Nutrigenomics in crustaceans: Current status and future prospects

Transcriptomics-based analysis of Macrobrachium rosenbergii growth retardation

Macrobrachium rosenbergii is an economically important crustacean in many parts of the world, but in recent years, growth retardation has become an increasingly serious issue. While the underlying causes remain unclear, this has inevitably impacted on aquaculture and production outputs. In this study, gill, hepatopancreas, and muscle tissue samples from M. rosenbergii, with distinct growth differences, underwent transcriptome sequencing and bioinformatics analyses using high-throughput sequencing. In total, 59,796 unigenes were annotated. Differential expression analyses showed that the most differentially expressed genes (DEGs) were screened in gill tissue (1790 DEGs). In muscle and hepatopancreas tissues, 696 and 598 DEGs were screened, respectively. These DEGs were annotated to Kyoto Encyclopedia of Genes and Genomes pathways, which identified several significantly enriched pathways related to growth metabolism, such as PI3K-AKT, glycolysis/gluconeogenesis, and starch and sucrose metabolism. These results suggest that low growth metabolism levels may be one cause of M. rosenbergii growth retardation. Our data provide support for further investigations into the causes and molecular mechanisms underpinning growth retardation in M. rosenbergii.

Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review

This review article offers a comprehensive overview of the current understanding of using metagenomic tools in food microbiome research. It covers the scientific foundation and practical application of genetic analysis techniques for microbial material from food, including bioinformatic analysis and data interpretation. The method discussed in the article for analyzing microorganisms in food without traditional culture methods is known as food metagenomics. This approach, along with other omics technologies such as nutrigenomics, proteomics, metabolomics, and transcriptomics, collectively forms the field of foodomics. Food metagenomics allows swift and thorough examination of bacteria and potential metabolic pathways by utilizing foodomic databases. Despite its established scientific basis and available bioinformatics resources, the research approach of food metagenomics outlined in the article is not yet widely implemented in industry. The authors believe that the integration of next-generation sequencing (NGS) with rapidly advancing digital technologies such as artificial intelligence (AI), the Internet of Things (IoT), and big data will facilitate the widespread adoption of this research strategy in microbial analysis for the food industry. This adoption is expected to enhance food safety and product quality in the near future.

Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata

To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.

Dietary effects of Saccharomyces cerevisiae and Allium sativum on growth, antioxidant status, hepatic and intestinal histoarchitecture, expression of growth- and immune-related genes, and resistance of Oreochromis niloticus to Aeromonas sobria

This study investigated the benefits of yeast, Saccharomyces cerevisiae and/or garlic, Allium sativum supplementation in diets of Nile tilapia with regard to growth, antioxidant status, hepatic and intestinal histoarchitecture, expression of growth- and immune-related genes, and resistance to Aeromonas sobria infection. Fish (with an initial weight of 9.43 ± 0.08 g) were allocated to twelve hapas, organized into four triplicate treatment groups defined as control (no supplementation), yeast (4 g/kg diet), garlic (30 g/kg diet), and a mixture of both. This trial continued over a 60-day feeding period. Results revealed that combined treatment (yeast + garlic) demonstrated the most promising outcomes regarding growth, with significantly higher final body weights, weight gains, and specific growth rates compared to other groups. Moreover, this combination enhanced hepatic antioxidant status, as evidenced by elevated levels of reduced glutathione and activities of catalase and superoxide dismutase enzymes, reflecting improved defense against oxidative stress. Histological assessments of the livers and intestines demonstrated structural enhancements in yeast and garlic treatments, suggesting improvements in organ health. In comparison to the control, the gene expression analyses unveiled increased expression of growth-related (igf-1 and ghr1) and immune-related (il-10, lyz, and hep) genes in the test groups, indicating a possible reinforcement of the growth and immune responses. The combined treatment also showed the highest resistance to A. sobria infection, as evidenced by improved survival rates and lower mortality compared with the other groups. These findings highlight the benefits of a combination of both yeast and garlic as a dietary supplementation regimen. In conclusion, this study suggests that the combined treatment regimen could be considered an effective strategy to promote the health and productivity of Nile tilapia under production conditions.

Phylogenetic and transcriptomic characterization of insulin and growth factor receptor tyrosine kinases in crustaceans

Receptor tyrosine kinases (RTKs) mediate the actions of growth factors in metazoans. In decapod crustaceans, RTKs are implicated in various physiological processes, such molting and growth, limb regeneration, reproduction and sexual differentiation, and innate immunity. RTKs are organized into two main types: insulin receptors (InsRs) and growth factor receptors, which include epidermal growth factor receptor (EGFR), fibroblast growth factor receptor (FGFR), vascular endothelial growth factor receptor (VEGFR), and platelet-derived growth factor receptor (PDGFR). The identities of crustacean RTK genes are incomplete. A phylogenetic analysis of the CrusTome transcriptome database, which included all major crustacean taxa, showed that RTK sequences segregated into receptor clades representing InsR (72 sequences), EGFR (228 sequences), FGFR (129 sequences), and PDGFR/VEGFR (PVR; 235 sequences). These four receptor families were distinguished by the domain organization of the extracellular N-terminal region and motif sequences in the protein kinase catalytic domain in the C-terminus or the ligand-binding domain in the N-terminus. EGFR1 formed a single monophyletic group, while the other RTK sequences were divided into subclades, designated InsR1-3, FGFR1-3, and PVR1-2. In decapods, isoforms within the RTK subclades were common. InsRs were characterized by leucine-rich repeat, furin-like cysteine-rich, and fibronectin type 3 domains in the N-terminus. EGFRs had leucine-rich repeat, furin-like cysteine-rich, and growth factor IV domains. N-terminal regions of FGFR1 had one to three immunoglobulin-like domains, whereas FGFR2 had a cadherin tandem repeat domain. PVRs had between two and five immunoglobulin-like domains. A classification nomenclature of the four RTK classes, based on phylogenetic analysis and multiple sequence alignments, is proposed.

Effects of L-ascorbic acid on growth, non-specific immunity, antioxidant capacity, and intestinal and hepatopancreatic histology of red swamp crayfish, Procambarus clarkii

This study investigated the dietary effects of coated L-ascorbic acid (LA) on growth, feed utilization, survival, serum biochemical indices, immunity, antioxidant capacity, and intestinal and hepatopancreatic histology of the pre-adult red swamp crayfish. Four isoproteinous and isolipidic diets were formulated to contain several LA levels as 0, 1300, 1600, and 1900 mg/kg and designated as control (LA0), LA13, LA16, and LA19, respectively. However, the analyzed LA concentrations in diets were 0.00, 199.57, 360.45, and 487.50 mg/kg in LA0, LA13, LA16, and LA19, respectively. Triplicate treatments of crayfish (21.60 ± 0.14 g) were fed the test diets and reared in fiberglass tanks with a density of 20 individuals per each for eight weeks. Results revealed that all LA treatments had significantly enhanced growth performance compared to the control. Of interest, the LA16 treatment recorded the highest final tank biomass, biomass gain, total feed intake, condition factor, and muscle yield among the other treatments. The tank feed conversion ratio was significantly decreased in LA treatments compared to the control. Moreover, dietary LA16 and LA19 had significantly higher survival rates (93.3%) compared to (85.0%) in the LA0 group. All dietary doses of LA significantly increased serum parameters (total protein, albumin, globulin, lysozyme activity) and respiratory burst activity compared to the LA0 treatment. Dietary LA16 significantly boosted the hepatopancreatic antioxidant capacity, manifested by decreased malondialdehyde concentrations, increased catalase, superoxide dismutase, and glutathione peroxidase enzyme activities, and reduced glutathione content compared to the LA-free diet. A normal histoarchitecture of the hepatopancreatic tubules was found in all LA treatments except with some minor degenerative changes in the tubular lumen, and hepatopancreatic cells associated with enlarged nuclei were found in the LA19. However, normal intestinal histoarchitecture was found in all treatments with no recorded intestinal lesions. Of interest, the polynomial regression performed on the analyzed LA concentrations suggested that 380 mg/kg would be suitable to provide maximal biomass gain for pre-adult crayfish. In conclusion, results revealed that coated LA could enhance the growth, immunity, and antioxidant capacity of pre-adult red swamp crayfish, suggesting its potential as a functional and necessary micronutrient for crayfish diets.

The first identification and functional analysis of two drosophila mothers against decapentaplegic protein genes (SpSmad1 and SpSmad2/3) and their involvement in the innate immune response in Scylla paramamosain

Smad，a member of the TGF-β superfamily，controls cell proliferation，growth and guiding cell differentiation, thus playing a crucial role in diseases. However, the presence as well as specific function of Smad in crabs is still unknown. In this study, two Smads (Smad1 and Smad2/3) were identified for the first time from the mud crab Scylla paramamosain. The complete open reading frames of SpSmad1 and SpSmad2/3 were 1,497bp and 1,338bp, encoding deduced proteins of 498 and 445 amino acids respectively. Moreover, under the administration of Vibrio alginolyticus and WSSV, the relative expression levels of SpSmad1 and SpSmad2/3 were significantly increased, indicating their involvement in the innate immune response of mud crabs. Knockdown of SpSmad1 and SpSmad2/3 in vivo not only led to the increasement of the expressions of NF-κB signaling genes and antimicrobial peptides genes, but also significantly affected the bacterial clearance process of mud crabs. Additionally, overexpression of SpSmad1 and SpSmad2/3 in HEK293T cells could markedly activate NF-κB signaling. These results indicated that Smad1 and Smad2/3 participated in the innate immunity of Scylla paramamosain, and might provide a better understanding of the presence and immune regulatory functions of Smad1 and Smad2/3 in crabs and even invertebrates.

Therapeutic uses and applications of bovine lactoferrin in aquatic animal medicine: an overview

Aquaculture is an important food sector throughout the globe because of its importance in ensuring the availability of nutritious and safe food for human beings. In recent years, this sector has been challenged with several obstacles especially the emergence of infectious disease outbreaks. Various treatment and control aspects, including antibiotics, antiseptics, and other anti-microbial agents, have been used to treat farmed fish and shrimp against diseases. Nonetheless, these medications have been prohibited and banned in many countries because of the development of antimicrobial-resistant bacterial strains, the accumulation of residues in the flesh of farmed fish and shrimp, and their environmental threats to aquatic ecosystems. Therefore, scientists and researchers have concentrated their research on finding natural and safe products to control disease outbreaks. From these natural products, bovine lactoferrin can be utilized as a functional feed supplement. Bovine lactoferrin is a multi-functional glycoprotein applied in various industries, like food preservation, and numerous medications, due to its non-toxic and ecological features. Recent research has proposed multiple advantages and benefits of using bovine lactoferrin in aquaculture. Reports showed its potential ability to enhance growth, reduce mortalities, regulate iron metabolism, decrease disease outbreaks, stimulate the antioxidant defense system, and recuperate the overall health conditions of the treated fish and shrimp. Besides, bovine lactoferrin can be considered as a safe antibiotic alternative and a unique therapeutic agent to decrease the negative impacts of infectious diseases. These features can be attributed to its well-known antibacterial, anti-parasitic, anti-inflammatory, immunostimulatory, and antioxidant capabilities. This literature review will highlight the implications of bovine lactoferrin in aquaculture, particularly highlighting its therapeutic features and ability to promote immunological defensive pathways in fish. The information included in this article would be valuable for further research studies to improve aquaculture's sustainability and the functionality of aquafeeds.

Transcriptome-based nutrigenomics analysis reveals the roles of dietary taurine in the muscle growth of juvenile turbot (Scophthalmus maximus)

The present study explored transcriptomics and gene regulation variations in the muscle of turbot fed with dietary taurine. A 70-day feeding trial was conducted using turbot (initial body weight: 3.66 ± 0.02 g) fed with different levels of dietary taurine: 0 % (C), 0.4 % (T2), 1.2 % (T4) and 2.0 % (T6). Two methods were used to analyze and verify the taurine effects on muscle growth: (1) real-time quantitative PCR (qRT-PCR) for the key muscle growth-related genes and (2) transcriptomic analysis by next-generation sequencing (NGS). The results showed that 1.2 % of dietary taurine supplementation significantly increased the expression of muscle growth stimulatory genes, including TauT, myoD, Myf5, myogenin and follistatin. And also, the 1.2 % level significantly decreased the expression of the muscle growth-restricting gene (myostatin). Meanwhile, transcriptomics analysis found that 1.2 % dietary taurine supplementation significantly increased the number of up-regulated genes linked to metabolic pathways. In contrast, taurine significantly enriched the actin cytoskeleton and metabolic pathways in the T4 and T2 groups, respectively. These findings align with the gene ontology (GO) analysis, which indicated a higher number of cellular component (CC) gene expressions at a 1.2 % of dietary taurine compared to a 0.4 % of dietary taurine supplementation. In conclusion, dietary taurine had positive impacts on the growth-stimulatory genes. Moreover, 1.2 % of dietary taurine supplementation is important to the metabolic pathway enrichment.

Dietary fulvic acid supplementation improves the growth performance and immune response of sea cucumber (Apostichopus japonicas)

The present study aims to explore the effects of dietary fulvic acid (FA) supplementation on the growth performance, digestive enzyme activity and immune response of sea cucumber (Apostichopus japonicas). FA was used to replace 0 (control), 0.1, 0.5 and 1 g cellulose in the basic diet of sea cucumber to formulate four experimental feeds with equivalent nitrogen and energy denoted as F0, F0.1, F0.3 and F1, respectively. No significant differences were observed in the survival rate among all groups (P > 0.05). Results show that the body weight gain rate, specific growth rate, intestinal trypsin, amylase and lipase activities, serum superoxide dismutase, catalase, lysozyme, alkaline and acid phosphatase activities and disease resistance ability against the pathogen, Vibrio splendidus of the sea cucumbers fed with FA-containing diets were significantly higher than those of the control group (P < 0.05). The optimum dose of dietary FA supplementation required for the maximum growth of sea cucumber was 0.54 g/kg. Therefore, dietary FA supplementation to the feed of sea cucumber can significantly improve its growth performance immune response.

Comparative Study on Growth Index and Nutritional Quality of Female Chinese Mitten Crab Eriocheir sinensis Selected at Different Growth Periods in Rice-Crab Culture Systems

Research was conducted on the growth performance and nutritional quality of Chinese mitten crabs (Eriocheir sinensis) during a 62-day growing period in a symbiotic coculture comprising rice and crab. Culture experiments were conducted in three rice fields of equal size (996 m²). On days 0 (July 15, D0), 15 (July 30, D15), 31 (August 15, D31), 46 (August 30, D46), and 62 (September 2, D62), tissue samples of 50 female E. sinensis were collected randomly from each rice field. The results showed that the serum growth hormone (GH) content and muscle ecdysone receptor (EcR) mRNA expression levels were higher in the D31 and D46 groups; the content of serum 20-hydroxyecdysone (20-HE) and the mRNA expression levels of retinoid X receptor (RXR), insulin-like growth factor 2 (IGF2), and chitinase (CHI) reached the maximum in the D31 group. Muscle crude protein content gradually increased; hepatopancreas crude protein and crude lipid content began to decrease after reaching the maximum value in the D0 and D15 groups, respectively; the contents of crude protein and crude lipid in the ovary significantly increased in the D46 and D62 groups (P < 0.05). The content of muscle essential amino acids (EAA) reached the maximum in the D46 group; the hepatopancreas EAA content began to decrease significantly in the D31 group (P < 0.05); and the EAA content of the ovary decreased significantly after reaching the maximum value in the D46 group (P < 0.05). The muscle contents of eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), polyunsaturated fatty acids (PUFA), and n-3 polyunsaturated fatty acids (n-3PUFA) and the ratio of n-3 polyunsaturated fatty acids/n-6 polyunsaturated fatty acids (n3/n6) decreased significantly in the D31 group (P < 0.05); the hepatopancreas contents of EPA, PUFA, n-3PUFA, and n-6 polyunsaturated fatty acids (n-6PUFA) and the ratio of n3/n6 began to decrease after reaching the maximum value in the D31 group, ethyl behenate (21:0), tetracosanoic acid (24:0), DPA, and DHA contents were detected for the first time in the D31 group; the ovary PUFA, n-3PUFA contents, and n3/n6 ratio of the D46 and D62 groups were significantly lower than those of the D31 group (P < 0.05). During the experimental conditions described here, female E. sinensis raised in rice fields reached rapid growth from August 15 to August 30. Additionally, the nutritional quality of the female E. sinensis edible tissues (muscle, hepatopancreas, and ovary) began to decline after August 15, when sufficient nutrients such as protein, lipid, EAA, and PUFA should be provided to the female E. sinensis.

Effects of Panax notoginseng Water Extract on Immune Responses and Digestive Enzymes in White Shrimp Litopenaeus vannamei

Panax notoginseng (Burk) F. H. Chen is a traditional Chinese herbal medicine commonly used in clinical applications. This study examined the effects of the Panax notoginseng water extract (PNWE) on the immune responses and digestive enzyme activity of Litopenaeus vannamei (L. vannamei). The PNWE (50, 100, and 200 μg (g shrimp)^-1) was injected into L. vannamei to analyze the immune response parameters, including the total haemocyte count (THC), granular haemocytes (GC), semi-granular haemocytes (SGC), hialin haemocyte (HC), the respiratory burst (RB), the phagocytic ratio (PR), the phagocytic index (PI), and phenoloxidase (PO). We evaluated the activity of the intestinal digestive enzymes (trypsin, chymotrypsin, amylase, and lipase), the histopathology, and the intestine Vibrio numbers. The results showed that different concentrations of the PNWE significantly increased THC, GC, SGC, PO and RB activity, the PR, and the PI of L. vannamei while reducing the HC. In addition, the PNWE also significantly increased the chymotrypsin, trypsin, and amylase activity of L. vannamei. Furthermore, 50 µg (g shrimp)^-1 of PNWE regulated the lipase activity. Additionally, different concentrations of the PNWE significantly reduced the Vibrio numbers in the intestine without damaging the hepatopancreas and intestine tissues. These results indicate that the PNWE improves the immune responses of L. vannamei by increasing the haemocyte count and regulating intestinal digestive enzymes.

Nuclease treatment enhanced the ameliorative effect of yeast culture on epidermal mucus, hepatic lipid metabolism, inflammation response and gut microbiota in high-fat diet-fed zebrafish

As a functional feed additive, yeast cultures are rich in nucleotides, and adding extra nuclease can significantly increase the content of nucleotides in yeast culture. In this experiment, the effects on growth, epidermal mucus, liver and intestinal health of zebrafish were evaluated by supplementing the yeast culture or nuclease-treated yeast culture with a high-fat diet (HFD). One-month-old zebrafish were fed four diets: normal diet (NORM), HFD, yeast culture diet (YC), and nuclease-treated yeast culture diet (YC (N)) for three weeks. Results showed that the complement 4 activity of the epidermal mucus in YC (N) group was significantly higher than those in HFD and YC groups (P < 0.05). The YC and YC (N) significantly reduced the content of hepatic triglyceride caused by HFD (P < 0.05). Moreover, compared with the YC group, the YC (N) significantly increased the expression of lipolysis genes, such as PPARα, PGC1α, ACOX3 (P < 0.05). Compared with the YC group, the YC (N) group significantly increased the expression of liver pro-inflammatory factors TNFα, IL-6, IL-1β and anti-inflammatory factors TGFβ, IL-10 (P < 0.05). The diet YC and YC (N) significantly improved the height of the intestinal villus (P < 0.05). Compared with the HFD group, the YC (N) group significantly increased the expression of intestinal pro-inflammatory factors TNFα, IL-6 and anti-inflammatory factors TGFβ, IL-10 (P < 0.05). The YC (N) group significantly decreased the abundance of intestinal Proteobacteria and Acinetobacter, and increased the abundance of intestinal Actinobacteria, Mycobacterium and Rhodobacter (P < 0.05). In conclusion, compared with the supplement of yeast culture, nuclease treated yeast culture can further alleviate the adverse effects of HFD on liver and intestinal health, and be used as feed additives for the nutritional and immune regulation of fish.

A new potential risk: The impacts of Klebsiella pneumoniae infection on the histopathology, transcriptome and metagenome of Chinese mitten crab (Eriocheir sinensis)

Klebsiella pneumoniae is a common conditional pathogen found in natural soil water sources and vegetation and can infect invertebrates, vertebrates, and plants. In this study, we isolated K. pneumoniae from the hepatopancreas of the Chinese mitten crab (Eriocheir sinensis) for the first time and then we analysed its effects of on the histopathological changes, the transcriptome of the hepatopancreas, and the gut microbiota of this crab species. The findings of this study showed that K. pneumoniae infection has led to significant structural changes in the hepatopancreas, such as the production of vacuolated tissue structures, disorganized cell arrangement, and lysis of some hepatopancreatic cells. Also, the infection caused activation of the antioxidant-related enzymes such as SOD and CAT by inducing oxidative stress. The transcriptome of the hepatopancreas identified 10,940 differentially expressed genes (DEGs) in the susceptible (SG) groups and control (CG) groups, and 8495 DEGs in the SG groups and anti-infective (AI) groups. The KEGG pathway revealed upregulated DEGs caused by K. pneumoniae infection that involved in the immune response and apoptotic functional pathways, and also downregulated DEGs involved in the digestive absorption, metabolic, and biosynthetic signaling pathways. Meanwhile, metagenics sequencing revealed that at the phylum, class, order, family, and genus levels, K. pneumoniae infection altered the composition of the gut microbiota of E. sinensis, through increasing the abundance of Prolixibacteraceae, Enterobacterales, and Roseimarinus and decreasing the abundance of Alphaproteobacteria. The flora structure has also been changed between the SG and AI groups, with the abundance of Firmicutes, Erysipelotrichales, and Erysipelotrichaceae that were significantly decreased in the SG groups than in the AI groups. But, the abundance of Acinetobacter was considerably higher than in the AI group. In summary, K. pneumoniae infection induced oxidative stress in E. sinensis, triggered changes in immune-related gene expression, and caused structural changes in the gut microbiota. This study provides data to support the analysis of bacterial infection probes in several crustacean species.