The zebrafish as a model for gastrointestinal tract-microbe interactions

Hydrodynamic confinement of bacteria within intestinal folds

The gut microbiota significantly influence host health by impacting metabolism, immune function and development. Understanding bacterial behaviours in intestinal folds is crucial owing to their role in biofilm formation, which protects bacteria from immune responses and antibiotics and is associated with colorectal cancer. In this study, we observed the behaviours of Escherichia coli bacteria in the intestinal folds of zebrafish larvae (Danio rerio). It is found that E. coli swims in the intestinal folds for extended periods and is confined in a groove on the wall. In order to clarify the mechanism of the confinement, we further performed numerical simulations using a boundary element method. Our simulations demonstrate that bacterial movement in the groove is constrained by hydrodynamic and steric forces. The groove configuration significantly influences bacterial confinement, with bacteria in a deep groove escaping more easily in the presence of background flow. Based on the aggregation rate of E. coli in the intestinal folds of zebrafish larvae, it is indicated that the groove trapping significantly reduces cell flux away from the wall. These findings enhance our understanding of bacterial accumulation and biofilm formation in the gut, with implications for other environments with geometric constraints.

Effect of dietary Clostridium butyricum supplementation on growth performance, immune function, and intestinal health of hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

Introduction

The aim of this study is to investigate the effects of supplementing Clostridium butyricum (C. butyricum) on hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂), with a particular focus on its impact on growth performance, blood composition, intestinal antioxidant capacity, gut microbiota, tight junction protein (ZO-1) expression, and inflammatory gene expression. The study seeks to uncover the potential health benefits of C. butyricum supplementation for hybrid grouper.

Methods

The experiment included four groups: a control group (CON) and three experimental groups, each supplemented with different strains of C. butyricum (KM, DZN, and CLH), with a concentration of 1 × 10⁷ colony-forming units per gram. These groups were designated as CB1 (KM), CB2 (DZN), and CB3 (CLH). The study evaluated growth performance, blood composition, intestinal antioxidant capacity, gut microbiota, ZO-1 protein expression, and inflammatory gene expression (IL-1β and Ikk-β).

Result

The results indicated that supplementation with C. butyricum had no significant effect on body weight gain (WG), feed efficiency (FE), or body composition. However, the CB3 group significantly increased the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in the intestine, as well as the expression of ZO-1. In addition, the CB3 group significantly increased serum lysozyme (LZM) activity, complement 4 (C4) levels, and immunoglobulin M (IgM) concentration, while significantly reducing the expression of pro-inflammatory genes (IL-1β and Ikk-β). After supplementation with C. butyricum, the level of malondialdehyde (MDA) in the intestine was significantly lower than that in the control group, indicating a reduction in intestinal oxidative stress. Supplementation with C. butyricum also altered the composition of the gut microbiota, promoting the growth of beneficial bacteria and inhibiting pathogenic bacteria, thereby further enhancing ZO-1 expression and intestinal barrier function.

Discussion

This study suggests that supplementing C. butyricum has a significant immunomodulatory effect on hybrid grouper, enhancing serum immune parameters, alleviating intestinal inflammation and oxidative stress, and promoting intestinal health. Although no significant impact was observed on growth performance, the role of C. butyricum in improving intestinal barrier function and modulating the gut microbiota highlights its potential for enhancing fish health.

Cichlid fishes are promising underutilized models to investigate helminth-host-microbiome interactions

The "Old Friends Hypothesis" suggests insufficient exposure to symbionts hinders immune development, contributing to increased immune-related diseases in the Global North. The microbiome is often the focus; helminths, potentially also offering health benefits, lack attention. Infection and effect of helminths are influenced and perhaps determined by micro-organisms. Mechanisms behind parasite-microbiome interactions are poorly understood, despite implications on host health. These interactions are typically studied for single helminth species in laboratory animal models, overlooking helminth diversity. Reviewing research on relationships between helminth and microbial diversity yielded 27 publications; most focused on human or other mammalian hosts, relying on natural exposure rather than experimental helminth inoculation. Only about half investigated host health outcomes. Remaining knowledge gaps warrant considering additional candidate model systems. Given the high helminthiasis burden and species diversity of helminths, we propose seeking models in the Global South, where a considerable proportion of research on diversity aspects of helminth-microbiome interactions took place. Low availability of genomic resources for helminths in the Global South, however, necessitates more integrative helminthological research efforts. Given substantial similarities in immune systems, several fishes are models for human health/disease. More effort could be done to establish this for cichlids, whose representatives in the African Great Lakes provide a well-delineated, closed natural system relevant to human health in view of fish-borne zoonoses and other water-borne parasites. A good baseline exists for these cichlids' genomics, parasitology, and microbiology. We suggest exploring African Great Lake cichlids as model hosts for interactions between microbial diversity, helminth diversity, and host health.

Zebrafish as a model for human epithelial pathology

Zebrafish (Danio rerio) have emerged as an influential model for studying human epithelial pathology, particularly because of their genetic similarity to humans and their unique physiological traits. This review explores the structural and functional homology between zebrafish and human epithelial tissues in organs, such as the gastrointestinal system, liver, and kidneys. Zebrafish possess significant cellular and functional homology with mammals, which facilitates the investigation of various diseases, including inflammatory bowel disease, nonalcoholic fatty liver disease, and polycystic kidney disease. The advantages of using zebrafish as a model organism include rapid external development, ease of genetic manipulation, and advanced imaging capabilities, allowing for the real-time observation of disease processes. However, limitations exist, particularly concerning the lack of organs in zebrafish and the potential for incomplete phenocopy of human conditions. Despite these challenges, ongoing research in adult zebrafish promises to enhance our understanding of the disease mechanisms and regenerative processes. By revealing the similarities and differences in epithelial cell function and disease pathways, this review highlights the value of zebrafish as a translational model for advancing our knowledge of human health and developing targeted therapies.

Small Fish, Big Answers: Zebrafish and the Molecular Drivers of Metastasis

Cancer metastasis is a leading cause of cancer-related deaths and represents one of the most challenging processes to study due to its complexity and dynamic nature. Zebrafish (Danio rerio) have become an invaluable model in metastasis research, offering unique advantages such as optical transparency, rapid development, and the ability to visualize tumor interactions with the microenvironment in real time. This review explores how zebrafish models have elucidated the critical steps of metastasis, including tumor invasion, vascular remodeling, and immune evasion, while also serving as platforms for drug testing and personalized medicine. Advances such as patient-derived xenografts and innovative genetic tools have further established zebrafish as a cornerstone in cancer research, particularly in understanding the molecular drivers of metastasis and identifying therapeutic targets. By bridging the experimental findings with clinical relevance, zebrafish continue transforming our understanding of cancer biology and therapy.

Effects of age on the response to spinal cord injury: optimizing the larval zebrafish model

Zebrafish are an increasingly popular model to study regeneration after spinal cord injury (SCI). The transparency of larval zebrafish makes them ideal to study cellular processes in real time. Standardized approaches, including age at the time of injury, are not readily available making comparisons of the results with other models challenging. In this study, we systematically examined the response to spinal cord transection of larval zebrafish at three different larval ages (3-, 5-, or 7-days post fertilization (dpf)) to determine whether the developmental complexity of the larvae affects the overall response to SCI. We then used imaging and behavioral analysis to evaluate whether differences existed based on the age of injury. Injury led to increased expression of cytokines associated with the immune response; however, we found that the timing of specific inflammatory markers changed with the age of the injury. We also observed changes in glial and axonal bridging with age. Young larvae (3 dpf) were better able to regenerate axons independent of the glial bridge, unlike older larvae (7 dpf), consistent with results seen in adult zebrafish. Finally, locomotor experiments demonstrated that some swimming behavior occurs independent of glial bridge formation, further highlighting the need for standardization of this model and functional recovery assays. Overall, we found differences based on the age of transection in larval zebrafish, underlining the importance of considering age when designing experiments aimed at understanding regeneration.

Systematic investigation on the pharmaceutical components and mechanism of the treatment against zebrafish enteritis by Sporisorium reilianum f. sp. reilianum based on histomorphology and pathology

ETHNOPHARMACOLOGICAL RELEVANCE

Sporisorium reilianum f. sp. reilianum (SSR) is a fungus isolated from a medicinal plant. Recorded in the "Compilation of National Chinese Herbal Medicine" and "Compendium of Materia Medica," it was used for preventing and treating intestinal diseases, enhancing immune function, etc. In this study, we investigated the chemical composition and bioactivity of SSR. Network pharmacology is utilized for predictive analysis and targeting pathway studies of anti-inflammatory bowel disease (IBD) mechanisms. Pharmacological activity against enteritis is evaluated using zebrafish (Danio rerio) as model animals.

AIM OF THE STUDY

To reveal the treatment of IBD by SSR used as traditional medicine and food, based on molecular biology identification of SSR firstly, and the pharmaceutical components & its toxicities, biological activity & mechanism of SSR were explored.

MATERIALS AND METHODS

Using chromatography and zebrafish IBD model induced by dextran sulfate sodium (DSS), nine compounds were first identified by nuclear magnetic resonance (NMR). The toxicity of ethanol crude extract and monomers from SSR were evaluated by evaluating the phenotypic characteristics of zebrafish embryos and larvae, histomorphology and pathology of the zebrafish model guided by network pharmacology were conducted.

RESULTS

The zebrafish embryo development did not show toxicity. The molecular docking and enrichment pathway results predicted that metabolites 3 & 4 (N-trans- feruloyl-3-methoxytyramine & N-cis-feruloyl-3-methoxytyramine) and 7 & 8 (4-N- trans-p-coumaroyltyramine & 4-N-cis--p-coumaroyltyramine) have anti-enteritis activities. This paper lays an experimental foundation for developing new drugs and functional foods.

Human norovirus disturbs intestinal motility and transit time through its capsid proteins

Human norovirus (HuNoV) accounts for over 700 million cases of gastroenteritis annually. Episodes of HuNoV disease are characterized by vomiting and diarrhea as the two most prominent symptoms. Despite its prevalence, our understanding of the pathophysiological mechanisms triggered upon HuNoV infection is limited, mainly due to a lack of suitable animal models. Our aim was to use the recent HuNoV zebrafish larvae model to study the effect of HuNoV infection on intestinal motility and investigate whether one viral protein could act as an enterotoxin, as seen with rotavirus. We studied whether HuNoV infection affects the contraction frequency of the intestinal bulb and the posterior intestine as well as the transit time. Infection of larvae, following injection of a HuNoV GII.4-containing stool sample in the yolk, resulted in an increased contraction frequency in the intestinal bulb. A comparable effect was observed in serotonin-treated larvae, corresponding to the natural function of serotonin. The higher replication efficacy of HuNoV GII.4 likely explains why they have a more marked effect on gut motility, when compared to other genotypes. Additionally, transit time of fluorescent food was prolonged in HuNoV GII.4 infected larvae, suggesting a loss of coordination in bowel movements upon infection. To identify the proteins responsible for the effect, individual HuNoV non-structural proteins and virus-like particles (VLPs) were injected intraperitoneally (ip). VLPs carrying VP1/VP2, but not those with only VP1, induced increased contraction frequencies in the intestinal bulb in a dose-dependent manner. In conclusion, our findings suggest that the viral capsid and potentially the minor capsid protein VP2 play a crucial role in the aetiology of symptoms associated with HuNoV, potentially acting as a viral enterotoxin. This work contributes to the understanding of the pathophysiological mechanisms in HuNoV-induced disease and further attests zebrafish as a valuable HuNoV disease model.

Natural-based solutions to mitigate dietary microplastics side effects in fish

Dietary microplastics (MPs) can be consumed by fish, crossing through the gastrointestinal tract. MPs smaller than 20 μm can easily translocate to other organs, such as liver, commonly triggering oxidative stress in fish. Given the current unlikelihood of their short-term elimination, strategies to mitigate MPs-related issues on fish are of considerable interest to the scientific community. In the present study, to reduce both the dietary MPs-induced oxidative stress and the accumulation of MPs, the effectiveness of microencapsulated astaxanthin (ASX) was evaluated in zebrafish (Danio rerio). Specifically, zebrafish were reared from larvae to adults (6 months) and fed diets containing MPs different in range-size (polymer A: 1-5 μm; polymer B: 40-47 μm) at different concentrations (50 or 500 mg/kg). After this period, fish from each experimental group were divided in two sub-groups that were fed, for an additional month, with the previous diets or with the same diets containing implemented with microencapsulated ASX (7 g/kg), respectively. Results showed that microencapsulated ASX was able to counteract the negative effects caused by MPs different in size. Particularly, in zebrafish fed diets containing polymer B microbeads, microencapsulated astaxanthin was able to restore the intestinal epithelium, affected by the abrasive role of MPs during gut transit. Differently, in zebrafish fed diets containing polymer A microbeads, absorbed at intestinal level and translocated mainly to the liver, the microencapsulated ASX decreased the oxidative stress response and reduced the MPs accumulation in target organs due to the antioxidant and the coagulant properties of the ASX and microcapsules wall, respectively. Taken together, the results highlighted that the aquafeeds' implementation with microencapsulated astaxanthin is a prospective tool to prevent MPs-related issues in fish.

Genomic insights into fish pathogenic bacteria: A systems biology perspective for sustainable aquaculture

Fish diseases significantly challenge global aquaculture, causing substantial financial losses and impacting sustainability, trade, and socioeconomic conditions. Understanding microbial pathogenesis and virulence at the molecular level is crucial for disease prevention in commercial fish. This review provides genomic insights into fish pathogenic bacteria from a systems biology perspective, aiming to promote sustainable aquaculture. It covers the genomic characteristics of various fish pathogens and their industry impact. The review also explores the systems biology of zebrafish, fish bacterial pathogens, and probiotic bacteria, offering insights into fish production, potential vaccines, and therapeutic drugs. Genome-scale metabolic models aid in studying pathogenic bacteria, contributing to disease management and antimicrobial development. Researchers have also investigated probiotic strains to improve aquaculture health. Additionally, the review highlights bioinformatics resources for fish and fish pathogens, which are essential for researchers. Systems biology approaches enhance understanding of bacterial fish pathogens by revealing virulence factors and host interactions. Despite challenges from the adaptability and pathogenicity of bacterial infections, sustainable alternatives are necessary to meet seafood demand. This review underscores the potential of systems biology in understanding fish pathogen biology, improving production, and promoting sustainable aquaculture.

A high-cholesterol zebrafish diet promotes hypercholesterolemia and fasting-associated liver steatosis

Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid-associated disorders. Unlike murine models, to which various standardized high lipid diets such as a high-cholesterol diet (HCD) are available, there has yet to be a uniformly adopted zebrafish HCD protocol. In this study, we have developed an improved HCD protocol and thoroughly tested its impact on zebrafish lipid deposition and lipoprotein regulation in a dose- and time-dependent manner. The diet stability, reproducibility, and fish palatability were also validated. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB-containing lipoproteins (ApoB-LPs) and increased plasma levels of cholesterol and cholesterol esters. Feeding of the HCD to larvae for 8 days produced hepatic steatosis that became more stable and sever after 1 day of fasting and was associated with an opaque liver phenotype (dark under transmitted light). Unlike larvae, adult fish fed HCD for 14 days followed by a 3-day fast did not develop a stable fatty liver phenotype, though the fish had higher ApoB-LP levels in plasma and an upregulated lipogenesis gene fasn in adipose tissue. In conclusion, our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.

Sex-Specific Effects of Environmental Exposure to the Antimicrobial Agents Benzalkonium Chloride and Triclosan on the Gut Microbiota and Health of Zebrafish (Danio rerio)

The use of disinfectants containing benzalkonium chloride (BAC) has become increasingly widespread in response to triclosan (TCS) restrictions and the COVID-19 pandemic, leading to the increasing presence of BAC in aquatic ecosystems. However, the potential environmental health impacts of BAC on fish remain poorly explored. In this study, we show that BAC and TCS can induce the gut dysbiosis in zebrafish (Danio rerio), with substantial effects on health. Breeding pairs of adult zebrafish were exposed to environmentally relevant concentrations of BAC and TCS (0.4-40 μg/L) for 42 days. Both BAC and TCS exposure perturbed the gut microbiota, triggering the classical NF-κB signaling pathway and resulting in downstream pathological toxicity associated with inflammatory responses, histological damage, inhibited ingestion, and decreased survival. These effects were dose-dependent and sex-specific, as female zebrafish were more susceptible than male zebrafish. Furthermore, we found that BAC induced toxicity to a greater extent than the restricted TCS at environmentally relevant concentrations, which is particularly concerning. Our results suggest that environmental exposure to antimicrobial chemicals can have ecological consequences by perturbing the gut microbiota, a previously underappreciated target of such chemicals. Rigorous ecological analysis should be conducted before widely introducing replacement antimicrobial compounds into disinfecting products.

Polystyrene nanoplastics-induced intestinal barrier disruption via inflammation and apoptosis in zebrafish larvae (Danio Rerio)

Plastics are one of the most pervasive materials on Earth, to which humans are exposed daily. Polystyrene (PS) is a common plastic packaging material. However, the impact of PS on human health remains poorly understood. Therefore, this study aimed to identify intestinal damage induced by PS nanoplastics (PS-NPs) in zebrafish larvae which have a high homology with humans. Four days post fertilization (dpf), zebrafish larvae were exposed to 0-, 10-, and 50-ppm PS-NPs for 48 h Initially, to ascertain if 100 nm PS-NPs could accumulate in the gastrointestinal (GI) tract of zebrafish larvae, the larvae were exposed to red fluorescence-labeled PS-NPs, and at 6 dpf, the larvae were examined using a fluorescence microscope. Analysis of the fluorescence intensity revealed that the GI tract of larvae exposed to 50-ppm exhibited a significantly stronger fluorescence intensity than the other groups. Nonfluorescent PS-NPs were then used in further studies. Scanning electron microscopy (SEM) confirmed the spherical shape of the PS-NPs. Fourier-transform infrared spectroscopy (FT-IR) analysis revealed chemical alterations in the PS-NPs before and after exposure to larvae. The polydispersity index (PDI) value derived using a Zetasizer indicated a stable dispersion of PS-NPs in egg water. Whole-mount apoptotic signal analysis via TUNEL assay showed increased apoptosis in zebrafish larval intestines exposed to 50-ppm PS-NPs. Damage to the intestinal tissue was assessed by Alcian blue (AB) and hematoxylin and eosin (H&E) staining. AB staining revealed increased mucin levels in the zebrafish larval intestines. Thin larval intestinal walls with a decrease in the density of intestinal epithelial cells were revealed by H&E staining. The differentially expressed genes (DEGs) induced by PS-NPs were identified and analyzed. In conclusion, exposure to PS-NPs may damage the intestinal barrier of zebrafish larvae due to increased intestinal permeability, and the in vivo gene network may change in larvae exposed to PS-NPs.

Resveratrol for inflammatory bowel disease in preclinical studies: a systematic review and meta-analysis

Background: Inflammatory bowel disease (IBD) is a chronic condition that can be managed with treatment, but it is challenging to get IBD cured. Resveratrol, a non-flavonoid polyphenolic organic compound derived from various plants, has a potential effect on IBD. The current research was set out to investigate the therapeutic effects of resveratrol on animal models of IBD. Methods: A comprehensive search of PubMed, Embase, Web of Science, and Chinese databases was performed. The literature search process was completed independently by two people and reviewed by a third person. The risk of bias in the included literature was assessed using the Collaborative Approach to Meta Analysis and Review of Animal Data from Experimental Stroke (CAMARADES) 10-point quality checklist. The meta-analysis utilized Review Manager 5.4 software to evaluate the efficacy of resveratrol, with histopathological index as the primary outcome measure. Subgroup analysis was conducted based on this indicator. Additionally, meta-analyses were carried out on different outcomes reported in the literature, including final disease activity index, final body weight change, colon length, splenic index, and inflammatory factors. Results: After conducting a thorough literature search and selection process, a total of 28 studies were ultimately included in the analysis. It was found that over half of the selected studies had more than five items with low risk of bias in the bias risk assessment. Relevant datas from included literature indicated that the histopathological index of the resveratrol group was significantly lower than that of the control group (WMD = -2.58 [-3.29, -1.87]). Subgroup analysis revealed that higher doses of resveratrol (>80 mg/kg) had a better efficacy (WMD = -3.47 [-4.97, -1.98]). Furthermore, The data summary and quantitative analysis results of SI and colon length also showed that resveratrol was effective in alleviating intestinal mucosal pathological injury of IBD. In terms of biochemical indicators, the summary analysis revealed that resveratrol affected interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10), tumor necrosis factor-α (TNF-α), transforming growth factor-β (TGF-β), interferon-γ (IFN-γ), malondialdehyde (MDA), myeloperoxidase (MPO), superoxide dismutase (SOD), and prostaglandin E2 (PGE2) significantly. These effects may be attributed to the mechanism of resveratrol in regulating immune response and inhibiting oxidative stress. Conclusion: This review suggests that resveratrol demonstrated a notable therapeutic impact in preclinical models of IBD, particularly at doses exceeding 80 mg/kg. This efficacy is attributed to the protective mechanisms targeting the intestinal mucosa involved in the pathogenesis of IBD through various pathways. As a result, resveratrol holds promising prospects for potential clinical use in the future.

Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models

Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.

Zebrafish: A trending model for gut-brain axis investigation

Zebrafish (Danio rerio) has ascended as a pivotal model organism in the realm of gut-brain axis research, principally owing to its high-throughput experimental capabilities and evolutionary alignment with mammals. The inherent transparency of zebrafish embryos facilitates unprecedented real-time imaging, affording unparalleled insights into the intricate dynamics of bidirectional communication between the gut and the brain. Noteworthy are the structural and functional parallels shared between the zebrafish and mammalian gut-brain axis components, rendering zebrafish an invaluable model for probing the molecular and cellular intricacies inherent in this critical physiological interaction. Recent investigations in zebrafish have systematically explored the impact of gut microbiota on neurodevelopment, behaviour, and disease susceptibility, underscoring the model's prowess in unravelling the multifaceted influence of microbial communities in shaping gut-brain interactions. Leveraging the genetic manipulability inherent in zebrafish, researchers have embarked on targeted explorations of specific pathways and molecular mechanisms, providing nuanced insights into the fundamental functioning of the gut-brain axis. This comprehensive review synthesizes pivotal findings and methodological advancements derived from zebrafish-based gut-brain axis research, accentuating the model's potential to significantly advance our understanding of this complex interplay. Furthermore, it underscores the translational significance of these insights, offering promising avenues for the identification of therapeutic targets in neuro-gastroenterological disorders and psychiatric conditions intricately linked with gut-brain interactions.

Utility of zebrafish-based models in understanding molecular mechanisms of neurotoxicity mediated by the gut-brain axis

The gut microbes perform several beneficial functions which impact the periphery and central nervous systems of the host. Gut microbiota dysbiosis is acknowledged as a major contributor to the development of several neuropsychiatric and neurological disorders including bipolar disorder, depression, anxiety, Parkinson's disease, Alzheimer's disease, attention deficit hyperactivity disorder, and autism spectrum disorder. Thus, elucidation of how the gut microbiota-brain axis plays a role in health and disease conditions is a potential novel approach to prevent and treat brain disorders. The zebrafish (Danio rerio) is an invaluable vertebrate model that possesses conserved brain and intestinal features with those of humans, thus making zebrafish a valued model to investigate the interplay between the gut microbiota and host health. This chapter describes current findings on the utility of zebrafish in understanding molecular mechanisms of neurotoxicity mediated via the gut microbiota-brain axis. Specifically, it highlights the utility of zebrafish as a model organism for understanding how anthropogenic chemicals, pharmaceuticals and bacteria exposure affect animals and human health via the gut-brain axis.

Zebrafish ApoB-Containing Lipoprotein Metabolism: A Closer Look

Zebrafish have become a powerful model of mammalian lipoprotein metabolism and lipid cell biology. Most key proteins involved in lipid metabolism, including cholesteryl ester transfer protein, are conserved in zebrafish. Consequently, zebrafish exhibit a human-like lipoprotein profile. Zebrafish with mutations in genes linked to human metabolic diseases often mimic the human phenotype. Zebrafish larvae develop rapidly and externally around the maternally deposited yolk. Recent work revealed that any disturbance of lipoprotein formation leads to the accumulation of cytoplasmic lipid droplets and an opaque yolk, providing a visible phenotype to investigate disturbances of the lipoprotein pathway, already leading to discoveries in MTTP (microsomal triglyceride transfer protein) and ApoB (apolipoprotein B). By 5 days of development, the digestive system is functional, making it possible to study fluorescently labeled lipid uptake in the transparent larvae. These and other approaches enabled the first in vivo description of the STAB (stabilin) receptors, showing lipoprotein uptake in endothelial cells. Various zebrafish models have been developed to mimic human diseases by mutating genes known to influence lipoproteins (eg, ldlra, apoC2). This review aims to discuss the most recent research in the zebrafish ApoB-containing lipoprotein and lipid metabolism field. We also summarize new insights into lipid processing within the yolk cell and how changes in lipid flux alter yolk opacity. This curious new finding, coupled with the development of several techniques, can be deployed to identify new players in lipoprotein research directly relevant to human disease.

Animal models of inflammatory bowel disease: category and evaluation indexes

Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, Drosophila melanogaster, and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.

Combined exposure with microplastics increases the toxic effects of PFOS and its alternative F-53B in adult zebrafish

Microplastics (MPs) can adsorb and desorb organic pollutants, which may alter their biotoxicities. Although the toxicity of perfluorooctane sulfonate (PFOS) and its alternative 6:2 chlorinated polyfluorinated ether sulfonate (F-53B) to organisms has been reported, the comparative study of their combined toxic effects with MPs on aquatic organisms is limited. In this study, adult female zebrafish were exposed to 10 μg/L PFOS/F-53B and 50 μg/L MPs alone or in combination for 14 days to investigate their single and combined toxicities. The results showed that the presence of MPs reduced the concentration of freely dissolved PFOS and F-53B in the exposure solution but did not affect their bioaccumulation in the zebrafish liver and gut. The combined exposure to PFOS and MPs had the greatest impact on liver oxidative stress, immunoinflammatory, and energy metabolism disorders. 16S rRNA gene sequencing analysis revealed that the combined exposure to F-53B and MPs had the greatest impact on gut microbiota. Functional enrichment analysis predicted that the alternations in the gut microbiome could interfere with signaling pathways related to immune and energy metabolic processes. Moreover, significant correlations were observed between changes in gut microbiota and immune and energy metabolism indicators, highlighting the role of gut microbiota in host health. Together, our findings demonstrate that combined exposure to PFOS/F-53B and MPs exacerbates liver immunotoxicity and disturbances in energy metabolism in adult zebrafish compared to single exposure, potentially through dysregulation of gut microbiota.

Bacterial accumulation in intestinal folds induced by physical and biological factors

BACKGROUND

The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment.

RESULTS

We discovered that E. coli spread was considerably suppressed within the intestinal folds, leading to a strong physical accumulation in the folds. Moreover, a higher concentration of E. coli on the dorsal side than on the ventral side was observed. Our in vitro microfluidic experiments and theoretical analysis revealed that the overall distribution of E. coli in the intestines was established by a combination of physical factor and bacterial taxis.

CONCLUSIONS

Our findings provide valuable insight into how the intestinal microenvironment affects bacterial motility and accumulation, enhancing our understanding of the behavioral and ecological dynamics of the intestinal microbiota.

Comparative histological description of the intestine in platyfish (Xiphophorus maculatus) and swordtail fish (Xiphophorus helleri)

This study aimed to provide a comprehensive analysis of the histological structure of intestinal tissues of platyfish (Xiphophorus maculatus) and swordtail fish (Xiphophorus helleri). Specifically, the objectives were: (1) to compare the structural adaptations of their intestines related to their distinct feeding habits, diet, and digestive strategies; and (2) to explore their potential as animal models for intestinal disease research. Through detailed examination of tissue morphology, cell types, and structural features, this study found that both species lack a stomach, with the intestine directly connected to the esophagus. Additionally, this study proposes a new division of the intestine into anterior and posterior segments based on distinct histological characteristics. The anterior segment may be adapted for temporary food storage and digestion and was characterized by elongated epithelial cells and thin intestinal folds. In contrast, the posterior segment displayed shorter villi and higher concentrations of goblet cells. This study is the first to describe in detail the intestinal morphology of platyfish and swordtail fish. These findings contribute significantly to the understanding of the comparative anatomy and physiology of these fish species, highlighting their potential as valuable models for intestinal biology research.

Gastrointestinal and brain barriers: unlocking gates of communication across the microbiota-gut-brain axis

Crosstalk between gut and brain has long been appreciated in health and disease, and the gut microbiota is a key player in communication between these two distant organs. Yet, the mechanisms through which the microbiota influences development and function of the gut-brain axis remain largely unknown. Barriers present in the gut and brain are specialized cellular interfaces that maintain strict homeostasis of different compartments across this axis. These barriers include the gut epithelial barrier, the blood-brain barrier and the blood-cerebrospinal fluid barrier. Barriers are ideally positioned to receive and communicate gut microbial signals constituting a gateway for gut-microbiota-brain communication. In this Review, we focus on how modulation of these barriers by the gut microbiota can constitute an important channel of communication across the gut-brain axis. Moreover, barrier malfunction upon alterations in gut microbial composition could form the basis of various conditions, including often comorbid neurological and gastrointestinal disorders. Thus, we should focus on unravelling the molecular and cellular basis of this communication and move from simplistic framing as 'leaky gut'. A mechanistic understanding of gut microbiota modulation of barriers, especially during critical windows of development, could be key to understanding the aetiology of gastrointestinal and neurological disorders.

Implications of exposure route for the bioaccumulation potential of nanopolystyrene particles

Microplastics and nanoplastics are found in marine biota across a wide range of trophic levels and environments. While a large portion of the information about plastic exposure comes from gastrointestinal (GI) data, the relevance of particle accumulation from an oral exposure compared with other types of exposure (e.g. dermal, respiratory) is unknown. To address this gap in knowledge, larval zebrafish (7 days post fertilization) were exposed to two different sizes of nanoplastics through either oral gavage or a waterborne exposure. Larvae were tracked for 48 h post exposure (hpe) to assess the migration and elimination of plastics. Larvae eliminated orally gavaged nanoplastics within 48 hpe. Oral gavage showed limited particle movement from the GI tract into other tissues. In contrast, waterborne nanoplastic-exposed larvae displayed notable fluorescence in tissues outside of the GI tract. The 50 nm waterborne-exposed larvae retained the particles past 48 hpe, and showed accumulation with neuromasts. For both sizes of plastic particles, the nanoplastics were eliminated from non-GI tract tissues by 24 hpe. Our results suggest that waterborne exposure leads to greater accumulation of plastic in comparison to oral exposure, suggesting that plastic accumulation in certain tissues is greater via routes of exposure other than oral consumption.

Vibrio cholerae arrests intestinal epithelial proliferation through T6SS-dependent activation of the bone morphogenetic protein pathway

To maintain an effective barrier, intestinal progenitor cells must divide at a rate that matches the loss of dead and dying cells. Otherwise, epithelial breaches expose the host to systemic infection by gut-resident microbes. Unlike most pathogens, Vibrio cholerae blocks tissue repair by arresting progenitor proliferation in the Drosophila model. At present, we do not understand how V. cholerae circumvents such a critical antibacterial defense. We find that V. cholerae blocks epithelial repair by activating the growth inhibitor bone morphogenetic protein (BMP) pathway in progenitors. Specifically, we show that interactions between V. cholerae and gut commensals initiate BMP signaling via host innate immune defenses. Notably, we find that V. cholerae also activates BMP and arrests proliferation in zebrafish intestines, indicating an evolutionarily conserved link between infection and failure in tissue repair. Our study highlights how enteric pathogens engage host immune and growth regulatory pathways to disrupt intestinal epithelial repair.

Exploring the impact of antibiotics, microplastics, nanoparticles, and pesticides on zebrafish gut microbiomes: Insights into composition, interactions, and health implications

This review addresses the impact of various chemical entities like pesticides, antibiotics, nanoparticles and microplastic on gut microbiota of zebrafish. Gut microbiota plays a vital role in metabolic regulation in every organism. As majority of metabolic pathways coordinated by microbiota, small alterations associated with mild to serious outcomes. Because of their unstoppable usage in day-to-day life, the present-day research on gut microbiota is mostly comprising aforementioned chemicals. It is better to understand how gut microbiome is dysbiosed by various environmental factors, to keep our microbiota safe. We tried to delineate the natural flora of zebrafish gut microbiome and the metabolic and other pathways associated and what are the common flora that was dysbiosed during the treatment. Based on the existing literature, we reviewed pesticides like Imazalil, Difenoconazole, Chlorpyrifos, Metamifop, Carbendazim, Imidacloprid, Phoxim, Niclosamide, Dieldrin, and antibiotics like Oxytetracycline, Enrofloxacin, Florfenicol, Sulfamethoxazole, Tetracycline, Streptomycin, Doxycycline, and in the category of nanoparticles, Titanium dioxide nanoparticles (nTiO2), Abalone viscera hydrolysates decorated silver nanoparticles (AVH-AgNPs), Lead-halide perovskite nanoparticles (LHP NPs), Copper nanoparticles (Cu-NPs), silver nanoparticles (Ag-NPs) and microplastic types like polyethylene and polystyrene microplastic. Other studies with miscellaneous chemical entities on zebrafish gut microbiome include Ferulic acid, Polychlorinated biphenyls, Cadmium, Disinfection by-products, Triclosan, microcystin-LR, Fluoride, and Amitriptyline.

Effects of Antibiotic Residues on Fish Gut Microbiome Dysbiosis and Mucosal Barrier-Related Pathogen Susceptibility in Zebrafish Experimental Model

The symbiotic community of microorganisms in the gut plays an important role in the health of the host. While many previous studies have been performed on the interactions between the gut microbiome and the host in mammals, studies in fish are still lacking. In this study, we investigated changes in the intestinal microbiome and pathogen susceptibility of zebrafish (Danio rerio) following chronic antibiotics exposure. The chronic antibiotics exposure assay was performed on zebrafish for 30 days using oxytetracycline (Otc), sulfamethoxazole/trimethoprim (Smx/Tmp), or erythromycin (Ery), which are antibiotics widely used in the aquaculture industry. The microbiome analysis indicated that Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in the gut microbiome of the zebrafish used in this study. However, in Smx/Tmp-treated zebrafish, the compositions of Fusobacteria and Proteobacteria were changed significantly, and in Ery-treated zebrafish, the compositions of Proteobacteria and Firmicutes were altered significantly. Although alpha diversity analysis showed that there was no significant difference in the richness, beta diversity analysis revealed a community imbalance in the gut microbiome of all chronically antibiotics-exposed zebrafish. Intriguingly, in zebrafish with dysbiosis in the gut microbiome, the pathogen susceptibility to Edwardsiella piscicida, a representative Gram-negative fish pathogen, was reduced. Gut microbiome imbalance resulted in a higher count of goblet cells in intestinal tissue and an upregulation of genes related to the intestinal mucosal barrier. In addition, as innate immunity was enhanced by the increased mucosal barrier, immune and stress-related gene expression in the intestinal tissue was downregulated. In this study, we provide new insight into the effect of gut microbiome dysbiosis on pathogen susceptibility.

Colonization of larval zebrafish (Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced enterocolitis

IMPORTANCE

Although inflammatory bowel diseases are on the rise, what factors influence IBD risk and severity, and the underlying mechanisms remain to be fully understood. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible to pro-inflammatory stimuli. It is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host in order to develop successful therapeutics. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models and can be utilized to address these gaps in knowledge.

Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 h post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and identify unexpected long-term cycling populations. Focused clustering and transcriptional trajectory analyses of non-skeletal muscle and endoderm identified transcriptional profiles and candidate transcriptional regulators of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and recently discovered best4+ cells. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.

Systematic analysis of proximal midgut- and anorectal-originating contractions in larval zebrafish using event feature detection and supervised machine learning algorithms

BACKGROUND

Zebrafish larvae are translucent, allowing in vivo analysis of gut development and physiology, including gut motility. While recent progress has been made in measuring gut motility in larvae, challenges remain which can influence results, such as how data are interpreted, opportunities for technical user error, and inconsistencies in methods.

METHODS

To overcome these challenges, we noninvasively introduced Nile Red fluorescent dye to fill the intraluminal gut space in zebrafish larvae and collected serial confocal microscopic images of gut fluorescence. We automated the detection of fluorescent-contrasted contraction events against the median-subtracted signal and compared it to manually annotated gut contraction events across anatomically defined gut regions. Supervised machine learning (multiple logistic regression) was then used to discriminate between true contraction events and noise. To demonstrate, we analyzed motility in larvae under control and reserpine-treated conditions. We also used automated event detection analysis to compare unfed and fed larvae.

KEY RESULTS

Automated analysis retained event features for proximal midgut-originating retrograde and anterograde contractions and anorectal-originating retrograde contractions. While manual annotation showed reserpine disrupted gut motility, machine learning only achieved equivalent contraction discrimination in controls and failed to accurately identify contractions after reserpine due to insufficient intraluminal fluorescence. Automated analysis also showed feeding had no effect on the frequency of anorectal-originating contractions.

CONCLUSIONS & INFERENCES

Automated event detection analysis rapidly and accurately annotated contraction events, including the previously neglected phenomenon of anorectal contractions. However, challenges remain to discriminate contraction events based on intraluminal fluorescence under treatment conditions that disrupt functional motility.

Single-cell resolution of the adult zebrafish intestine under conventional conditions and in response to an acute Vibrio cholerae infection

Vibrio cholerae is an aquatic bacterium that causes severe and potentially deadly diarrheal disease. Despite the impact on global health, our understanding of host mucosal responses to Vibrio remains limited, highlighting a knowledge gap critical for the development of effective prevention and treatment strategies. Using a natural infection model, we combine physiological and single-cell transcriptomic studies to characterize conventionally reared adult zebrafish guts and guts challenged with Vibrio. We demonstrate that Vibrio causes a mild mucosal immune response characterized by T cell activation and enhanced antigen capture; Vibrio suppresses host interferon signaling; and ectopic activation of interferon alters the course of infection. We show that the adult zebrafish gut shares similarities with mammalian counterparts, including the presence of Best4+ cells, tuft cells, and a population of basal cycling cells. These findings provide important insights into host-pathogen interactions and emphasize the utility of zebrafish as a natural model of Vibrio infection.

A high-cholesterol zebrafish diet promotes hypercholesterolemia and fasting-associated liver triglycerides accumulation

Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid-associated disorders. In this study, we provide an improved protocol to assay the impact of a high-cholesterol diet (HCD) on zebrafish lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB-containing lipoproteins (ApoB-LP) and increased plasma levels of cholesterol and cholesterol esters. Feeding of the HCD to larvae (8 days followed by a 1 day fast) and adult female fish (2 weeks, followed by 3 days of fasting) was also associated with a fatty liver phenotype that presented as severe hepatic steatosis. The HCD feeding paradigm doubled the levels of liver triacylglycerol (TG), which was striking because our HCD was only supplemented with cholesterol. The accumulated liver TG was unlikely due to increased de novo lipogenesis or inhibited β-oxidation since no differentially expressed genes in these pathways were found between the livers of fish fed the HCD versus control diets. However, fasted HCD fish had significantly increased lipogenesis gene fasn in adipose tissue and higher free fatty acids (FFA) in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes, which supplied more FFA during fasting, promoting hepatic steatosis. In conclusion, our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.

Toxic effects of benfluralin on zebrafish embryogenesis via the accumulation of reactive oxygen species and apoptosis

The dinitroaniline herbicide benfluralin is used weed control in conventional systems and poses a high risk of accumulation in aquatic systems. Previous studies have shown the toxic effects of benfluralin on non-target organisms; however, its developmental toxicity in vertebrates has not yet been reported. This study demonstrated the developmental toxicity of benfluralin and its mechanism of action, using zebrafish as an aquatic vertebrate model. Benfluralin induces morphological and physiological alterations in body length, yolk sac, and heart edema. We also demonstrated a reactive oxygen species (ROS) increase of approximately 325.53 % compared with the control group after 20 μM benfluralin-treatment. In addition, the malformation of the heart and vascular structures was identified using transgenic flk1:eGFP zebrafish models at 20 μM concentration benfluralin exposure. Moreover, benfluralin induced small livers, approximately 59.81 % of normal liver size, via abnormal development of the liver as observed in the transgenic L-fabp:dsRed zebrafish. Benfluralin also inhibits normal growth via abnormal expression of cell cycle regulatory genes and increases oxidative stress, inflammation, and apoptosis. Collectively, we elucidated the mechanisms associated with benfluralin toxicity, which lead to various abnormalities and developmental toxicities in zebrafish. Therefore, this study provides information on the parameters used to assess developmental toxicity in other aquatic organisms, such as herbicides, pesticides, and environmental contaminants.

Histomorphological Changes in Fish Gut in Response to Prebiotics and Probiotics Treatment to Improve Their Health Status: A Review

The gastrointestinal tract (GIT) promotes the digestion and absorption of feeds, in addition to the excretion of waste products of digestion. In fish, the GIT is divided into four regions, the headgut, foregut, midgut, and hindgut, to which glands and lymphoid tissues are associated to release digestive enzymes and molecules involved in the immune response and control of host-pathogens. The GIT is inhabited by different species of resident microorganisms, the microbiota, which have co-evolved with the host in a symbiotic relationship and are responsible for metabolic benefits and counteracting pathogen infection. There is a strict connection between a fish's gut microbiota and its health status. This review focuses on the modulation of fish microbiota by feed additives based on prebiotics and probiotics as a feasible strategy to improve fish health status and gut efficiency, mitigate emerging diseases, and maximize rearing and growth performance. Furthermore, the use of histological assays as a valid tool for fish welfare assessment is also discussed, and insights on nutrient absorptive capacity and responsiveness to pathogens in fish by gut morphological endpoints are provided. Overall, the literature reviewed emphasizes the complex interactions between microorganisms and host fish, shedding light on the beneficial use of prebiotics and probiotics in the aquaculture sector, with the potential to provide directions for future research.

Delineating the protective action of cordycepin against cadmium induced oxidative stress and gut inflammation through downregulation of NF-κB pathway

Cadmium (Cd) exposure is known to cause gut inflammation. In this study, we investigated the protective effects of cordycepin, a natural compound with pharmacological properties, against gut inflammation induced by Cd exposure. Using zebrafish larvae and colon cell line models, we examined the impact of cordycepin on Cd-induced toxicity and inflammation. Zebrafish larvae were exposed to Cd (2 µg/mL) and treated with different concentrations of cordycepin (12.5, 25 and 50 µg/mL). Cordycepin treatment significantly reduced Cd-induced embryotoxicity in zebrafish larvae. It also alleviated Cd-induced oxidative stress by reducing reactive oxygen species (ROS), lipid peroxidation and apoptosis. Furthermore, cordycepin treatment normalized the levels of liver-related biomarkers affected due to Cd exposure. Additionally, cordycepin (50 µg/mL) demonstrated a significant reduction in Cd bioaccumulation and downregulated the expression of inflammatory genes in both zebrafish larval gut and colon cell lines. These findings suggest that cordycepin could be an effective agent against Cd-induced gut inflammation.

A mucin-regulated adhesin determines the spatial organization and inflammatory character of a bacterial symbiont in the vertebrate gut

In a healthy gut, microbes are often aggregated with host mucus, yet the molecular basis for this organization and its impact on intestinal health are unclear. Mucus is a viscous physical barrier separating resident microbes from epithelia, but it also provides glycan cues that regulate microbial behaviors. Here, we describe a mucin-sensing pathway in an Aeromonas symbiont of zebrafish, Aer01. In response to the mucin-associated glycan N-acetylglucosamine, a sensor kinase regulates the expression of an aggregation-promoting adhesin we named MbpA. Upon MbpA disruption, Aer01 colonizes to normal levels but is largely planktonic and more pro-inflammatory. Increasing cell surface MbpA rescues these traits. MbpA-like adhesins are common in human-associated bacteria, and the expression of an Akkermansia muciniphila MbpA-like adhesin in MbpA-deficient Aer01 restores lumenal aggregation and reverses its pro-inflammatory character. Our work demonstrates how resident bacteria use mucin glycans to modulate behaviors congruent with host health.

Epigenetic effects of short-chain fatty acids from the large intestine on host cells

Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.

Potential of algae-derived alginate oligosaccharides and β-glucan to counter inflammation in adult zebrafish intestine

Alginate oligosaccharides (AOS) are natural bioactive compounds with anti-inflammatory properties. We performed a feeding trial employing a zebrafish (Danio rerio) model of soybean-induced intestinal inflammation. Five groups of fish were fed different diets: a control (CT) diet, a soybean meal (SBM) diet, a soybean meal+β-glucan (BG) diet and 2 soybean meal+AOS diets (alginate products differing in the content of low molecular weight fractions - AL, with 31% < 3kDa and AH, with 3% < 3kDa). We analyzed the intestinal transcriptomic and plasma metabolomic profiles of the study groups. In addition, we assessed the expression of inflammatory marker genes and histological alterations in the intestine. Dietary algal β-(1, 3)-glucan and AOS were able to bring the expression of certain inflammatory genes altered by dietary SBM to a level similar to that in the control group. Intestinal transcriptomic analysis indicated that dietary SBM changed the expression of genes linked to inflammation, endoplasmic reticulum, reproduction and cell motility. The AL diet suppressed the expression of genes related to complement activation, inflammatory and humoral response, which can likely have an inflammation alleviation effect. On the other hand, the AH diet reduced the expression of genes, causing an enrichment of negative regulation of immune system process. The BG diet suppressed several immune genes linked to the endopeptidase activity and proteolysis. The plasma metabolomic profile further revealed that dietary SBM can alter inflammation-linked metabolites such as itaconic acid, taurochenodeoxycholic acid and enriched the arginine biosynthesis pathway. The diet AL helped in elevating one of the short chain fatty acids, namely 2-hydroxybutyric acid while the BG diet increased the abundance of a vitamin, pantothenic acid. Histological evaluation revealed the advantage of the AL diet: it increased the goblet cell number and length of villi of the intestinal mucosa. Overall, our results indicate that dietary AOS with an appropriate amount of < 3kDa can stall the inflammatory responses in zebrafish.

Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii

Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.

Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused analyses of non-skeletal muscle and the endoderm identified transcriptional profiles of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and homologs of recently discovered human best4+ enterocytes. The transcriptional regulators of these populations remain unknown, so we reconstructed gene expression trajectories to suggest candidates. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.

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.

On the Novel Process of Pristine Microplastic Bio-fragmentation by Zebrafish (Danio rerio)

Microplastics are highly persistent particles that deliberately contaminate our ecosystem. These small-sized particles can pass through filtering systems into the water bodies, affecting various forms of aquatic and terrestrial life. However, little is known about their fragmentation process within the organism's body. In previous studies, commercially available microplastics were used that are rarely found in the environment naturally, hence they cannot mimic the effects on our surroundings. Therefore, using the zebrafish, Danio rerio we have evaluated the process of bio-fragmentation of ingested pristine polyethene microplastics which are widely used in our daily life. We have also examined their faecal pellets through Field Emission Scanning Electron Microscopy (FE-SEM) and Fourier transform infrared spectroscopy (FTIR). Our results show that zebrafish can potentially bio-fragment the pristine microplastic particles into nano-plastic within a short period of 24 h. Additionally, zebrafish cannot recognize the pristine microplastic particles and can ingest them as food. No mortality occurred during the experiment. Thus, we have identified a natural pathway of microplastic bio-fragmentation, introducing an emerging role of zebrafish in biogeochemical cycling and the fate of plastics.

Zebrafish as a Model of Cardiac Pathology and Toxicity: Spotlight on Uremic Toxins

Chronic kidney disease (CKD) is an increasing health care problem. About 10% of the general population is affected by CKD, representing the sixth cause of death in the world. Cardiovascular events are the main mortality cause in CKD, with a cardiovascular risk 10 times higher in these patients than the rate observed in healthy subjects. The gradual decline of the kidney leads to the accumulation of uremic solutes with a negative effect on every organ, especially on the cardiovascular system. Mammalian models, sharing structural and functional similarities with humans, have been widely used to study cardiovascular disease mechanisms and test new therapies, but many of them are rather expensive and difficult to manipulate. Over the last few decades, zebrafish has become a powerful non-mammalian model to study alterations associated with human disease. The high conservation of gene function, low cost, small size, rapid growth, and easiness of genetic manipulation are just some of the features of this experimental model. More specifically, embryonic cardiac development and physiological responses to exposure to numerous toxin substances are similar to those observed in mammals, making zebrafish an ideal model to study cardiac development, toxicity, and cardiovascular disease.

Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut

BACKGROUND

Prebiotic feed additives aim to improve gut health by influencing the microbiota and the gut barrier. Most studies on feed additives concentrate on one or two (monodisciplinary) outcome parameters, such as immunity, growth, microbiota or intestinal architecture. A combinatorial and comprehensive approach to disclose the complex and multifaceted effects of feed additives is needed to understand their underlying mechanisms before making health benefit claims. Here, we used juvenile zebrafish as a model species to study effects of feed additives by integrating gut microbiota composition data and host gut transcriptomics with high-throughput quantitative histological analysis. Zebrafish received either control, sodium butyrate or saponin-supplemented feed. Butyrate-derived components such as butyric acid or sodium butyrate have been widely used in animal feeds due to their immunostimulant properties, thereby supporting intestinal health. Soy saponin is an antinutritional factor from soybean meal that promotes inflammation due to its amphipathic nature.

RESULTS

We observed distinct microbial profiles associated with each diet, discovering that butyrate (and saponin to a lesser extent) affected gut microbial composition by reducing the degree of community-structure (co-occurrence network analysis) compared to controls. Analogously, butyrate and saponin supplementation impacted the transcription of numerous canonical pathways compared to control-fed fish. For example, both butyrate and saponin increased the expression of genes associated with immune response and inflammatory response, as well as oxidoreductase activity, compared to controls. Furthermore, butyrate decreased the expression of genes associated with histone modification, mitotic processes and G-coupled receptor activity. High-throughput quantitative histological analysis depicted an increase of eosinophils and rodlet cells in the gut tissue of fish receiving butyrate after one week of feeding and a depletion of mucus-producing cells after 3 weeks of feeding this diet. Combination of all datasets indicated that in juvenile zebrafish, butyrate supplementation increases the immune and the inflammatory response to a greater extent than the established inflammation-inducing anti-nutritional factor saponin. Such comprehensive analysis was supplemented by in vivo imaging of neutrophil and macrophage transgenic reporter zebrafish (mpeg1:mCherry/mpx:eGFPi¹¹⁴) larvae. Upon exposure to butyrate and saponin, these larvae displayed a dose-dependent increase of neutrophils and macrophages in the gut area.

CONCLUSION

The omics and imaging combinatorial approach provided an integrated evaluation of the effect of butyrate on fish gut health and unraveled inflammatory-like features not previously reported that question the usage of butyrate supplementation to enhance fish gut health under basal conditions. The zebrafish model, due to its unique advantages, provides researchers with an invaluable tool to investigate effects of feed components on fish gut health throughout life.

The microbiota regulates hematopoietic stem and progenitor cell development by mediating inflammatory signals in the niche

The commensal microbiota regulates the self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) in bone marrow. Whether and how the microbiota influences HSPC development during embryogenesis is unclear. Using gnotobiotic zebrafish, we show that the microbiota is necessary for HSPC development and differentiation. Individual bacterial strains differentially affect HSPC formation, independent of their effects on myeloid cells. Early-life dysbiosis in chd8-/- zebrafish impairs HSPC development. Wild-type microbiota promote HSPC development by controlling basal inflammatory cytokine expression in kidney niche, and chd8-/- commensals elicit elevated inflammatory cytokines that reduce HSPCs and enhance myeloid differentiation. We identify an Aeromonas veronii strain with immuno-modulatory activities that fails to induce HSPC development in wild-type fish but selectively inhibits kidney cytokine expression and rebalances HSPC development in chd8-/- zebrafish. Our studies highlight the important roles of a balanced microbiome during early HSPC development that ensure proper establishment of lineal precursor for adult hematopoietic system.

Tyramine-induced gastrointestinal dysregulation is attenuated via estradiol associated mechanisms in a zebrafish larval model

Development of targeted therapeutics to alleviate gastrointestinal (GI) inflammation and its debilitating consequences are required. In this context, the trace aminergic system may link together sex, diet and inflammation. Utilising a zebrafish larval model of GI inflammation, the current study aimed to investigate mechanisms by which excess amounts of trace amines (TAs) may influence GI health. In addition, we probed the potential role of 17β-estradiol (E2) and its receptors, given the known female-predominance of many GI disorders. To assess GI functionality and integrity, live imaging techniques (neutral red staining) and post-mortem immunofluorescent staining of tight junction proteins (occludin and ZO-1) were analyzed respectively. In addition, behavioural assays, as an indication of overall wellbeing, as well as whole body H₂O₂ and prostaglandin E2 assays were performed to inform on oxidative and inflammatory status. Excess β-phenethylamine (PEA), tryptamine (TRP) and ρ-tyramine (TYR) resulted in adverse GI and systemic effects. In this regard, clear beneficial effects of E2 to modulate the effects of PEA, TRP and TYR was evident. Moreover, agmatine displayed potential protective effects on GI epithelium and whole body oxidative status, however, potential to induce systemic inflammation suggests the importance of dosage and administration optimisation. Taken together, TYR seems like the most prominent TA to have damaging GI effects, feasibly exacerbating GI inflammation. In this context, the relative lack of E2 may provide mechanistic insights into the reported female-predominance of GI disorders. Moreover, an effective therapeutic in this context may be required to maintain GI TA load despite fluctuating E2 levels.

Aeromonas hydrophila induction method in adult zebrafish (Danio rerio) as animal infection models

Background and Aim: Zebrafish are frequently used as model organisms in scientific research as their genes mirror those of humans. Aeromonas hydrophila bacteria can infect humans and animals, mainly fish. This study aimed to identify the concentration and route of A. hydrophila infection in adult zebrafish. Zebrafish had been used as a challenge test by analyzing their hematological profiles, blood glucose levels, and survival rates. Materials and Methods: Induction of cell supernatant free (CSF) from A. hydrophila bacteria in adult zebrafish was carried out via bath immersion (BI), intraperitoneal injection (IPI), intramuscular injection (IMI), and healthy zebrafish as a control (C). The bacterial concentrations were 107, 109, and 1011 colony-forming units (CFU)/mL. At 24 h post-infection, the outcomes of infection were evaluated based on survival rates, hematological profiles, and blood glucose levels. A one-way analysis of variance with a confidence level of 95% was employed to examine the data. Results: In the BI, IPI, and IMI treatment groups, the survival rate of the fish reached a peak of 100%, 22%–100%, and 16%–63%, respectively, compared with the injection technique. In the IMI2 group, a 109 CFU/mL bacterial concentration was determined to correspond to the lethal dosage 50. All infection groups had lower erythrocyte and hemoglobin counts but higher leukocyte counts than the control group. The blood sugar levels of the healthy and infected groups were not significantly different. Conclusion: The route of A. hydrophila infection through Intramuscular injection with a concentration of 109 CFU/mL indicated a high performance compared to other techniques. This method could be developed as a reproducible challenge test.

Lactobacillus rhamnosus GG treatment potentiates ethanol-induced behavioral changes through modulation of intestinal epithelium in Danio rerio

The gut-brain axis directly regulates the brain homeostatic environment; an imbalance in gut microbial composition following ethanol exposure is maleficent. In this context, involvement of probiotics as prophylactic intervention against ethanol-induced neurotoxicity is elusive in the literature. Therefore, the present study was aimed to determine the impact of chronic ethanol exposure on the neurobehavioral response of zebrafish and possible neuroprotection through co-supplementation of probiotic Lactobacillus rhamnosus GG (LGG). Zebrafish were divided into naive, control, ethanol (0.01% v/v), LGG, and ethanol co-supplemented with LGG groups. Neurobehavioral assessment was performed after 7 days of chronic waterborne exposure to ethanol with LGG co-supplementation followed by histopathological studies. The findings indicated that there was a clear alteration in locomotor activity and habitat preference, with animals preferentially migrating toward altered zones on exposure to ethanol. However, co-supplementation of LGG showed restoration against ethanol-induced neurobehavioral and cognitive dysfunction. Brain tissue pyknosis and intestinal epithelial disruption were significantly mitigated on LGG co-supplementation against ethanol in zebrafish. The present study provides a novel approach toward supplementation of probiotics such as LGG in modulation of gut commensal microbiota influencing zebrafish behavior. Moreover, the findings delineate the possible role of probiotics as a curative administration to counter ethanol-persuaded neurological outcomes.

E. coli Common pili promote the fitness and virulence of a hybrid aEPEC/ExPEC strain within diverse host environments

Pathogenic subsets of Escherichia coli include diarrheagenic (DEC) strains that cause disease within the gut and extraintestinal pathogenic E. coli (ExPEC) strains that are linked with urinary tract infections, bacteremia, and other infections outside of intestinal tract. Among DEC strains is an emergent pathotype known as atypical enteropathogenic E. coli (aEPEC), which can cause severe diarrhea. Recent sequencing efforts revealed that some E. coli strains possess genetic features that are characteristic of both DEC and ExPEC isolates. BA1250 is a newly reclassified hybrid strain with characteristics of aEPEC and ExPEC. This strain was isolated from a child with diarrhea, but its genetic features indicate that it might have the capacity to cause disease at extraintestinal sites. The spectrum of adhesins encoded by hybrid strains like BA1250 are expected to be especially important in facilitating colonization of diverse niches. E. coli common pilus (ECP) is an adhesin expressed by many E. coli pathogens, but how it impacts hybrid strains has not been ascertained. Here, using zebrafish larvae as surrogate hosts to model both gut colonization and extraintestinal infections, we found that ECP can act as a multi-niche colonization and virulence factor for BA1250. Furthermore, our results indicate that ECP-related changes in activation of envelope stress response pathways may alter the fitness of BA1250. Using an in silico approach, we also delineated the broader repertoire of adhesins that are encoded by BA1250, and provide evidence that the expression of at least a few of these varies in the absence of functional ECP.

Zebrafish: an efficient vertebrate model for understanding role of gut microbiota

Gut microbiota plays a critical role in the maintenance of host health. As a low-cost and genetically tractable vertebrate model, zebrafish have been widely used for biological research. Zebrafish and humans share some similarities in intestinal physiology and function, and this allows zebrafish to be a surrogate model for investigating the crosstalk between the gut microbiota and host. Especially, zebrafish have features such as high fecundity, external fertilization, and early optical transparency. These enable the researchers to employ the fish to address questions not easily addressed in other animal models. In this review, we described the intestine structure of zebrafish. Also, we summarized the methods of generating a gnotobiotic zebrafish model, the factors affecting its intestinal flora, and the study progress of gut microbiota functions in zebrafish. Finally, we discussed the limitations and challenges of the zebrafish model for gut microbiota studies. In summary, this review established that zebrafish is an attractive research tool to understand mechanistic insights into host-microbe interaction.