Transcriptome analysis provides insights into the immune responsive pathways and genes in the head kidney of tiger grouper (Epinephelus fuscoguttatus) fed with Spatholobus suberectus, Phellodendron amurense, or Eclipta prostrata

Long-Term Phellodendri Cortex Supplementation in the Tiger Grouper (Epinephelus fuscoguttatus): Dual Effects on Intestinal Health Revealed by Transcriptome Analysis

The tiger grouper (Epinephelus fuscoguttatus), an important mariculture fish in Southeast Asia, faces increasing health issues in recent years. Phellodendri Cortex (PC) is a traditional Chinese herbal medicine that exhibits a variety of beneficial effects on tiger groupers. The effects of PC, however, varies with the period of dietary intervention. This study aims to investigate the long-term effects of 1% PC supplementation on tiger groupers, focusing on growth, immunity, disease resistance, and intestinal gene expression. The tiger groupers (with an initial mean weight of 27.5 ± 0.5 g) were fed with a diet of Phellodendri Cortex supplementation and a control diet for 8 weeks. Our results indicate that the long-term PC supplementation did not affect growth or Vibrio disease resistance in tiger groupers. However, the transcriptome analysis revealed potential damage to the structural and functional integrity of the groupers' intestines. On the other hand, anti-inflammatory and cathepsin inhibition effects were also observed, offering potential benefits to fish enteritis prevention and therapy. Therefore, long-term PC supplementation in grouper culture should be applied with caution.

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Effects of Five Prebiotics on Growth, Antioxidant Capacity, Non-Specific Immunity, Stress Resistance, and Disease Resistance of Juvenile Hybrid Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

To explore the short-term health benefits of five prebiotics on hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂), six experimental groups fed with different diets (basal diet, diet control (CON); basal diet + 0.2% fructooligosaccharide (FOS), diet FOS; basal diet + 0.5% chitosan, diet chitosan (CTS); basal diet + 0.2% mannan-oligosaccharide (MOS), diet MOS; basal diet + 0.1% β-glucan (GLU), Diet GLU; basal diet + 0.05% xylooligosaccharide (XOS), diet XOS) were set up, and a 4-week feeding trial was conducted. MOS and XOS significantly improved the growth of hybrid grouper compared to the CON group (p < 0.05). Antioxidant enzyme assay showed that the activity of glutathione peroxidase (GPx) was significantly enhanced in the MOS group, and the content of malondialdehyde (MDA) in the XOS group was significantly lower than in the CON group (p < 0.05). The catalase (CAT) activities were significantly enhanced in all prebiotic-supplemented groups compared with the CON group (p < 0.05). Non-specific immunity assay showed that the activities of alkaline phosphatase (AKP) and lysozyme (LZM) were significantly increased in all prebiotic-supplemented groups compared with the CON group (p < 0.05). The total protein content in the XOS group was significantly increased (p < 0.05), and the albumin (ALB) activity in the MOS group was more significantly increased than that in the CON group. Histological examination of the intestine revealed that muscle thickness was significantly increased in all prebiotic-supplemented groups compared to the CON group (p < 0.05). Villi length, villi width, muscle thickness all increased significantly in the MOS group (p < 0.05). In addition, the crowding stress and ammonia nitrogen stress experiments revealed that the survival rates of the MOS and XOS groups after stresses were significantly higher than those of the CON group (p < 0.05). Though MOS and XOS exhibited similar anti-stress effects, the antioxidant and non-specific immunity parameters they regulated were not the same, indicating that the specific mechanisms of MOS and XOS's anti-stress effects were probably different. After being challenged with Vibrio harvey, MOS and GLU groups showed significantly higher post-challenge survival rates than the CON group (p < 0.05). These findings indicated that among the five prebiotics, MOS and XOS showed the best overall short-term beneficial effects and could be considered promising short-term feed additives to improve the stress resistance of juvenile hybrid grouper.

A Review of the Pharmacological Potential of Spatholobus suberectus Dunn on Cancer

Spatholobus suberectus Dunn (SSD) has been extensively employed in Traditional Chinese Medicine to treat several ailments. SSD and its active compounds are effective therapeutic agents for treating a variety of diseases with negligible side effects. Therefore, we aimed to investigate its phytochemistry, pharmacology, and potential therapeutic effects exclusively in cancer prevention and treatment. Phytochemical and pharmacological information was collected and arranged in a rational order. SSD has been frequently attributed to having antioxidant, anti-diabetic, anti-inflammatory, hematopoietic, neuroprotective, antimicrobial, and anticancer properties. Evidence has indicated that the bioactive constituents in SSD have attracted increasing scientific attention due to their preventive role in cancers. Further, the present review provides the current information on the health implications of SSD, thus allowing for future clinical trials to explore its restorative benefits. All data of in vitro and animal investigations of SSD, as well as its effect on human health, were obtained from an electronic search and library database. The diverse pharmacological potential of SSD provides an opportunity for preclinical drug discovery, and this comprehensive review strongly indicates that SSD is an excellent anti-tumorigenic agent that modulates or prevents breast cancer.

Bio-active components in medicinal plants: A mechanistic review of their effects on fish growth and physiological parameters

World population is increasing at a tremendous rate so is the demand for animal-based protein. Aquaculture is a promising industry that has the potential to supply high quality protein for mankind with minimum environmental impact. In the past decade, aquaculture practices have been shifting from extensive to intensive culture. To achieve maximum production per unit area, high stocking densities are maintained in intensive aquaculture. If not managed properly, this may lead to stress in fish. Fish under stress condition show decreased growth, suppressed appetite, weakened immunity and increased susceptibility to infections. Chemicals, vaccines and antibiotics are used for the treatment of diseased fish. Use of synthetic chemicals, vaccines and antibiotics is not sustainable because pathogens develop resistance against them and they have high residues. Moreover, certain chemicals used for the treatment of fish diseases are not safe for humans therefore, are banned in some countries. Plant parts and their extracts are used in traditional medicines to cure many diseases and to improve health of mankind. In aquaculture industry, use of plants and their derivatives in fish feed to improve health status of fish is increasing. Several plants improve growth and overall health status of fish, some provide protection against pathogens by improving the immune system while others increase appetite by direct action on neuro-endocrine axis of fish. This review provides an in depth and up to date information about use of medicinal plants and their derivatives to improve growth and physiological status of fish and their possible mechanism of action.

Transcriptome analysis reveals the molecular mechanism of long-term exposure of Eriocheir sinensis to low concentration of trichlorfon

Trichlorphon, a common organophosphorus pesticide (OPs), is widely used in aquaculture to prevent aquatic insects from infecting cultured objects as well as to control the excessive proliferation of plankton in water bodies. However, its repeated use time can contaminate water bodies and impart direct/indirect toxicity to beneficial aquatic species. However, the underlying mechanism regarding toxicity and cellular metabolism remains unclear. Understanding the mechanism would enable the standardized use and management of OPs and their use in the aquatic environment. Here, low concentration of trichlorphon (5 × 10^-5 g/L) was used to construct a hepatopancreatic transcriptional library 30 d, 60 d and 90 d after exposure using RNA-Seq. We detected 649, 148, and 2949 DEGs in the hepatopancreas of E. sinensis for the Tri01 vs. Ctr01, Tri02 vs. Ctr02 and Tri03 vs. Ctr03 library, respectively. The results of KEGG pathway enrichment analysis showed that DEGs were mainly enriched in signal transduction, carbohydrate metabolism, transport and catabolism, endocrine system, and digestive system. Also, under trichlorfon stress, DEGs of E. sinensis were enriched in thyroid hormone signaling pathways, protein digestion and absorption, cancer pathways, etc. The significant DEGs were mainly related to metabolism and the apoptosis and autophagy pathways. This study lays a foundation for further revealing the effects of long-term trichlorfon stress on E. sinensis as well as the potential physiological toxicity. The relevant transcriptome data could provide a reference for the molecular toxicological evaluation of trichlorfon in aquaculture.

The Gene Regulatory Roles of Herbal Extracts on the Growth, Immune System, and Reproduction of Fish

The crucial need for safe and healthy aquatic animals obligates researchers in aquaculture to investigate alternative and beneficial additives. Medicinal herbals and their extracts are compromised with diverse effects on the performances of aquatic animals. These compounds can affect growth performance and stimulate the immune system when used in fish diet. In addition, the use of medicinal herbs and their extracts can reduce oxidative stress induced by several stressors during fish culture. Correspondingly, aquatic animals could gain increased resistance against infectious pathogens and environmental stressors. Nevertheless, the exact mode of action where these additives can affect aquatic animals' performances is still not well documented. Understanding the mechanistic role of herbal supplements and their derivatives is a vital tool to develop further the strategies and application of these additives for feasible and sustainable aquaculture. Gene-related studies have clarified the detailed information on the herbal supplements' mode of action when administered orally in aquafeed. Several review articles have presented the potential roles of medicinal herbs on the performances of aquatic animals. However, this review article discusses the outputs of studies conducted on aquatic animals fed dietary, medicinal herbs, focusing on the gene expression related to growth and immune performances. Furthermore, a particular focus is directed to the expected influence of herbal supplements on the reproduction of aquatic animals.

Antioxidant system of soiny mullet (Liza haematocheila) is responsive to dietary poly-β-hydroxybutyrate (PHB) supplementation based on immune-related enzyme activity and de novo transcriptome analysis

As a dietary supplement, poly-β-hydroxybutyrate (PHB) has been reported to positively influence growth, boost the immune system and enhance disease resistance in fish and shellfish. However, the protective mechanism is little known. Thus, the present study was conducted to evaluate the effect of PHB supplementation on immune-related enzyme activity and transcriptome-based gene expression in soiny mullet (Liza haematocheila). Results showed that dietary PHB supplementation could increase antioxidant enzyme activity, including total antioxidant capacity, catalase and superoxide dismutase. A total of 7,082,094,175 and 7,650,341,357 raw reads with mean length of 757 bp were obtained from control and PHB (dietary PHB supplementation at 2%) groups, respectively. There were 46,106 differentially expressed genes (DEGs) between control and PHB groups, including 21,828 upregulated and 24,278 downregulated DEGs. All the DEGs were classified into three gene ontology categories, and 312 DEGs related with immune system process and 760 with the response to a stimulus. Additionally, all DEGs were allocated to 261 Kyoto Encyclopedia of Gene and Genome pathways, and major immune-related pathways were detected, including MAPK/PI3K-Akt/TNF/NF-κB/TCR/TLR signaling pathways. Moreover, the regulation of several observed immune-related genes was confirmed by qRT-PCR. Altogether, this study suggests that antioxidant system is more effective for dietary PHB supplementation and lays the foundation for further study on the precise immunostimulatory mechanism of PHB. Hopefully, it provides insights into exploring biomarker for assessment of immunostimulants in fish culture.

Transcriptome comparative analysis of immune tissues from asymptomatic and diseased Epinephelus moara naturally infected with nervous necrosis virus

Epinephelus moara is an economically important fish in Southeast Asian countries but is suffering from nervous necrosis virus (NNV) infection. A deeper understanding of the host-NNV interaction mechanisms makes sense for disease control, however, at present, the pathogenesis of natural NNV infection and the resistance mechanism in host remains poorly understood. In this study, asymptomatic and diseased E. moara with clinical symptoms of viral nervous necrosis (VNN) from a grouper farm were both detected with a positive RT-PCR signal of NNV, then transcriptome sequencing of their immune tissues (liver, spleen and kidney) were performed for comparation analysis. The de novo assemblies yielded 53,789 unigenes which had a length varied from 201 to 19,675 bp and a N50 length of 2115 bp, and 29,451 unigenes were functionally annotated, with 83, 250 and 5632 unigenes being differentially expressed in liver, spleen and kidney respectively. KEGG pathway enrichment analysis of the DEGs showed many DEGs were enriched in immune related pathways. Although the expression of class I major histocompatibility complex (MHC) was significantly higher in three immune tissues of the diseased grouper, many immune related genes, including humoral immune molecules (such as antibodies), the cellular mediated cytotoxic molecules (such as perforin) and some adhesion related genes were down regulated in the diseased grouper. Our results provided many unigenes that might play important roles in NNV resistance for further research. Furthermore, a total of 8666 unigenes containing 11,623 simple sequence repeats (SSRs) were identified, which provided useful information for screening molecular markers associated with NNV resistance in E. moara.

Characterization and expression of galectin-3 after Streptococcus agalactiae and Aeromonas hydrophila challenge in GIFT strain Nile tilapia (Oreochromis niloticus)

In mammals, Galectin-3 has been revealed to be widely expressed in immune cells and played important role in immune reactions. However, Galectin-3 is frequently less reported in teleost. In the present study, a molecular characterization and expression analysis of galectin-3 were conducted in GIFT strain Nile tilapia. The full-length cDNA is 1034 bp with 690 bp of protein coding sequences. The result of qRT-PCR showed that the mRNA of galectin-3 was widely expressed in various tissues (heart, liver, spleen, gill, kidney, brain, intestine, skin, muscle, and ovary), and the higher expression was observed in immune-related tissues (liver and spleen). The time-course expression analysis revealed that galectin-3 was significantly up-regulated in intestine (5 h, 50 h, and 7 d), liver (5 h, 50 h, and 7 d), spleen (5 and 50 h), head-kidney (5 and 50 h), gill (5 h and 7 d) after Streptococcus agalactiae challenge, and significantly up-regulated in intestine (18, 24, 36, 72, and 96 h), liver (6, 18, 24, 96 h, and 6 d), spleen (18, 24, 36, 72, and 96 h), head-kidney (6, 12, 18, 24, 36, 72, and 96 h), and gill (12, 18, 24, and 36 h) after Aeromonas hydrophila challenge. Taken together, these data suggest that galectin-3 plays a role in immune responses in Nile tilapia after bacterial challenge.

Cloning, expression prolife, and immune characterization of a novel stat family member (stat5bl) in Chinese tongue sole (Cynoglossus semilaevis)

STAT plays important roles in innate immunity during JAK/STAT signaling pathway, and STAT5 is particularly focused due to the existence of duplicated forms in fish and mammal. In Chinese tongue sole, stat5bl was suggested to be a candidate related to Vibrio harveyi resistance based on previous QTL screening. In this study, the full length of stat5bl cDNA was cloned and its expression patterns were analyzed. stat5bl was predominantly expressed in immune tissues, where the highest level was observed in liver, followed by skin and gill. Time course expression patterns were examined in six tissues (liver, skin, gill, kidney, intestine, spleen) after V. harveyi infection. stat5bl could be up-regulated by V. harveyi infection in all tissues except liver, despite the timepoints of peak were different. In contrast, stat5bl was significantly downregulated in liver. To elucidate the role of stat5bl in liver, in vitro RNAi were performed using primary liver cell culture. Knockdown of stat5bl could regulate the expression of genes closely related to JAK/STAT pathway. This study would enlarge our understanding of stat5bl in fish immunity.

Effects of dietary administration of Lactococcus lactis HNL12 on growth, innate immune response, and disease resistance of humpback grouper (Cromileptes altivelis)

Lactic acid bacteria are a common group of probiotics that have been widely studied and used in aquaculture. In the present study, we isolated Lactococcus lactis HNL12 from the gut of wild humpback grouper (Cromileptes altivelis) and explored its probiotic properties. For this purpose, L. lactis HNL12 was added to the commercial fish feed. The results showed that HNL12 had high auto-aggregation ability and strong tolerance to simulated gastrointestinal stress. When C. altivelis consumed a diet containing 0 (control), 10⁶, 10⁸, or 10¹⁰ CFU/g HNL12 for four weeks, all of the groupers fed a diet with HNL12 had significantly increased percent weight gain (PWG), especially those fed with 10⁸ CFU/g, which had a PWG of 231.45%. Compared to the control, fish fed with L. lactis HNL12 exhibited significantly increased survival rates following injection with Vibrio harveyi after one month. Immunological analysis showed that C. altivelis fed with HNL12 had (i) enhanced respiratory burst activity of head kidney macrophages, superoxide dismutase, acid phosphatase, and lysozyme activities of serum; (ii) an improved survival rate from 36% to 70%; and (iii) upregulated expression of a broad spectrum of immunity. Meanwhile, de novo transcriptome assembly yielded 89,314 unigenes, which were annotated by at least one of the reference databases (Nr, Swiss-Prot, GO, COG and KEGG). A total of 307 genes showed significantly different expression between the groups fed with or without added HNL12. GO and KEGG enrichment analyses of the significantly different expression gene categories and pathways were related to infectious diseases, antigen processing and presentation, and other immune system responses. These results indicate that L. lactis HNL12 is effective for enhancing the growth, immunity, and disease resistance of C. altivelis; this study also provides insight into the use of probiotics for commercial applications.

Cloning, characterization and functional analysis of dctn5 in immune response of Chinese tongue sole (Cynoglossus semilaevis)

In mammals, microtubule-dependent trafficking could participate the immune response, where the motor proteins are suggested to play an important role in this process, while the related study in fish was rare. In this study, dctn5, a subunit of dyactin complex for docking motor protein, was obtained by previous immune QTL screening. The full-length cDNAs of two dctn5 transcript variants were cloned and identified (named dctn5_tv1 and dctn5_tv2, respectively). Tissue distribution showed that dctn5_tv1 was widely distributed and high transcription was observed in immune tissue (skin), while dctn5_tv2 was predominantly detected in gonad and very low in other tissues. Time-course expression analysis revealed that dctn5_tv1 could be up-regulated in gill, intestine, skin, spleen, and kidney after Vibrio harveyi challenge. Moreover, recombinant Dctn5_tv1 exhibited high antimicrobial activity against Escherichia coli and Streptococcus agalactiae due to binding to bacteria cells. Taken together, these data suggest Dctn5_tv1 is involved in immune response of bacterial invasion in Chinese tongue sole.

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.