Intestinal microbiome adjusts the innate immune setpoint during colonization through negative regulation of MyD88

The interactions between the host immunity and intestinal microorganisms in fish

There is a huge quantity of microorganisms in the gut of fish, which exert pivotal roles in maintaining host intestinal and general health. The fish immunity can sense and shape the intestinal microbiota and maintain the intestinal homeostasis. In the meantime, the intestinal commensal microbes regulate the fish immunity, control the extravagant proliferation of pathogenic microorganisms, and ensure the intestinal health of the host. This review summarizes developments and progress on the known interactions between host immunity and intestinal microorganisms in fish, focusing on the recent advances in zebrafish (Danio rerio) showing the host immunity senses and shapes intestinal microbiota, and intestinal microorganisms tune host immunity. This review will offer theoretical references for the development, application, and commercialization of intestinal functional microorganisms in fish. KEY POINTS: • The interactions between the intestinal microorganisms and host immunity in zebrafish • Fish immunity senses and shapes the microbiota • Intestinal microbes tune host immunity in fish.

Acute copper oxide nanoparticles exposure alters zebrafish larval microbiome

Copper oxide nanoparticles (CuO NPs) are being used in healthcare industries due to its antimicrobial properties. The increased consumption of NPs could lead to the rise of these NPs in the environment affecting the biological systems. Altered microbiome has been correlated to disease pathology in humans as well as xenobiotic toxicity in experimental animal models. However, CuO NPs-induced microbiome alterations in vertebrates have not been reported so far. In this study, for the first time, zebrafish larvae at 96 hpf (hours post fertilization) were exposed to CuO NPs for 24 h at 10, 20, and 40 ppm. After exposure, the control and treated larvae were subjected to 16S rRNA amplicon sequencing followed by relative taxa abundance, alpha and beta diversity analysis, single factor analysis, LEfSe, Deseq2, and functional profiling. No significant alteration was detected in the microbial richness and diversity, however, specific taxa constituting the core microbiome such as phylum Proteobacteria were significantly increased and Bacterioidetes and Firmicutes were decreased in the treated groups, indicating a core microbiota dysbiosis. Further, the family Lachnospiraceae, and genus Syntrophomonas involved in butyrate production and the metabolism of lipids and glucose were significantly altered. In addition, the opportunistic pathogens belonging to order Flavobacteriales were increased in CuO NPs treated groups. Moreover, the taxa involved in host immune response (Shewanella, Delftia, and Bosea) were found to be enriched in CuO NPs exposed larvae. These results indicate that CuO NPs exposure causes alteration in the core microbiota, which could cause colitis or inflammatory bowel disease.

Synbiotic Agents and Their Active Components for Sustainable Aquaculture: Concepts, Action Mechanisms, and Applications

Aquaculture is a fast-emerging food-producing sector in which fishery production plays an imperative socio-economic role, providing ample resources and tremendous potential worldwide. However, aquatic animals are exposed to the deterioration of the ecological environment and infection outbreaks, which represent significant issues nowadays. One of the reasons for these threats is the excessive use of antibiotics and synthetic drugs that have harmful impacts on the aquatic atmosphere. It is not surprising that functional and nature-based feed ingredients such as probiotics, prebiotics, postbiotics, and synbiotics have been developed as natural alternatives to sustain a healthy microbial environment in aquaculture. These functional feed additives possess several beneficial characteristics, including gut microbiota modulation, immune response reinforcement, resistance to pathogenic organisms, improved growth performance, and enhanced feed utilization in aquatic animals. Nevertheless, their mechanisms in modulating the immune system and gut microbiota in aquatic animals are largely unclear. This review discusses basic and current research advancements to fill research gaps and promote effective and healthy aquaculture production.

Probiotic components of Bacillus siamensis LF4 mitigated β-conglycinin caused cell injury via modulating TLR2/MAPKs/NF-κB signaling in Lateolabrax maculatus

β-conglycinin is a recognized factor in leading to intestinal inflammation and limiting application of soybean meal in aquaculture. Our previous study reported that heat-killed B. siamensis LF4 could effectively mitigate inflammatory response and apoptosis caused by β-conglycinin in spotted seabass (Lateolabrax maculatus) enterocytes, but the mechanisms involved are not fully understood. In the present study, therefore, whole cell wall (CW), peptidoglycan (PG) and lipoteichoic acid (LTA) and cell-free supernatant (CFS) have been collected from B. siamensis LF4 and their mitigative function on β-conglycinin-induced adverse impacts and mechanisms underlying were evaluated. The results showed that β-conglycinin-induced cell injury, characterized with significantly decreased cell viability and increased activities of lactate dehydrogenase, glutamic oxaloacetic transaminase, glutamic propylic transaminase (P < 0.05), were reversed by subsequent heat-killed B. siamensis LF4 and its CW, LTA, PG and CFS treatment. Enterocytes co-cultured with heat-killed B. siamensis LF4 and its CW, LTA, PG and CFS (especially PG) significantly increased expressions of anti-inflammatory genes (IL-2, IL-4, IL-10 and TGF-β1), tight junction proteins (ZO-1, occludin and claudin-b) and antimicrobial peptides (β-defensin, hepcidin-1, NK-lysin and piscidin-5), and decreased expressions of pro-inflammatory genes (IL-1β, IL-8 and TNF-α) and apoptosis-related genes (caspase 3, caspase 8 and caspase 9) (P < 0.05), indicating their excellent mitigation effects on β-conglycinin-induced cell damages. In addition, heat-killed B. siamensis LF4 and its CW, LTA, PG and CFS significantly increased TLR2 mRNA level (especially in PG treatment), and decreased MAPKs (JNK, ERK, p38 and AP-1) and NF-κB related genes expressions. In conclusion, heat-killed B. siamensis LF4 and its CW, LTA, PG and CFS could modulating TLR2/MAPKs/NF-κB signaling and alleviating β-conglycinin-induced enterocytes injury in spotted seabass (L. maculatus), and PG presented the best potential.

Maturation of the medaka immune system depends on reciprocal interactions between the microbiota and the intestinal tract

The interactions between the host immune system and intestinal microorganisms have been studied in many animals, including fish. However, a detailed analysis has not been performed in medaka, an established fish model for biological studies. Here, we investigated the effect of immunodeficiency on the microbiota composition and the effect of gut bacteria on intestinal epithelial development and immune responses in medaka. Chronological analysis of the intestinal microbiota of interleukin 2 receptor subunit gamma (il2rg) mutant medaka showed a gradual decrease in the evenness of operational taxonomic units, mainly caused by the increased abundance of the Aeromonadaceae family. Exposure of wild-type medaka to high doses of an intestine-derived opportunistic bacterium of the Aeromonadaceae family induced an inflammatory response, suggesting a harmful effect on adult il2rg mutants. In addition, we established germ-free conditions in larval medaka and observed large absorptive vacuoles in intestinal epithelial cells, indicating a block in epithelial maturation. Transcriptome analysis revealed a decrease in the expression of genes involved in the defense response, including the antimicrobial peptide gene hepcidin, whose expression is induced by lipopolysaccharide stimulation in normal larvae. These results show that reciprocal interactions between the microbiome and the intestinal tract are required for the maturation of the medaka immune system.

Antibiotic-Induced Dysbiosis of the Gut Microbiota Impairs Gene Expression in Gut-Liver Axis of Mice

Antibiotics can be a double-edged sword. The application of broad-spectrum antibiotics leads to the suppression of microorganisms in the human body without selective targeting, including numerous non-pathogenic microorganisms within the gut. As a result, dysbiosis of the gut microbiota can occur. The gut microbiota is a vast and intricate ecosystem that has been connected with various illnesses. Significantly, the gut and liver function in a closely coupled anatomical and physiological relationship referred to as the "gut-liver axis". Consequently, metabolites stemming from the gut microbiota migrate via the portal vein to the liver, thereby influencing gene expression and proper physiological activity within the liver. This study aimed to investigate the dysbiosis of gut microbiota ecology and the disruption of gene expression resulting from oral antibiotics and their subsequent recovery. In the experiment, mice were tube-fed neomycin (0.5 mg/mL) and ampicillin (1 mg/mL) for 21 days (ABX group) to conduct 16s rRNA sequencing. By simultaneously analyzing public datasets PRJDB6615, which utilized the same antibiotics, it was found that nearly 50% of the total microbiota abundance was attributed to the f__Lactobacillaceae family. Additionally, datasets GSE154465 and GSE159761, using the same antibiotics, were used to screen for differentially expressed genes pre-and post-antibiotic treatment. Quantitative real-time PCR was employed to evaluate gene expression levels before and after antibiotic treatment. It was discovered that oral antibiotics significantly disrupted gene expression in the gut and liver, likely due to the dysregulation of the gut microbiota ecology. Fecal microbiota transplantation (FMT) was found to be an effective method for restoring gut microbiota dysbiosis. To further enhance the restoration of gut microbiota and gene expression, an antioxidant, vitamin C, was added to the FMT process to counteract the oxidative effect of antibiotics on microorganisms. The results showed that FMTs with vitamin C were more effective in restoring gut microbiota and gene expression to the level of the fecal transplant donor.

The role of the microbiome on fish mucosal immunity under changing environments

The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.

Small fish, big discoveries: zebrafish shed light on microbial biomarkers for neuro-immune-cardiovascular health

Zebrafish (Danio rerio) have emerged as a powerful model to study the gut microbiome in the context of human conditions, including hypertension, cardiovascular disease, neurological disorders, and immune dysfunction. Here, we highlight zebrafish as a tool to bridge the gap in knowledge in linking the gut microbiome and physiological homeostasis of cardiovascular, neural, and immune systems, both independently and as an integrated axis. Drawing on zebrafish studies to date, we discuss challenges in microbiota transplant techniques and gnotobiotic husbandry practices. We present advantages and current limitations in zebrafish microbiome research and discuss the use of zebrafish in identification of microbial enterotypes in health and disease. We also highlight the versatility of zebrafish studies to further explore the function of human conditions relevant to gut dysbiosis and reveal novel therapeutic targets.

Short-Term Alternate Feeding between Terrestrially Sourced Oil- and Fish Oil-Based Diets Modulates the Intestinal Microecology of Juvenile Turbot

A nine-week feeding trial was conducted to investigate changes in the intestinal microbiota of turbot in response to alternate feeding between terrestrially sourced oil (TSO)- and fish oil (FO)-based diets. The following three feeding strategies were designed: (1) continuous feeding with the FO-based diet (FO group); (2) weekly alternate feeding between soybean oil (SO)- and FO-based diets (SO/FO group); and (3) weekly alternate feeding between beef tallow (BT)- and FO-based diets (BT/FO group). An intestinal bacterial community analysis showed that alternate feeding reshaped the intestinal microbial composition. Higher species richness and diversity of the intestinal microbiota were observed in the alternate-feeding groups. A PCoA analysis showed that the samples clustered separately according to the feeding strategy, and among the three groups, the SO/FO group clustered relatively closer to the BT/FO group. The alternate feeding significantly decreased the abundance of Mycoplasma and selectively enriched specific microorganisms, including short-chain fatty acid (SCFA)-producing bacteria, digestive bacteria (Corynebacterium and Sphingomonas), and several potential pathogens (Desulfovibrio and Mycobacterium). Alternate feeding may maintain the intestinal microbiota balance by improving the connectivity of the ecological network and increasing the competitive interactions within the ecological network. The alternate feeding significantly upregulated the KEGG pathways of fatty acid and lipid metabolism, glycan biosynthesis, and amino acid metabolism in the intestinal microbiota. Meanwhile, the upregulation of the KEGG pathway of lipopolysaccharide biosynthesis indicates a potential risk for intestinal health. In conclusion, short-term alternate feeding between dietary lipid sources reshapes the intestinal microecology of the juvenile turbot, possibly resulting in both positive and negative effects.

Preclinical study models of psoriasis: State-of-the-art techniques for testing pharmaceutical products in animal and nonanimal models

Local and systemic treatments exist for psoriasis, but none can do more than control its symptoms because of its numerous unknown mechanisms. The lack of validated testing models or a defined psoriatic phenotypic profile hinders antipsoriatic drug development. Despite their intricacy, immune-mediated diseases have no improved and precise treatment. The treatment actions may now be predicted for psoriasis and other chronic hyperproliferative skin illnesses using animal models. Their findings confirmed that a psoriasis animal model could mimic a few disease conditions. However, their ethical approval concerns and inability to resemble human psoriasis rightly offer to look for more alternatives. Hence, in this article, we have reported various cutting-edge techniques for the preclinical testing of pharmaceutical products for the treatment of psoriasis.

The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

BACKGROUND

The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems.

RESULTS

Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities.

CONCLUSIONS

Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.

Commensal Bacillus siamensis LF4 induces antimicrobial peptides expression via TLRs and NLRs signaling pathways in intestinal epithelial cells of Lateolabrax maculatus

Antimicrobial peptides (AMPs) play an important role in modulating intestinal microbiota, and our previous study showed that autochthonous Baccilus siamensis LF4 could shape the intestinal microbiota of spotted seabass (Lateolabrax maculatus). In the present study, a spotted seabass intestinal epithelial cells (IECs) model was used to investigate whether autochthonous B. siamensis LF4 could modulate the expression of AMPs in IECs. And then, the IECs were treated with active, heat-inactivated LF4 and its supernatant to illustrate their AMPs inducing effects and the possible signal transduction mechanisms. The results showed that after 3 h of incubation with 10⁸ CFU/mL B. siamensis LF4, lactate dehydrogenase (LDH), glutamic oxaloacetic transaminase (GOT), glutamic propylic transaminase (GPT) activities in supernatant decreased significantly and obtained minimum values, while supernatant alkaline phosphatase (AKP) activity, β-defensin protein level and IECs Na⁺/K⁺-ATPase activity, AMPs (β-defensin, hepcidin-1, NK-lysin, piscidin-5) genes expression increased significantly and obtained maximum values (P < 0.05). Further study demonstrated that the active, heat-inactivated LF4 and its supernatant treatments could effectively decrease the LDH, GOT, and GPT activities in IECs supernatant, increase AKP activity and β-defensin (except LF4 supernatant treatment) protein level in IECs supernatant and Na⁺/K⁺-ATPase and AMPs genes expression in IECs. Treatment with active and heat-inactivated B. siamensis LF4 resulted in significantly up-regulated the expressions of TLR1, TLR2, TLR3, TLR5, NOD1, NOD2, TIRAP, MyD88, IRAK1, IRAK4, TRAF6, TAB1, TAB2, ERK, JNK, p38, AP-1, IKKα, IKKβ and NF-κB genes. Treatment with B. siamensis LF4 supernatant also resulted in up-regulated these genes, but not the genes (ERK, JNK, p38, and AP-1) in MAPKs pathway. In summary, active, heat-inactivated and supernatant of B. siamensis LF4 can efficiently induce AMPs expression through activating the TLRs/NLRs-MyD88-dependent signaling, active and heat-inactivated LF4 activated both the downstream MAPKs and NF-κB pathways, while LF4 supernatant only activated NF-κB pathway.

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.

Transcriptomic and Metabolomic Studies Reveal That Toll-like Receptor 2 Has a Role in Glucose-Related Metabolism in Unchallenged Zebrafish Larvae (Danio rerio)

Toll-like receptors (TLRs) have been implicated in the regulation of various metabolism pathways, in addition to their function in innate immunity. Here, we investigate the metabolic function of TLR2 in a larval zebrafish system. We studied larvae from a tlr2 mutant and the wild type sibling controls in an unchallenged normal developmental condition using transcriptomic and metabolomic analyses methods. RNAseq was used to evaluate transcriptomic differences between the tlr2 mutant and wild-type control zebrafish larvae and found a signature set of 149 genes to be significantly altered in gene expression. The expression level of several genes was confirmed by qPCR analyses. Gene set enrichment analysis (GSEA) revealed differential enrichment of genes between the two genotypes related to valine, leucine, and isoleucine degradation and glycolysis and gluconeogenesis. Using ¹H nuclear magnetic resonance (NMR) metabolomics, we found that glucose and various metabolites related with glucose metabolism were present at higher levels in the tlr2 mutant. Furthermore, we confirmed that the glucose level is higher in tlr2 mutants by using a fluorometric assay. Therefore, we have shown that TLR2, in addition to its function in immunity, has a function in controlling metabolism during vertebrate development. The functions are associated with transcriptional regulation of various enzymes involved in glucose metabolism that could explain the different levels of glucose, lactate, succinate, and malate in larvae of a tlr2 mutant.

Vitamin E supplementation in diet ameliorates growth of Nile tilapia by upgrading muscle health

Vitamin E (VE), an important lipid-soluble antioxidant, has great influence on growth and maintenance in animal. The effects of VE supplemented diet on growth and feed usage in Nile tilapia (Oreochromis niloticus) was investigated in this study. Three formulated diets containing VE (0, 50 and 100 mg/kg) were fed to Nile tilapia (3.56 ± 0.16 g) in glass aquaria maintaining three replicate groups for 56 days (8 weeks). Survival, growth performance including weight gain, percent weight gain, and specific growth rate (WG, % WG, and SGR), and feed utilization comprising protein efficiency ratio and feed conversion ratio (PER and FCR) were calculated. Hemato-biochemical indices including hemoglobin level (Hb), white blood cell (WBC), red blood cell (RBC) and glucose level were analyzed. In addition, muscle morphology was examined after completion of the experiment. At the end of the trial, WG, %WG, SGR, FCR and PER increased significantly which had dietary VE supplimentation. However, no distinct changes were observed in Hb level, RBC count, WBC count and glucose level among these different dietary groups. Dietary VE treatments significantly upgraded the muscle fiber diameter and lowered the intra-muscle gap. Moreover, quantity of hyperplastic muscle fiber as well as nucleus also significantly enhanced by VE. Morphological structure of muscle characterized by a huge proportion of hyperplastic muscle that may be supposed to contribute the enhanced growth of Nile tilapia receiving VE supplemented diet. Therefore these results suggested that VE incorporation into the feed can be effective to improve the feed efficiency and maximize the growth of O. niloticus.

Prodrug Integrated Envelope on Probiotics to Enhance Target Therapy for Ulcerative Colitis

Ulcerative colitis (UC), affecting millions of patients worldwide, is associated with disorders of the gut microbiota. Probiotics-based therapy positively regulating the community structure of gut microbiota is regarded as an efficient intervention for UC. However, oral probiotics delivery is restricted by limited bioactivity, short retention time, complex pathological condition, and single therapeutic efficacy. Here, a bioengineered probiotic decorated with a multifunctional prodrug coating is constructed to ameliorate the aforementioned shortcomings. The results of UC mice induced by dextran sulfate sodium demonstrate that the intrinsic features of the fabricated coating integrate gut microbes protection, colon-targeted drug release, prolonged drug retention, and inflammation regulation. In parallel, the probiotics Lactobacillus rhamnosus GG (LGG) could regulate the composition of the gut microbiota and improve epithelial barrier function, thereby synergistically ameliorating UC. These results provide ample shreds of evidence of the therapeutic effect on UC, therefore, demonstrate a great promise as the potential therapeutic strategy for UC treatment.

Effects of carbamazepine on gut microbiota, ARGs and intestinal health in zebrafish

Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal health, resistome, microbiota, and their relationship after CBZ exposure has been rarely reported. This study aimed to explore the impacts of CBZ on gut microbiota, antibiotic resistance genes (ARGs) and the expression of intestinal health related genes as well as their interaction using the zebrafish model. 16 S ribosomal RNA sequencing indicated CBZ altered the composition of gut microbiota. Using high-throughput quantitative polymerase chain reaction (HT-qPCR), we found the number and abundance of ARGs were impacted by CBZ levels and exposure duration. We also observed the upregulated expression of the pro-inflammatory gene IL6 and downregulated expression of toll-like receptor gene TLR2 and intestinal barrier gene TJP2a at different exposure times. Correlation analyses revealed that Geobacillus, Rhodococcus, Ralstonia, Delftia, Luteolibacter and Escherichia-Shigella might be the main bacterial genera carrying ARGs. Meanwhile, Cetobacterium and Aeromonas could be the dominant bacteria affecting intestinal health related genes. Our results could contribute to understanding the health risks of CBZ to the intestinal microecology of aquatic animals.

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.

The road not taken: host genetics in shaping intergenerational microbiomes

The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.

Detecting Intestinal Goblet Cells of the Broadgilled Hagfish Eptatretus cirrhatus (Forster, 1801): A Confocal Microscopy Evaluation

Simple Summary

The intestinal epithelium of fish, similar to mammals, consists mainly of enterocytes and goblet cells. Goblet cells play a key role in the secretion of mucus, which, in addition to promoting the digestion of nutrients, is the first protective barrier against bacteria, viruses, and pathogens. Our study aims to evaluate the presence, localization, and co-localization of 5-HT, TLR2, iNOS, and Piscidin1 in goblet cells of the intestine of Eptatretus cirrhatus. The results obtained by confocal microscopy show, for the first time, the positivity of goblet cells to the antibodies tested, suggesting the involvement of these cells in the intestinal immunity of broadgilled hagfish.

Abstract

The fish intestine operates as a complicated interface between the organism and the environment, providing biological and mechanical protections as a result of a viscous layer of mucus released by goblet cells, which serves as a barrier against bacteria, viruses, and other pathogens, and contributes to the functions of the immune system. Therefore, goblet cells have a role in preserving the health of the body by secreting mucus and acting as sentinels. The ancient jawless fish broadgilled hagfish (Eptatretus cirrhatus, Forster, 1801) has a very basic digestive system because it lacks a stomach. By examining the presence, localization, and co-localization of 5-HT, TLR2, iNOS, and Piscidin1, this study intends to provide insight into the potential immune system contributions arranged by the gut goblet cells of broadgilled hagfish. Our results characterize intestinal goblet cells of broadgilled hagfish, for the first time, with the former antibodies, suggesting the hypothesis of conservation of the roles played by these cells also in primitive vertebrates. Moreover, this study deepens the knowledge about the still little-known immune system of hagfish.

Arbutin improves gut development and serum lipids via Lactobacillus intestinalis

Arbutin has been widely studied in whitening, anti-inflammatory, and antioxidant. However, the interaction between arbutin and intestinal microbes has been rarely studied. Thus, mice were treated with arbutin concentrations of 0, 0.1, 0.2, 0.4, and 1 mg/ml. We found that arbutin promoted gut development such as villus length, villus areas, and villus length/crypt depth (L/D). Total cholesterol (TC), high-density lipoprotein (HDL), and low-density lipoprotein (LDL) were significantly reduced by low concentrations of arbutin. Importantly, we analyzed the microbial composition in the control and 0.4 mg/ml arbutin group and found that the abundance of Lactobacillus intestinalis (L. intestinalis) was highest and enhanced in arbutin. Further, mice were fed with oral antibiotics and antibiotics + 0.4 mg/ml arbutin and then we transplanted fecal microbes from oral 0.4 mg/ml arbutin mice to mice pretreated with antibiotics. Our results showed that arbutin improves gut development, such as villus width, villus length, L/D, and villus areas. In addition, L. intestinalis monocolonization was carried out after a week of oral antibiotics and increased villus length, crypt depth, and villus areas. Finally, in vitro arbutin and L. intestinalis co-culture showed that arbutin promoted the growth and proliferation of L. intestinalis. Taken together, our results suggest that arbutin improves gut development and health of L. intestinalis. Future studies are needed to explore the function and mechanism of L. intestinalis affecting gut development.

Gut microbiome modulation mediated by probiotics: Positive impact on growth and health status of Labeo rohita

The current study was targeted to determine the effect of probiotics on the growth, physiology, and gut microbiology of Labeo rohita fingerlings. One hundred and twenty fishes were divided into four dietary groups, each in triplicate for a feeding trial of 90 days. These treatments included T0 (control, basal diet) used as the reference, and three probiotic-supplemented diets represented as Tbc (Bacillus cereus), Tgc (Geotrichum candidum), and Tmc (B. cereus and G. candidum). The probiotics were supplemented at a level of 1 × 10⁹ CFU/g feed. Fishes nurtured on probiotic-added diet showed significantly high physiological improvement (p < 0.05) in terms of growth, feed utilization capacity, hematological profile, and digestive enzymes as compared to control. The fish were subjected to a challenge test after a 90-day feeding trial. The Tmc exhibited maximum fish growth when challenged by Staphylococcus aureus and showed fish survival when compared to control, in which fish mortality was examined. Fish gut microbial composition was modulated by probiotic treatments, especially in Tgc and Tmc as compared to control. The absence of opportunistic pathogens such as Staphylococcus saprophyticus and Sporobolomyces lactosus and detection of lower levels of Trichosporon and Cryptococcus in treated groups indicate the gut modulation driven by applied probiotics. The G. candidum QAUGC01 was retrieved in yeast metagenomics data, which might be due to the production of polyamines by them that facilitated adherence and consequent persistence. In conclusion, it can be suggested that the probiotic-supplemented diet could enhance fish growth and feed efficiency through community modulation and digestive enzymes, which could be a milestone in local aquaculture.

Aeromonas hydrophila Induces Skin Disturbance through Mucosal Microbiota Dysbiosis in Striped Catfish (Pangasianodon hypophthalmus)

Bacterial pathogens are well equipped to adhere to and initiate infection in teleost fish. Fish skin mucus serves as the first barrier against environmental pathogens. The mucus harbors commensal microbes that impact host physiological and immunological responses. However, how the skin mucosal microbiota responds to the presence of pathogens remains largely unexplored. Thus, little is known about the status of skin mucus prior to infection with noticeable symptoms. In this study, we investigated the interactions between pathogens and the skin mucosal microbiota as well as the fish skin immune responses in the presence of pathogens. Striped catfish (Pangasianodon hypophthalmus) were challenged with different concentrations of the bacterial pathogen Aeromonas hydrophila (AH), and the skin immune response and the mucosal microbiota were examined by quantitative PCR (qPCR) and 16S rRNA gene sequence analysis. We determined that the pathogen concentration needed to stimulate the skin immune response was associated with significant mucosal microbiota changes, and we reconfirmed these observations using an ex vivo fish skin model. Further analysis indicated that changes in the microbiota were attributed to a significant increase in opportunistic pathogens over AH. We concluded that the presence and increase of AH result in dysbiosis of the mucosal microbiota that can stimulate skin immune responses. We believe that our work sheds light on host-pathogen-commensal microbiota interactions and therefore contributes to aquaculture fish health.

IMPORTANCE The fish skin mucosal microbiota is essential in modulating the host response to the presence of pathogens. Our study provides a platform to study both the correlation and causation of the interactions among the pathogen, fish skin, and the skin mucosal microbiota. Based on these findings, we provide the first mechanistic information on how mucosal microbiota changes induced by the pathogen AH result in skin disturbance with immune stimulation in striped catfish in the natural state and a potential direction for early-infection screening. Thus, this study is highly significant in the prevention of fish disease.

Microbiota-dependent TLR2 signaling reduces silver nanoparticle toxicity to zebrafish larvae

Many host-microbiota interactions depend on the recognition of microbial constituents by toll-like receptors of the host. The impacts of these interactions on host health can shape the hosts response to environmental pollutants such as nanomaterials. Here, we assess the role of toll-like receptor 2 (TLR2) signaling in the protective effects of colonizing microbiota against silver nanoparticle (nAg) toxicity to zebrafish larvae. Zebrafish larvae were exposed to nAg for two days, from 3 to 5 days post-fertilization. Using an il1ß-reporter line, we first characterized the accumulation and particle-specific inflammatory effects of nAg in the total body and intestinal tissues of the larvae. This showed that silver gradually accumulated in both the total body and intestinal tissues, yet specifically caused particle-specific inflammation on the skin of larvae. Subsequently, we assessed the effects of microbiota-dependent TLR2 signaling on nAg toxicity. This was done by comparing the sensitivity of loss-of-function zebrafish mutants for TLR2, and each of the TLR2-adaptor proteins MyD88 and TIRAP (Mal), under germ-free and microbially-colonized conditions. Irrespective of their genotype, microbially-colonized larvae were less sensitive to nAg than their germ-free siblings, supporting the previously identified protective effect of microbiota against nAg toxicity. Under germ-free conditions, tlr2, myd88 and tirap mutants were equally sensitive to nAg as their wildtype siblings. However, when colonized by microbiota, tlr2 and tirap mutants were more sensitive to nAg than their wildtype siblings. The sensitivity of microbially-colonized myd88 mutants did not differ significantly from that of wildtype siblings. These results indicate that the protective effect of colonizing microbiota against nAg-toxicity to zebrafish larvae involves TIRAP-dependent TLR2 signaling. Overall, this supports the conclusion that host-microbiota interactions affect nanomaterial toxicity to zebrafish larvae.

Zebrafish: an underutilized tool for discovery in host-microbe interactions

Zebrafish are relatively new to the field of host-pathogen interactions, although they have been a valuable vertebrate model for decades in developmental biology and neuroscience. Transparent zebrafish larvae have most components of the human innate immune system, and adult zebrafish also produce cells of the adaptive immune system. Recent discoveries using zebrafish infection models include mechanisms of pathogen survival and host cell sensing of microbes. These discoveries were enabled by zebrafish technology, which is constantly evolving and providing new opportunities for immunobiology research. Recent tools include CRISPR/Cas9 mutagenesis, in vivo biotinylation, and genetically encoded biosensors. We argue that the zebrafish model - which remains underutilized in immunology - provides fertile ground for a new understanding of host-microbe interactions in a transparent host.

Application of zebrafish in the study of the gut microbiome

Zebrafish (Danio rerio) have attracted much attention over the past decade as a reliable model for gut microbiome research. Owing to their low cost, strong genetic and development coherence, efficient preparation of germ-free (GF) larvae, availability in high-throughput chemical screening, and fitness for intravital imaging in vivo, zebrafish have been extensively used to investigate microbiome-host interactions and evaluate the toxicity of environmental pollutants. In this review, the advantages and disadvantages of zebrafish for studying the role of the gut microbiome compared with warm-blooded animal models are first summarized. Then, the roles of zebrafish gut microbiome on host development, metabolic pathways, gut-brain axis, and immune disorders and responses are addressed. Furthermore, their applications for the toxicological assessment of aquatic environmental pollutants and exploration of the molecular mechanism of pathogen infections are reviewed. We highlight the great potential of the zebrafish model for developing probiotics for xenobiotic detoxification, resistance against bacterial infection, and disease prevention and cure. Overall, the zebrafish model promises a brighter future for gut microbiome research.

Plastic nanoparticles cause mild inflammation, disrupt metabolic pathways, change the gut microbiota and affect reproduction in zebrafish: A full generation multi-omics study

Plastic pollution has become a major concern on a global scale. The plastic is broken down into minuscule particles, which have an impact on the biosystems, however long-term impacts through an entire generation is largely unknown. Here, we present the first whole generation study exposing fish to a 500 nm polystyrene plastic particle at environmentally relevant concentrations. Short- and long-term adverse effects were investigated in the zebrafish model organism using a holistic multi-omics approach. The particles accumulated in the yolk sac of young larvae and short-term biological impacts included immune-relevant gene regulation related to inflammation and tolerance as well as disruption of metabolic processes, such as the fatty acid and lipid pathways. The long-term effects comprised gene regulations pointing towards skin and/or gill inflammation, dysbiosis of the gut microbiota, a tendency towards decreased condition factor in adult males as well as a lowered reproductive capability. From this study, it can be concluded that exposures to plastic nanoparticles have an impact on population as well as ecosystem level in fish and likely also in other vertebrates.

A cell atlas of microbe-responsive processes in the zebrafish intestine

Gut microbial products direct growth, differentiation, and development in animal hosts. However, we lack system-wide understanding of cell-specific responses to the microbiome. We profiled cell transcriptomes from the intestine, and associated tissue, of zebrafish larvae raised in the presence or absence of a microbiome. We uncovered extensive cellular heterogeneity in the conventional zebrafish intestinal epithelium, including previously undescribed cell types with known mammalian homologs. By comparing conventional to germ-free profiles, we mapped microbial impacts on transcriptional activity in each cell population. We revealed intricate degrees of cellular specificity in host responses to the microbiome that included regulatory effects on patterning and on metabolic and immune activity. For example, we showed that the absence of microbes hindered pro-angiogenic signals in the developing vasculature, causing impaired intestinal vascularization. Our work provides a high-resolution atlas of intestinal cellular composition in the developing fish gut and details the effects of the microbiome on each cell type.

Passive exposure to cannabidiol oil does not cause microbiome dysbiosis in larval zebrafish

The use of cannabidiol oil derived products has dramatically increased in popularity and is predicted to grow steadily over the next decade. Given its relative stability, cannabidiol is likely to accumulate in the environment and affect aquatic animals and their host-associated microbiomes. Here, using zebrafish larvae, a model system in environmental toxicology, we show that passive exposure to a concentration as high as 200 µg/L cannabidiol oil did not affect larvae survival and had limited effects on their host-associated microbial communities. We found that the changes in community structure were limited to a decrease in two sequence variants identified as Methylobacterium-Methylorubrum sp. and one ASV identified as Staphylococcus sp., as well as the increase of one sequence variant identified as Chryseobacterium sp., a bacterium commensal to zebrafish. More importantly, we found that cannabidiol oil did not affect the overall richness and diversity of the exposed fish microbiomes. These results suggest that passive exposure to cannabidiol oil is unlikely to impact aquatic organisms in significant ways.

Recent progress in the understanding of the gut microbiota of marine fishes

As the significance of the gut microbiota has become increasingly realized, a large number of related studies have emerged. With respect to the gut microbial composition of fish, the predominant gut microbes and core gut microbiota have been reported by many researchers. Our understanding of fish gut microbiota, especially its functional roles, has fallen far behind that of terrestrial vertebrates, although previous studies using gnotobiotic zebrafish models have revealed that the gut microbiota performs a significant role in gut development, nutrient metabolism and immune responses. Given that environmental factors of marine habitats are very different from those of freshwater habitats, a distinct difference may exist in the gut microbiota between freshwater and marine fish. Therefore, this review aims to address the advances in marine fish gut microbiota in terms of methodologies, the gut microbial composition, and gnotobiotic models of marine fish, the important factors (host genotype and three environmental factors: temperature, salinity and diet) that drive marine fish gut microbiota, and significant roles of the gut microbiota in marine fish.

A Link between Chronic Kidney Disease and Gut Microbiota in Immunological and Nutritional Aspects

Chronic kidney disease (CKD) is generally progressive and irreversible, structural or functional renal impairment for 3 or more months affecting multiple metabolic pathways. Recently, the composition, dynamics, and stability of a patient's microbiota has been noted to play a significant role during disease onset or progression. Increasing urea concentration during CKD can lead to an acceleration of the process of kidney injury leading to alterations in the intestinal microbiota that can increase the production of gut-derived toxins and alter the intestinal epithelial barrier. A detailed analysis of the relationship between the role of intestinal microbiota and the development of inflammation within the symbiotic and dysbiotic intestinal microbiota showed significant changes in kidney dysfunction. Several recent studies have determined that dietary factors can significantly influence the activation of immune cells and their mediators. Moreover, dietary changes can profoundly affect the balance of gut microbiota. The aim of this review is to present the importance and factors influencing the differentiation of the human microbiota in the progression of kidney diseases, such as CKD, IgA nephropathy, idiopatic nephropathy, and diabetic kidney disease, with particular emphasis on the role of the immune system. Moreover, the effects of nutrients, bioactive compounds on the immune system in development of chronic kidney disease were reviewed.

Virus Infection Is an Instigator of Intestinal Dysbiosis Leading to Type 1 Diabetes

In addition to genetic predisposition, environmental determinants contribute to a complex etiology leading to onset of type 1 diabetes (T1D). Multiple studies have established the gut as an important site for immune modulation that can directly impact development of autoreactive cell populations against pancreatic self-antigens. Significant efforts have been made to unravel how changes in the microbiome function as a contributor to autoimmune responses and can serve as a biomarker for diabetes development. Large-scale longitudinal studies reveal that common environmental exposures precede diabetes pathology. Virus infections, particularly those associated with the gut, have been prominently identified as risk factors for T1D development. Evidence suggests recent-onset T1D patients experience pre-existing subclinical enteropathy and dysbiosis leading up to development of diabetes. The start of these dysbiotic events coincide with detection of virus infections. Thus viral infection may be a contributing driver for microbiome dysbiosis and disruption of intestinal homeostasis prior to T1D onset. Ultimately, understanding the cross-talk between viral infection, the microbiome, and the immune system is key for the development of preventative measures against T1D.

Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease

Human Angiotensin I Converting Enzyme 2 (ACE2) plays an essential role in blood pressure regulation and SARS-CoV-2 entry. ACE2 has a highly conserved, one-to-one ortholog (ace2) in zebrafish, which is an important model for human diseases. However, the zebrafish ace2 expression profile has not yet been studied during early development, between genders, across different genotypes, or in disease. Moreover, a network-based meta-analysis for the extraction of functionally enriched pathways associated with differential ace2 expression is lacking in the literature. Herein, we first identified significant development-, tissue-, genotype-, and gender-specific modulations in ace2 expression via meta-analysis of zebrafish Affymetrix transcriptomics datasets (n_datasets = 107); and the correlation analysis of ace2 meta-differential expression profile revealed distinct positively and negatively correlated local functionally enriched gene networks. Moreover, we demonstrated that ace2 expression was significantly modulated under different physiological and pathological conditions related to development, tissue, gender, diet, infection, and inflammation using additional RNA-seq datasets. Our findings implicate a novel translational role for zebrafish ace2 in organ differentiation and pathologies observed in the intestines and liver.

Zebrafish larvae as experimental model to expedite the search for new biomarkers and treatments for neonatal sepsis

Neonatal sepsis is a major cause of death and disability in newborns. Commonly used biomarkers for diagnosis and evaluation of treatment response lack sufficient sensitivity or specificity. Additionally, new targets to treat the dysregulated immune response are needed, as are methods to effectively screen drugs for these targets. Available research methods have hitherto not yielded the breakthroughs required to significantly improve disease outcomes, we therefore describe the potential of zebrafish (Danio rerio) larvae as preclinical model for neonatal sepsis. In biomedical research, zebrafish larvae combine the complexity of a whole organism with the convenience and high-throughput potential of in vitro methods. This paper illustrates that zebrafish exhibit an immune system that is remarkably similar to humans, both in terms of types of immune cells and signaling pathways. Moreover, the developmental state of the larval immune system is highly similar to human neonates. We provide examples of zebrafish larvae being used to study infections with pathogens commonly causing neonatal sepsis and discuss known limitations. We believe this species could expedite research into immune regulation during neonatal sepsis and may hold keys for the discovery of new biomarkers and novel treatment targets as well as for screening of targeted drug therapies.

Probiotic Bacteria with High Alpha-Gal Content Protect Zebrafish against Mycobacteriosis

Mycobacteriosis affects wild fish and aquaculture worldwide, and alternatives to antibiotics are needed for an effective and environmentally sound control of infectious diseases. Probiotics have shown beneficial effects on fish growth, nutrient metabolism, immune responses, disease prevention and control, and gut microbiota with higher water quality. However, the identification and characterization of the molecules and mechanisms associated with probiotics is a challenge that requires investigation. To address this challenge, herein we used the zebrafish model for the study of the efficacy and mechanisms of probiotic interventions against tuberculosis. First, bacteria from fish gut microbiota were identified with high content of the surface glycotope Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal) that has been shown to induce protective immune responses. The results showed that probiotics of selected bacteria with high α-Gal content, namely Aeromonas veronii and Pseudomonas entomophila, were biosafe and effective for the control of Mycobacterium marinum. Protective mechanisms regulating immunity and metabolism activated in response to α-Gal and probiotics with high α-Gal content included modification of gut microbiota composition, B-cell maturation, anti-α-Gal antibodies-mediated control of mycobacteria, induced innate immune responses, beneficial effects on nutrient metabolism and reduced oxidative stress. These results support the potential of probiotics with high -Gal content for the control of fish mycobacteriosis and suggested the possibility of exploring the development of combined probiotic treatments alone and in combination with -Gal for the control of infectious diseases.

The Gut-Brain-Microbiome Axis and Its Link to Autism: Emerging Insights and the Potential of Zebrafish Models

Research involving autism spectrum disorder (ASD) most frequently focuses on its key diagnostic criteria: restricted interests and repetitive behaviors, altered sensory perception, and communication impairments. These core criteria, however, are often accompanied by numerous comorbidities, many of which result in severe negative impacts on quality of life, including seizures, epilepsy, sleep disturbance, hypotonia, and GI distress. While ASD is a clinically heterogeneous disorder, gastrointestinal (GI) distress is among the most prevalent co-occurring symptom complex, manifesting in upward of 70% of all individuals with ASD. Consistent with this high prevalence, over a dozen family foundations that represent genetically distinct, molecularly defined forms of ASD have identified GI symptoms as an understudied area with significant negative impacts on quality of life for both individuals and their caregivers. Moreover, GI symptoms are also correlated with more pronounced irritability, social withdrawal, stereotypy, hyperactivity, and sleep disturbances, suggesting that they may exacerbate the defining behavioral symptoms of ASD. Despite these facts (and to the detriment of the community), GI distress remains largely unaddressed by ASD research and is frequently regarded as a symptomatic outcome rather than a potential contributory factor to the behavioral symptoms. Allowing for examination of both ASD's impact on the central nervous system (CNS) as well as its impact on the GI tract and the associated microbiome, the zebrafish has recently emerged as a powerful tool to study ASD. This is in no small part due to the advantages zebrafish present as a model system: their precocious development, their small transparent larval form, and their parallels with humans in genetics and physiology. While ASD research centered on the CNS has leveraged these advantages, there has been a critical lack of GI-centric ASD research in zebrafish models, making a holistic view of the gut-brain-microbiome axis incomplete. Similarly, high-throughput ASD drug screens have recently been developed but primarily focus on CNS and behavioral impacts while potential GI impacts have not been investigated. In this review, we aim to explore the great promise of the zebrafish model for elucidating the roles of the gut-brain-microbiome axis in ASD.

Macrophage cytokine responses to commensal Gram-positive Lactobacillus salivarius strains are TLR2-independent and Myd88-dependent

The mechanisms through which cells of the host innate immune system distinguish commensal bacteria from pathogens are currently unclear. Toll-like receptors (TLRs) are a class of pattern recognition receptors (PRRs) expressed by host cells which recognize microbe-associated molecular patterns (MAMPs) common to both commensal and pathogenic bacteria. Of the different TLRs, TLR2/6 recognize bacterial lipopeptides and trigger cytokines responses, especially to Gram-positive and Gram-negative pathogens. We report here that TLR2 is dispensable for triggering macrophage cytokine responses to different strains of the Gram-positive commensal bacterial species Lactobacillus salivarius. The L. salivarius UCC118 strain strongly upregulated expression of the PRRs, Mincle (Clec4e), TLR1 and TLR2 in macrophages while downregulating other TLR pathways. Cytokine responses triggered by L. salivarius UCC118 were predominantly TLR2-independent but MyD88-dependent. However, macrophage cytokine responses triggered by another Gram-positive commensal bacteria, Bifidobacterium breve UCC2003 were predominantly TLR2-dependent. Thus, we report a differential requirement for TLR2-dependency in triggering macrophage cytokine responses to different commensal Gram-positive bacteria. Furthermore, TNF-α responses to the TLR2 ligand FSL-1 and L. salivarius UCC118 were partially Mincle-dependent suggesting that PRR pathways such as Mincle contribute to the recognition of MAMPs on distinct Gram-positive commensal bacteria. Ultimately, integration of signals from these different PRR pathways and other MyD88-dependent pathways may determine immune responses to commensal bacteria at the host-microbe interface.

The adapter protein Myd88 plays an important role in limiting mycobacterial growth in a zebrafish model for tuberculosis

Tuberculosis (TB) is the most prevalent bacterial infectious disease in the world, caused by the pathogen Mycobacterium tuberculosis (Mtb). In this study, we have used Mycobacterium marinum (Mm) infection in zebrafish larvae as an animal model for this disease to study the role of the myeloid differentiation factor 88 (Myd88), the key adapter protein of Toll-like receptors. Previously, Myd88 has been shown to enhance innate immune responses against bacterial infections, and in the present study, we have investigated the effect of Myd88 deficiency on the granuloma morphology and the intracellular distribution of bacteria during Mm infection. Our results show that granulomas formed in the tail fin from myd88 mutant larvae have a more compact structure and contain a reduced number of leukocytes compared to the granulomas observed in wild-type larvae. These morphological differences were associated with an increased bacterial burden in the myd88 mutant. Electron microscopy analysis showed that the majority of Mm in the myd88 mutant are located extracellularly, whereas in the wild type, most bacteria were intracellular. In the myd88 mutant, intracellular bacteria were mainly present in compartments that were not electron-dense, suggesting that these compartments had not undergone fusion with a lysosome. In contrast, approximately half of the intracellular bacteria in wild-type larvae were found in electron-dense compartments. These observations in a zebrafish model for tuberculosis suggest a role for Myd88-dependent signalling in two important phenomena that limit mycobacterial growth in the infected tissue. It reduces the number of leukocytes at the site of infection and the acidification of bacteria-containing compartments inside these cells.

Gut immunity in European sea bass (Dicentrarchus labrax): a review

In this review, we summarize and discuss the trends and supporting findings in scientific literature on the gut mucosa immune role in European sea bass (Dicentrarchus labrax L.). Overall, the purpose is to provide an updated overview of the gastrointestinal tract functional regionalization and defence barriers. A description of the available information regarding immune cells found in two immunologically-relevant intestinal compartments, namely epithelium and lamina propria, is provided. Attention has been also paid to mucosal immunoglobulins and to the latest research investigating gut microbiota and dietary manipulation impacts. Finally, we review oral vaccination strategies, as a safe method for sea bass vaccine delivery.

Conserved anti-inflammatory effects and sensing of butyrate in zebrafish

Short-chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated with gut microbiota dysbiosis in mammals. We aimed to determine if SCFAs are produced by the zebrafish microbiome and if SCFAs exert conserved effects on zebrafish immunity as an example of the non-mammalian vertebrate immune system. We demonstrate that bacterial communities from adult zebrafish intestines synthesize all three main SCFA in vitro, although SCFA were below our detectable limits in zebrafish intestines in vivo. Immersion in butyrate, but not acetate or propionate, reduced the recruitment of neutrophils and M1-type pro-inflammatory macrophages to wounds. We found conservation of butyrate sensing by neutrophils via orthologs of the hydroxycarboxylic acid receptor 1 (hcar1) gene. Neutrophils from Hcar1-depleted embryos were no longer responsive to the anti-inflammatory effects of butyrate, while macrophage sensitivity to butyrate was independent of Hcar1. Our data demonstrate conservation of anti-inflammatory butyrate effects and identify the presence of a conserved molecular receptor in fish.

The Link between Oral and Gut Microbiota in Inflammatory Bowel Disease and a Synopsis of Potential Salivary Biomarkers

The objective of this review is to provide recent evidence for the oral–gut axis connection and to discuss gastrointestinal (GI) immune response, inflammatory bowel disease (IBD) pathogenesis, and potential salivary biomarkers for determining GI health. IBD affects an estimated 1.3% of the US adult population. While genetic predisposition and environment play a role, abnormal immune activity and microbiota dysbiosis within the gastrointestinal tract are also linked in IBD pathogenesis. It has been inferred that a reduced overall richness of bacterial species as well as colonization of opportunistic bacteria induce systemic inflammation in the GI tract. Currently, there is supporting evidence that both oral and gut microbiota may be related to the development of IBD. Despite this, there are currently no curative therapies for IBD, and diagnosis requires samples of blood, stool, and invasive diagnostic imaging techniques. Considering the relative ease of collection, emerging evidence of association with non-oral diseases may imply that saliva microbiome research may have the potential for gut diagnostic or prognostic value. This review demonstrates a link between saliva and intestinal profiles in IBD patients, suggesting that saliva sampling has the potential to serve as a non-invasive biomarker for gut diseases such as IBD in the oral–gut axis.

Drainage of inflammatory macromolecules from the brain to periphery targets the liver for macrophage infiltration

Many brain pathologies are associated with liver damage, but a direct link has long remained elusive. Here, we establish a new paradigm for interrogating brain-periphery interactions by leveraging zebrafish for its unparalleled access to the intact whole animal for in vivo analysis in real time after triggering focal brain inflammation. Using traceable lipopolysaccharides (LPS), we reveal that drainage of these inflammatory macromolecules from the brain led to a strikingly robust peripheral infiltration of macrophages into the liver independent of Kupffer cells. We further demonstrate that this macrophage recruitment requires signaling from the cytokine IL-34 and Toll-like receptor adaptor MyD88, and occurs in coordination with neutrophils. These results highlight the possibility for circulation of brain-derived substances to serve as a rapid mode of communication from brain to the liver. Understanding how the brain engages the periphery at times of danger may offer new perspectives for detecting and treating brain pathologies.

Single-Cell RNA Sequencing Reveals Size-Dependent Effects of Polystyrene Microplastics on Immune and Secretory Cell Populations from Zebrafish Intestines

Microplastics (MPs) as widespread contamination pose a high risk for aquatic organisms. However, the current understanding of MP toxicity is based on cell population-averaged measurements. Our aim was to gain a comprehensive understanding of the size-dependent effects of polystyrene MPs (PS-MPs) on intestinal cell populations in zebrafish and characterize the interplay of MPs, intestinal cells, and intestinal microbiota. Here, we used single-cell RNA sequencing to determine the transcriptome heterogeneity of 12 000 intestinal cells obtained from zebrafish exposed to 100 nm, 5 μm, and 200 μm PS-MPs for 21 days. Eight intestinal cell populations were identified. Combined with changes in intestinal microbiota, our findings highlight a previously unrecognized end point that all three sizes of PS-MPs induced dysfunction of intestinal immune cells (including effects on phagosomes and the regulation of immune system processes) and increased the abundance of pathogenic bacteria. However, only 100 nm PS-MPs altered the expression of genes related to phagocyte-produced reactive oxygen species (ROS) generation and increased mucus secretion by secretory cells. Microsize PS-MPs specifically changed the lysosome (5 μm) and cell surface receptor signaling (200 μm) processes of the macrophages. Our findings pinpoint to cell-specific and size-dependent responses to PS-MPs in fish intestine, which can provide a reference for future study directions.

The Differences between Luminal Microbiota and Mucosal Microbiota in Mice

The differences between luminal microbiota (LM) and mucosal microbiota (MAM) were little known, especially in duodenum. In this study, LM and MAM in colon and duodenum of mice were investigated through 16S rRNA high-throughput sequencing. The lowest bacterial diversity and evenness were observed in duodenal LM (D_LM), followed by duodenal MAM (D_MAM). Meanwhile, the bacterial diversity and evenness were obviously increased in D_MAM than these in D_LM, while no significant difference was observed between colonic MAM (C_MAM) and colonic LM (C_LM). PCoA analysis also showed that bacterial communities of LM and MAM in duodenum were completely separated, while these in colon overlapped partly. The ratio of Firmicutes to Bacteroidetes (F/B) in D_MAM was significantly higher than that in D_LM. Lactobacillus was largely enriched and was the characteristic bacteria in D_LM. The characteristic bacteria in D_MAM were Turicibacter, Parasutterella, Marvinbryantia and Bifidobacterium, while in C_LM they were Ruminiclostridium_6, Ruminiclostridium_9, Ruminococcaceae_UCG_007 and Lachnospiraceae_UCG_010, and in C_MAM they were Lachnospiraceae_NK4A136, Mucispirillum, Alistipes, Ruminiclostridium and Odoribacter. The networks showed that more interactions existed in colonic microbiota (24 nodes and 74 edges) than in duodenal microbiota (17 nodes and 29 edges). The 16S rDNA function prediction results indicated that bigger differences of function exist between LM and MAM in duodenum than these in colon. In conclusion, microbiota from intestinal luminal content and mucosa were different both in colon and in duodenum, and bacteria in colon interacted with each other much more closely than those in duodenum.

Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health

Aquafeed companies aim to provide solutions to the various challenges related to nutrition and health in aquaculture. Solutions to promote feed efficiency and growth, as well as improving the fish health or protect the fish gut from inflammation may include dietary additives such as prebiotics and probiotics. The general assumption is that feed additives can alter the fish microbiota which, in turn, interacts with the host immune system. However, the exact mechanisms by which feed influences host-microbe-immune interactions in fish still remain largely unexplored. Zebrafish rapidly have become a well-recognized animal model to study host-microbe-immune interactions because of the diverse set of research tools available for these small cyprinids. Genome editing technologies can create specific gene-deficient zebrafish that may contribute to our understanding of immune functions. Zebrafish larvae are optically transparent, which allows for in vivo imaging of specific (immune) cell populations in whole transgenic organisms. Germ-free individuals can be reared to study host-microbe interactions. Altogether, these unique zebrafish features may help shed light on the mechanisms by which feed influences host-microbe-immune interactions and ultimately fish health. In this review, we first describe the anatomy and function of the zebrafish gut: the main surface where feed influences host-microbe-immune interactions. Then, we further describe what is currently known about the molecular pathways that underlie this interaction in the zebrafish gut. Finally, we summarize and critically review most of the recent research on prebiotics and probiotics in relation to alterations of zebrafish microbiota and immune responses. We discuss the advantages and disadvantages of the zebrafish as an animal model for other fish species to study feed effects on host-microbe-immune interactions.

Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection

Background

The function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we analyzed the response of tlr2 zebrafish mutant larvae to infection with Mycobacterium marinum (Mm), a close relative to Mtb, as a model for tuberculosis. We measured infection phenotypes and transcriptome responses using RNA deep sequencing in mutant and control larvae.

Results

tlr2 mutant embryos at 2 dpf do not show differences in numbers of macrophages and neutrophils compared to control embryos. However, we found substantial changes in gene expression in these mutants, particularly in metabolic pathways, when compared with the heterozygote tlr2^+/− control. At 4 days after Mm infection, the total bacterial burden and the presence of extracellular bacteria were higher in tlr2^−/− larvae than in tlr2^+/−, or tlr2^+/+ larvae, whereas granuloma numbers were reduced, showing a function of Tlr2 in zebrafish host defense. RNAseq analysis of infected tlr2^−/− versus tlr2^+/− shows that the number of up-regulated and down-regulated genes in response to infection was greatly diminished in tlr2 mutants by at least 2 fold and 10 fold, respectively. Analysis of the transcriptome data and qPCR validation shows that Mm infection of tlr2 mutants leads to decreased mRNA levels of genes involved in inflammation and immune responses, including il1b, tnfb, cxcl11aa/ac, fosl1a, and cebpb. Furthermore, RNAseq analyses revealed that the expression of genes for Maf family transcription factors, vitamin D receptors, and Dicps proteins is altered in tlr2 mutants with or without infection. In addition, the data indicate a function of Tlr2 in the control of induction of cytokines and chemokines, such as the CXCR3-CXCL11 signaling axis.

Conclusion

The transcriptome and infection burden analyses show a function of Tlr2 as a protective factor against mycobacteria. Transcriptome analysis revealed tlr2-specific pathways involved in Mm infection, which are related to responses to Mtb infection in human macrophages. Considering its dominant function in control of transcriptional processes that govern defense responses and metabolism, the TLR2 protein can be expected to be also of importance for other infectious diseases and interactions with the microbiome.

The Responses of Germ-Free Zebrafish (Danio rerio) to Varying Bacterial Concentrations, Colonization Time Points, and Exposure Duration

Colonizing germ-free (GF) zebrafish with specific bacterial species provides the possibility of understanding the influence on host biological processes including gene expression, development, immunity, and behavioral responses. It also enlightens our understanding on the host-microbe interactions within the physiological context of a living host. However, the responses of GF zebrafish to various colonization conditions such as bacterial concentrations, colonization time points, and exposure duration remain unclear. To address this issue, we explored the responses of GF zebrafish by using two bacterial species at varying concentrations, colonization time points and exposure duration. Therefore, we mono-associated GF zebrafish with Escherichia coli DH5α or Bacillus subtilis WB800N at concentrations ranging from 10² to 10⁷ CFU/ml either at 3 day post fertilization (dpf) or 5 dpf for 24 or 48 h. We evaluated the responses of GF zebrafish by analyzing the survival rate, colonization efficiency, nutrients metabolism, intestinal cell proliferation, innate immunity, stress, and behavior responses by comparing it to conventionally raised zebrafish (CONR) and GF zebrafish. The results indicated that the final bacteria concentrations ranging from 10² to 10⁴ CFU/ml did not cause any mortality when GF mono-associated larvae were exposed to either E. coli DH5α or B. subtilis WB800N at 3 or 5 dpf, while concentrations ranging from 10⁶ to 10⁷ CFU/ml increased the mortality, particularly for 5 dpf owing to the decrease in dissolved oxygen level. The E. coli DH5α mainly induced the expression of genes related to nutrients metabolism, cell proliferation and immunity, while B. subtilis WB800N mainly upregulated the expression of genes related to immunity and stress responses. Moreover, our data revealed that GF zebrafish showed higher levels of physical activity than CONR and the microbial colonization reduced the hyperactivity of GF zebrafish, suggesting colonization of bacteria affected behavior characteristics. This study provides useful information on bacterial colonization of GF zebrafish and the interaction between the host and microbiota.