Current basis and future directions of zebrafish nutrigenomics

A Bacterial-Sourced Protein Diet Induces Beneficial Shifts in the Gut Microbiome of the Zebrafish, Danio rerio

Background

Bacterial-sourced single-cell proteins (SCPs) offer an alternative protein source for diet formulation for Zebrafish (Danio rerio) and other aquaculture models. In addition, the use of a single-cell bacterial protein source derived from multiple species provides a unique insight into the interplay among nutrients in the diet, microbial populations in the diet, and the gut microbiome in D. rerio.

Objective

Our objective in this study was to evaluate the impact of dietary replacement of fish protein hydrolysate in a standard reference (SR) with a single-cell bacterial protein source on D. rerio gut microbiome.

Methods

We investigated gut microbial compositions of D. rerio fed an open-formulation standard reference (SR) diet or a bacterial-sourced protein (BP) diet, utilizing microbial taxonomic co-occurrence networks, and predicted functional profiles.

Results

Microbial communities in the SR diet were primarily composed of Firmicutes. In contrast, the BP diet was mainly composed of Proteobacteria. Alpha diversity revealed significant differences in microbial communities between the 2 diets, and between the guts of D. rerio fed either of the 2 diets. D. rerio fed with the SR diet resulted in abundance of Aeromonas and Vibrio. In contrast, D. rerio fed with a BP diet displayed a large abundance of members from the Rhodobacteraceae family. Taxonomic co-occurrence networks display unique microbial interactions, and key taxons in D. rerio gut samples were dependent on diet and gender. Predicted functional profiling of the microbiome across D. rerio fed SR or BP diets revealed distinct metabolic pathway differences. Female D. rerio fed the BP diet displayed significant upregulation of pathways related to primary and secondary bile acid synthesis. Male D. rerio fed the BP diet revealed similar pathway shifts and, additionally, a significant upregulation of the polyketide sugar unit biosynthesis pathway.

Conclusions

The use of a BP dramatically affects the composition and activity of the gut microbiome. Future investigations should further address the interplay among biological systems and diet and may offer insights into potential health benefits in preclinical and translational animal models.

Obesity Impairs Cognitive Function with No Effects on Anxiety-like Behaviour in Zebrafish

Over the last decade, the zebrafish has emerged as an important model organism for behavioural studies and neurological disorders, as well as for the study of metabolic diseases. This makes zebrafish an alternative model for studying the effects of energy disruption and nutritional quality on a wide range of behavioural aspects. Here, we used the zebrafish model to study how obesity induced by overfeeding regulates emotional and cognitive processes. Two groups of fish (n = 24 per group) were fed at 2% (CTRL) and 8% (overfeeding-induced obesity, OIO) for 8 weeks and tested for anxiety-like behaviour using the novel tank diving test (NTDT). Fish were first tested using a short-term memory test (STM) and then trained for four days for a long-term memory test (LTM). At the end of the experiment, fish were euthanised for biometric sampling, total lipid content, and triglyceride analysis. In addition, brains (eight per treatment) were dissected for HPLC determination of monoamines. Overfeeding induced faster growth and obesity, as indicated by increased total lipid content. OIO had no effect on anxiety-like behaviour. Animals were then tested for cognitive function (learning and memory) using the aversive learning test in Zantiks AD units. Results show that both OIO and CTRL animals were able to associate the aversive stimulus with the conditioned stimulus (conditioned learning), but OIO impaired STM regardless of fish sex, revealing the effects of obesity on cognitive processes in zebrafish. Obese fish did not show a deficiency in monoaminergic transmission, as revealed by quantification of total brain levels of dopamine and serotonin and their metabolites. This provides a reliable protocol for assessing the effect of metabolic disease on cognitive and behavioural function, supporting zebrafish as a model for behavioural and cognitive neuroscience.

Body Metrics and the Gut Microbiome in Response to Macronutrient Limitation in the Zebrafish Danio rerio

Background

Healthy and predictable physiologic homeostasis is paramount in animal models for biomedical research. Proper macronutrient intake is an essential and controllable environmental factor for maintaining animal health and promoting experimental reproducibility.

Objective and Methods

Evaluate reductions in dietary macronutrient composition on body weight metrics, composition, and gut microbiome in Danio rerio.

Methods

D. rerio were fed reference diets deficient in either protein or lipid content for 14 weeks.

Results

Diets of reduced-protein or reduced-fat resulted in lower weight gain than the standard reference diet in male and female D. rerio. Females fed the reduced-protein diet had increased total body lipid, suggesting increased adiposity compared with females fed the standard reference diet. In contrast, females fed the reduced-fat diet had decreased total body lipid compared with females fed the standard reference diet. The microbial community in male and female D. rerio fed the standard reference diet displayed high abundances of Aeromonas, Rhodobacteraceae, and Vibrio. In contrast, Vibrio spp. were dominant in male and female D. rerio fed a reduced-protein diet, whereas Pseudomonas displayed heightened abundance when fed the reduced-fat diet. Predicted functional metagenomics of microbial communities (PICRUSt2) revealed a 3- to 4-fold increase in the KEGG (Kyoto Encyclopedia of Genes and Genomes) functional category of steroid hormone biosynthesis in both male and female D. rerio fed a reduced-protein diet. In contrast, an upregulation of secondary bile acid biosynthesis and synthesis and degradation of ketone bodies was concomitant with a downregulation in steroid hormone biosynthesis in females fed a reduced-fat diet.

Conclusions

These study outcomes provide insight into future investigations to understand nutrient requirements to optimize growth, reproductive, and health demographics to microbial populations and metabolism in the D. rerio gut ecosystem. These evaluations are critical in understanding the maintenance of steady-state physiologic and metabolic homeostasis in D. rerio. Curr Dev Nutr 20xx;x:xx.

Swimming against ALS: How to model disease in zebrafish for pathophysiological and behavioral studies

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that leads to progressive disability and motor impairment. Existing therapies provide modest improvements in patient survival, raising a need for new treatments for ALS. Zebrafish is a promising model animal for translational and fundamental research in ALS - it is an experimentally tractable vertebrate, with high homology to humans and an ample experimental toolbox. These advantages allow high-throughput study of behavioral and pathophysiological phenotypes. The last decade saw an increased interest in modelling ALS in zebrafish, leading to the current abundance and variety of available methods and models. Additionally, the rise of gene editing techniques and toxin combination studies has created novel opportunities for ALS studies in zebrafish. In this review, we address the relevance of zebrafish as a model animal for ALS studies, the strategies for model induction and key phenotypical evaluation. Furthermore, we discuss established and emerging zebrafish models of ALS, analyzing their validity, including their potential for drug testing, and highlighting research opportunities in this area.

Feeding Rate and Protein Quality Differentially Affect Growth and Feeding Efficiency Response Variables of Zebrafish (Danio rerio)

Manipulating feeding rate and protein quality may improve growth and feeding efficiency of cultured species. However, whether feeding rate, protein quality, or their interaction has a greater effect on growth and feeding efficiency response variables is unknown. To determine whether feeding rate and protein quality individually or interactively affect growth and feeding efficiency, juvenile Zebrafish (Danio rerio) were either offered nutritionally similar diet consisting of either menhaden fishmeal protein or a 100% replacement of fishmeal with soybean meal-based protein restrictively or to satiation. Total length, weight, feed intake, and feed conversion ratio (FCR) were measured throughout the duration of the study. Protein quality and feeding rate individually and interactively affected feed intake and FCR: Zebrafish offered feed to satiation had higher growth and FCR than those fed restrictively, and Zebrafish fed soybean meal-based diet showed lower growth and higher FCR and feed intake compared to those fed fishmeal-based diet, although magnitude of response depended on feeding rate. These findings likely indicate lower digestibility of soybean meal or the presence of antinutritional factors in soybean meal that led to impaired nutrient absorption of fish offered soybean meal-based diet. Differences in measured response variables between protein qualities and feeding rates highlight the importance of determining interactive effects in nutritional studies.

Starter feed for carnivorous species as a practical replacement of bloodworms for a vertebrate model organism in ageing, the turquoise killifish Nothobranchius furzeri

The absence of a controlled diet is unfortunate in a promising model organism for ageing, the turquoise killifish (Nothobranchius furzeri Jubb, 1971). Currently captive N. furzeri are fed bloodworms but it is not known whether this is an optimal diet. Replacing bloodworms with a practical dry feed would reduce diet variability. In the present study, we estimated the nutritional value of the diet ingested by wild fish and determined the fish-body amino acid profile as a proxy for their nutritional requirements. We compared the performance of fish fed four commercial feeds containing 46%-64% protein to that achieved with bloodworms and that of wild fish. Wild fish target a high-protein (60%) diet and this is supported by their superior performance on high-protein diets in captivity. In contrast, feeds for omnivores led to slower growth, lower fecundity and unnatural liver size. In comparison to wild fish, a bloodworm diet led to lower body condition, overfeeding and male liver enlargement. Out of the four dry feeds tested, the fish fed Aller matched wild fish in body condition and liver size, and was comparable to bloodworms in terms of growth and fecundity. A starter feed for carnivorous species appears to be a practical replacement for bloodworms for N. furzeri. The use of dry feeds improved performance in comparison to bloodworms and thus may contribute to reducing response variability and improving research reproducibility in N. furzeri research.

Crème de la Créature: Dietary Influences on Behavior in Animal Models

In humans, alterations in cognitive, motivated, and affective behaviors have been described with consumption of processed diets high in refined sugars and saturated fats and with high body mass index, but the causes, mechanisms, and consequences of these changes remain poorly understood. Animal models have provided an opportunity to answer these questions and illuminate the ways in which diet composition, especially high-levels of added sugar and saturated fats, contribute to brain physiology, plasticity, and behavior. Here we review findings from invertebrate (flies) and vertebrate models (rodents, zebrafish) that implicate these diets with changes in multiple behaviors, including eating, learning and memory, and motivation, and discuss limitations, open questions, and future opportunities.

Evaluation of the Potential of Marine Algae Extracts as a Source of Functional Ingredients Using Zebrafish as Animal Model for Aquaculture

Research on immunotherapeutic agents has become a focus for the treatment of fish diseases. The ability of algae to produce secondary metabolites of potential interest as immunotherapeutics has been documented. The present research intended to assess antiviral and antibacterial activities of macro- and microalgae extracts against viral and bacterial pathogens and explore their immunomodulatory potential using zebrafish (Danio rerio) larvae as a model organism. The cytotoxicity and antiviral activity of eight methanolic and ethanolic extracts from two macroalgae (Fucus vesiculosus, Ulva rigida) and two microalgae (Nannochloropsis gaditana, Chlorella sp.) were analyzed in established fish cell lines. Six extracts were selected to evaluate antibacterial activity by disk diffusion and growth inhibition assays. The three most promising extracts were characterized in terms of fatty acid composition, incorporated at 1% into a plant-based diet, and evaluated their effect on zebrafish immune response and intestinal morphology in a short-term feeding trial. All extracts exhibited in vitro antiviral activity against viral hemorrhagic septicemia and/or infectious pancreatic necrosis viruses. Methanolic extracts from F. vesiculosus and U. rigida were richer in saturated fatty acids and exhibited in vitro antibacterial action against several bacteria. Most promising results were obtained in vivo with F. vesiculosus methanol extract, which exerted an anti-inflammatory action when incorporated alone into diets and induced pro-inflammatory cytokine expression, when combined with the other extracts. Moreover, dietary inclusion of the extracts improved intestinal morphology. In summary, the results obtained in this study support the potential of algae as natural sources of bioactive compounds for the aquaculture industry.

Multiple toxicity endpoints induced by carbon nanofibers in Amazon turtle juveniles: Outspreading warns about toxicological risks to reptiles

The toxicity of carbon-based nanomaterials (CNs) has been observed in different organisms; however, little is known about the impact of water polluted with carbon nanofibers (CNFs) on reptiles. Thus, the aim of the current study was to assess the chronic effects (7.5 months) of 1 and 10 mg/L of CNF on Podocnemis expansa (Amazon turtle) juveniles (4 months old) based on different biomarkers. Increased total organic carbon (TOC) concentrations observed in the liver and brain (which suggests CNF uptake) were closely correlated to changes in REDOX systems of turtles exposed to CNFs, mainly to higher nitrite, hydrogen peroxide and lipid peroxidation levels. Increased levels of antioxidants such as total glutathione, catalase and superoxide dismutase in the exposed animals were also observed. The uptake of CNFs and the observed biochemical changes were associated with higher frequency of erythrocyte nuclear abnormalities (assessed through micronucleus assays), as well as with both damage in erythrocyte DNA (assessed through comet assays) and higher apoptosis and necrosis rates in erythrocytes of exposed turtles. Cerebral and hepatic acetylcholinesterase (AChE) increased in turtles exposed to CNFs, and this finding suggested the neurotoxic effect of these nanomaterials. Data in the current study reinforced the toxic potential of CNFs and evidenced the biochemical, mutagenic, genotoxic, cytotoxic, and neurotoxic effects of CNFs on P. expansa.

Standardized Reference Diets for Zebrafish: Addressing Nutritional Control in Experimental Methodology

The ideal of experimental methodology in animal research is the reduction or elimination of environmental variables or consistency in their application. In lab animals, diet has been recognized as a very influential response variable. Reproducibility in research using rodents required the development of a unique diet of consistent ingredient and nutrient composition to allow for cross-comparisons of lab results, spatially and temporally. These diets are commonly referred to as standard reference diets (SRDs). The established validity of published nutritional requirements combined with the cooperation of commercial partners led to species-specific reference diets commonly used by the research community. During the last several decades, zebrafish (Danio rerio) have become a widespread alternative animal model, but specific knowledge of their nutrition is lacking. We present a short-term approach for developing an SRD for zebrafish, similar to that eventually attained for rodents over decades. Imminent development of an open-formulation, commercially produced SRD for zebrafish will notably advance translational biomedical science. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Incoherent Fluctuation of Folate Pools and Differential Regulation of Folate Enzymes Prioritize Nucleotide Supply in the Zebrafish Model Displaying Folate Deficiency-Induced Microphthalmia and Visual Defects

Objective

Congenital eye diseases are multi-factorial and usually cannot be cured. Therefore, proper preventive strategy and understanding the pathomechanism underlying these diseases become important. Deficiency in folate, a water-soluble vitamin B, has been associated with microphthalmia, a congenital eye disease characterized by abnormally small and malformed eyes. However, the causal-link and the underlying mechanism between folate and microphthalmia remain incompletely understood.

Methods

We examined the eye size, optomotor response, intracellular folate distribution, and the expression of folate-requiring enzymes in zebrafish larvae displaying folate deficiency (FD) and ocular defects.

Results

FD caused microphthalmia and impeded visual ability in zebrafish larvae, which were rescued by folate and dNTP supplementation. Cell cycle analysis revealed cell accumulation at S-phase and sub-G1 phase. Decreased cell proliferation and increased apoptosis were found in FD larvae during embryogenesis in a developmental timing-specific manner. Lowered methylenetetrahydrofolate reductase (mthfr) expression and up-regulated methylenetetrahydrofolate dehydrogenase (NADP⁺-dependent)-1-like (mthfd1L) expression were found in FD larvae. Knocking-down mthfd1L expression worsened FD-induced ocular anomalies; whereas increasing mthfd1L expression provided a protective effect. 5-CH₃-THF is the most sensitive folate pool, whose levels were the most significantly reduced in response to FD; whereas 10-CHO-THF levels were less affected. 5-CHO-THF is the most effective folate adduct for rescuing FD-induced microphthalmia and defective visual ability.

Conclusion

FD impeded nucleotides formation, impaired cell proliferation and differentiation, caused apoptosis and interfered active vitamin A production, contributing to ocular defects. The developmental timing-specific and incoherent fluctuation among folate adducts and increased expression of mthfd1L in response to FD reflect the context-dependent regulation of folate-mediated one-carbon metabolism, endowing the larvae to prioritize the essential biochemical pathways for supporting the continuous growth in response to folate depletion.

Toxic effects of naturally-aged microplastics on zebrafish juveniles: A more realistic approach to plastic pollution in freshwater ecosystems

We aim at evaluating the toxicity of naturally-aged polystyrene microplastics (MPs) in Danio rerio at intermediate development stage. Animal models were stactically exposed to 4 × 10⁴ and 4 × 10⁶ microparticles/m³ for five days - this concentration is environmentally relevant. We evaluated MP's impact on animals' nutritional status and REDOX balance, as well as its potential neuro- and cytotoxic action on them. Initially, MPs did not induce any change in total carbohydrates, triglycerides and total cholesterol levels. MP accumulation was associated with oxidative stress induction, which was inferred by the nitrite and thiobarbituric acid reactive substances levels. Furthermore, we observed that such stress was not counterbalanced by increase in the assessed enzymatic (total glutathione, catalase and superoxide dismutase) and non-enzymatic (total thiols, reduced glutathione and DPPH radical scavenging activity) antioxidants. The association between high acetylcholinesterase activity and numerical changes in neuroblasts distributed on animals' body surface confirmed MP's neurotoxic potential. MP's ability to induce apoptosis and necrosis processes in animals' erythrocytes suggested its cytotoxic action; therefore, the present study is pioneer in providing insight on how MPs can affect young freshwater fish at environmental concentrations. It is essential knowing the magnitude of these pollutants' impact on the ichthyofauna.

The reduction of lipid-sourced energy production caused by ATGL inhibition cannot be compensated by activation of HSL, autophagy, and utilization of other nutrients in fish

The adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL)-mediated lipolysis play important roles in lipid catabolism. ATGL is considered the central rate-limiting enzyme in the mobilization of fatty acids in mammals. Currently, severe fat accumulation has been commonly detected in farmed fish globally. However, the ATGL-mediated lipolysis and the potential synergy among ATGL, HSL, and autophagy, which is another way for lipid breakdown, have not been intensively understood in fish. In the present study, we added Atglistatin as an ATGL-specific inhibitor into the zebrafish diet and fed to the fish for 5 weeks. The results showed that the Atglistatin-treated fish exhibited severe fat deposition, reduced oxygen consumption, and fatty acid β-oxidation, accompanied with increased oxidative stress and inflammation. Furthermore, the Atglistatin-treated fish elevated total and phosphorylation protein expressions of HSL. However, the free fatty acids and lipase activities in organs were still systemically reduced in the Atglistatin-treated fish, and the autophagy marker LC3 was also decreased in the liver. On the other hand, glycogenolysis was stimulated but blood glucose was higher in the Atglistatin-treated fish. The transcriptomic analysis also provided the hint that the protein turnover efficiency in Atglistatin-treated fish was likely to be accelerated, but the protein content in whole fish was not affected. Taken together, ATGL plays crucial roles in energy homeostasis such that its inhibition causes loss of lipid-sourced energy production, which cannot be compensated by activation of HSL, autophagy, and utilization of other nutrients.