this review, we provided a comprehensive overview of the literature on zebrafish bone-related assays and evaluated their performance towards an integration into screening pipelines for the discovery of mineralogenic/osteogenic compounds. Tools available to standardize fish housing and feeding procedures, synchronize embryo production, and automatize specimen sorting and image acquisition/analysis toward faster and more accurate screening outputs were also presented.