Integrative Transcriptomic and Small RNA Sequencing Reveals Immune-Related miRNA-mRNA Regulation Network for Soybean Meal-Induced Enteritis in Hybrid Grouper, Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂

Long- and short-term dietary β-glucan improves intestinal health and disease resistance in pearl gentian grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀)

β-Glucans are immunostimulants and are widely used in aquaculture industry. The present study was conducted to evaluate the effects of different periods of β-glucan management on growth performance, intestinal health, and disease resistance in pearl gentian grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀). A commercial feed was used as control diet (CD), and the β-glucan diet (βD) was based on CD and further supplemented with 0.1% β-glucan. Grouper in control and long-term β-glucan diet (LGD) groups were fed with CD and βD for 8 weeks, respectively. Groupers in short-term β-glucan diet (SGD) group were fed with CD for the first 4 weeks and βD for the last 4 weeks. We found that LGD and SGD had no effect on growth performance but reduced the mortalities of grouper after challenging with Vibrio harveyi. In addition, both LGD and SGD increased intestinal morphology, enhanced antioxidant capacity, enhanced immunity, inhibited apoptosis, altered the transcriptional profile, and activated mitogen-activated protein kinase (MAPK) and nuclear factor kappa-B (NF-κB) signaling pathway in the intestine of grouper. Furthermore, the effect of LGD on most of the above parameters was comparable to that of SGD. In conclusion, LGD and SGD did not affect growth rate parameters but enhanced the intestinal health and disease resistance of pearl gentian grouper.

An integrated study of glutamine alleviates enteritis induced by glycinin in hybrid groupers using transcriptomics, proteomics and microRNA analyses

Glutamine has been used to improve intestinal development and immunity in fish. We previously found that dietary glutamine enhances growth and alleviates enteritis in juvenile hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂). This study aimed to further reveal the protective role of glutamine on glycinin-induced enteritis by integrating transcriptome, proteome, and microRNA analyses. Three isonitrogenous and isolipidic trial diets were formulated: a diet containing 10% glycinin (11S group), 10% glycinin diet supplemented with 2% alanine-glutamine (Gln group), and a diet containing neither glycinin nor alanine-glutamine (fishmeal, FM group). Each experimental diet was fed to triplicate hybrid grouper groups for 8 weeks. The analysis of intestinal transcriptomic and proteomics revealed a total of 570 differentially expressed genes (DEGs) and 169 differentially expressed proteins (DEPs) in the 11S and FM comparison group. Similarly, a total of 626 DEGs and 165 DEPs were identified in the Gln and 11S comparison group. Integration of transcriptome and proteome showed that 117 DEGs showed consistent expression patterns at both the transcriptional and translational levels in the Gln and 11S comparison group. These DEGs showed significant enrichment in pathways associated with intestinal epithelial barrier function, such as extracellular matrix (ECM)-receptor interaction, tight junction, and cell adhesion molecules (P < 0.05). Further, the expression levels of genes (myosin-11, cortactin, tenascin, major histocompatibility complex class I and II) related to these pathways above were significantly upregulated at both the transcriptional and translational levels (P < 0.05). The microRNA results showed that the expression levels of miR-212 (target genes colla1 and colla2) and miR-18a-5p (target gene colla1) in fish fed Gln group were significantly lower compared to the 11S group fish (P < 0.05). In conclusion, ECM-receptor interaction, tight junction, and cell adhesion molecules pathways play a key role in glutamine alleviation of hybrid grouper enteritis induced by high-dose glycinin, in which miRNAs and target mRNAs/proteins participated cooperatively. Our findings provide valuable insights into the RNAs and protein profiles, contributing to a deeper understanding of the underlying mechanism for fish enteritis.

Potential mechanisms of different methylation degrees of pectin driving intestinal microbiota and their metabolites to modulate intestinal health of Micropterus salmoides

Four diets containing 8 % cellulose, low methyl-esterified pectin (LMP), high methyl-esterified pectin (HMP) and MMP (half LMP and half HMP) were designed to evaluate the potential mechanisms by which different esterification degrees of pectin drive intestinal microbiota and their metabolites modulating the intestinal health of Micropterus salmoides. The results showed that both dietary LMP and HMP consistently upregulated intestinal zonula occludens protein 1 (Zo-1), Caludin-1, and Caludin-4, and downregulated intestinal tumor necrosis factor-alpha (TNF-α), interleukin-8 (IL-8), and interleukin-1 beta (IL-1β) gene expression (P < 0.05). Dietary HMP separately upregulated intestinal Occludin, nuclear factor erythroid2-related factor 2 (Nrf2), B-cell lymphoma-2 (Bcl-2), and Bcl-2 associated agonist of cell death (BAD) gene expression, as well as the digesta propionate content, OTUs, Sobs, Shannon, Chao, and ACE indices (P < 0.05), whereas dietary LMP decreased digesta arginine, 4-aminobutyric, L-tyrosine, and phenylalanine contents (P < 0.05). Moreover, dietary HMP decreased plasma lipopolysaccharide and d-lactic acid contents and increased intestinal superoxide dismutase and glutathione peroxidase activities and immunoglobulin (Ig) receptor and IgM levels (P < 0.05). Collectively, dietary HMP improves intestinal health by increasing intestinal flora α-diversity and enhancing intestinal mechanical barrier, anti-inflammatory, antioxidant, and immune functions. On the contrary, the interference of dietary LMP with butyrate, tyrosine, arginine, and 4-aminobutyric acid metabolism is the main reason for its detrimental effects on intestinal health.

Glutamine improves growth and intestinal health in juvenile hybrid groupers fed high-dose glycinin

Glutamine addition can improve immunity and intestinal development in fish. This study examined the protective roles of glutamine on growth suppression and enteritis induced by glycinin in juvenile hybrid groupers (female Epinephelus fuscoguttatus × male Epinephelus lanceolatus). The experiment set four isonitrogenous and isolipidic trial diets: a diet containing 10% glycinin (11S), 10% of 11S diet supplemented with 1% or 2% alanine-glutamine (1% or 2% Ala-Gln), and a diet containing neither 11S nor Ala-Gln (FM). A feeding trial was conducted in hybrid grouper for 8 weeks. Weight gain and specific growth rates in Groups 1% and 2% Ala-Gln were significantly higher than those of the 11S group but were similar to those of the FM group. The intestinal muscular layer thickness, plica height and width of the 2% Ala-Gln group were significantly higher than those of Group 11S. The enterocyte proliferation efficiency of the 11S group was significantly lower compared to other groups. Compared with the 11S group, Groups 1% and 2% Ala-Gln fish had increased intestinal lysozyme activities, complement 3 and immunoglobulin M as well as cathelicidin contents. The mRNA levels of tnf-α, il-1β, ifn-α, and hsp70 genes were more downregulated in Groups 1% and 2% Ala-Gln than in Group 11S. Compared with FM group, fish from the 11S group had significantly lower mRNA levels of myd88, ikkβ, and nf-κb p65 genes. These three values in the 2% Ala-Gln group were significantly lower than those in Group 11S but not significantly different from those of Group FM. The relative abundance of Vibrio in Group 11S was higher than that in Groups FM and 2% Ala-Gln. Intestinal glutamine, glutaminase, glutamic acid, α-ketoglutarate, malate dehydrogenase and ATP contents were higher in Groups 1% and 2% Ala-Gln than in Group 11S. These results suggest that glutamine is a useful feed additive to enhance growth and intestinal immunity, alleviate inflammation, and modulate gut microbiota in hybrid grouper fed high-dose glycinin.

Dietary High Glycinin Reduces Growth Performance and Impairs Liver and Intestinal Health Status of Orange-Spotted Grouper (Epinephelus coioides)

The aim of the study was to investigate whether the negative effects of dietary glycinin are linked to the structural integrity damage, apoptosis promotion and microbiota alteration in the intestine of orange-spotted grouper (Epinephelus coioides). The basal diet (FM diet) was formulated to contain 48% protein and 11% lipid. Fish meal was replaced by soybean meal (SBM) in FM diets to prepare the SBM diet. Two experimental diets were prepared, containing 4.5% and 10% glycinin in the FM diets (G-4.5 and G-10, respectively). Triplicate groups of 20 fish in each tank (initial weight: 8.01 ± 0.10 g) were fed the four diets across an 8 week growth trial period. Fish fed SBM diets had reduced growth rate, hepatosomatic index, liver total antioxidant capacity and GSH-Px activity, but elevated liver MDA content vs. FM diets. The G-4.5 exhibited maximum growth and the G-10 exhibited a comparable growth with that of the FM diet group. The SBM and G-10 diets down-regulated intestinal tight junction function genes (occludin, claudin-3 and ZO-1) and intestinal apoptosis genes (caspase-3, caspase-8, caspase-9, bcl-2 and bcl-xL), but elevated blood diamine oxidase activity, D-lactic acid and endotoxin contents related to intestinal mucosal permeability, as well as the number of intestinal apoptosis vs FM diets. The intestinal abundance of phylum Proteobacteria and genus Vibrio in SBM diets were higher than those in groups receiving other diets. As for the expression of intestinal inflammatory factor genes, in SBM and G-10 diets vs. FM diets, pro-inflammatory genes (TNF-α, IL-1β and IL-8) were up-regulated, but anti-inflammatory genes (TGF-β1 and IL-10) were down-regulated. The results indicate that dietary 10% glycinin rather than 4.5% glycinin could decrease hepatic antioxidant ability and destroy both the intestinal microbiota profile and morphological integrity through disrupting the tight junction structure of the intestine, increasing intestinal mucosal permeability and apoptosis. These results further trigger intestinal inflammatory reactions and even enteritis, ultimately leading to the poor growth of fish.

Specific Blood Plasma Circulating miRs Are Associated with the Physiological Impact of Total Fish Meal Replacement with Soybean Meal in Diets for Rainbow Trout (Oncorhynchus mykiss)

High dietary SBM content is known to induce important physiological alterations, hampering its use as a major FM alternative. Rainbow trout (Oncorhynchus mykiss) juveniles were fed two experimental diets during 9 weeks: (i) a FM diet containing 12% FM; and (ii) a vegetable meal (VM) diet totally devoid of FM and based on SBM (26%). Fish fed the VM diet did not show reduced growth performance when compared with fish fed the FM diet. Nevertheless, fish fed the VM diet had an increased viscerosomatic index, lower apparent fat digestibility, higher aminopeptidase enzyme activity and number of villi fusions, and lower α-amylase enzyme activity and brush border integrity. Small RNA-Seq analysis identified six miRs (omy-miR-730a-5p, omy-miR-135c-5p, omy-miR-93a-3p, omy-miR-152-5p, omy-miR-133a-5p, and omy-miR-196a-3p) with higher expression in blood plasma from fish fed the VM diet. Bioinformatic prediction of target mRNAs identified several overrepresented biological processes known to be associated with high dietary SBM content (e.g., lipid metabolism, epithelial integrity disruption, and bile acid status). The present research work increases our understanding of how SBM dietary content has a physiological impact in farmed fish and suggests circulating miRs might be suitable, integrative, and less invasive biomarkers in fish.

G protein-coupled bile acid receptor 1 reduced hepatic immune response and inhibited NFκB, PI3K/AKT, and PKC/P38 MAPK signaling pathway in hybrid grouper

The mammalian G protein-coupled bile acid receptor 1 (TGR5) is involved in the inflammatory response. However, the functions of TGR5 in the immune response of fish remain unclear. In this study, the full-length sequence of tgr5 from hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) was cloned, and the function of TGR5 in the immune response was explored. The results showed that the ORF of tgr5 gene in hybrid grouper was 1029 bp and encoded 342 amino acids. Activation of TGR5 by INT-777 significantly decreased the activities and mRNA expression of TNFα and IL1β, whereas inhibition of TGR5 by SBI-115 showed the opposite effect. SBI-115 treatment significantly increased the expression of phosphorylated inhibitor κB α (p-IKBα) protein. After the INT-777 treatment, the concentration of protein kinase C (PKC) and expression of the p38 mitogen-activated protein kinases (p38a), p38b and p38c, were significantly decreased in vivo. INT-777 agonist significantly decreased the expression of phosphorylated phosphoinositide 3-kinase (p-PI3K) protein and the ratio of phosphorylated and nonphosphorylated serine/threonine-protein kinase (p-AKT/AKT). In conclusion, activation of hepatic TGR5 inhibited the PKC/P38 MAPK, PI3K/AKT, NFκB signaling pathway and improved hepatic immune responses of hybrid grouper in vivo and in vitro.

Farnesoid X receptor regulates PI3K/AKT/mTOR signaling pathway, lipid metabolism, and immune response in hybrid grouper

Some diseases related to lipid metabolism increase yearly in cultured fish, and the farnesoid X receptor (FXR) is a nuclear protein that plays a key role in inflammatory responses and lipid metabolism. However, the roles of FXR in hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) remain poorly understood. The main objective of this study was to explore the roles of hepatic FXR in triggering the immune response and the potential functions of FXR in regulating the lipid metabolism. In the present study, the full-length sequence of fxr from hybrid grouper was cloned and characterized for the first time. Upon the Vibrio parahaemolyticus stimulation, the transcriptional level of fxr was rapidly elevated in the head kidney tissue in the early stage of infection. In vivo and vitro, activation of FXR by obeticholic acid (OA) significantly increased the concentrations and mRNA levels of hepatic inflammatory cytokines. These effects were inversed when FXR was inhibited by guggulsterone (GU). Moreover, the activation of FXR to suppress the PI₃K/AKT/mTOR signaling pathway improves hepatic lipid metabolism and reduces hepatic lipid accumulation in vivo and vitro. In addition, the inhibition of FXR activated the PI₃K/AKT/mTOR pathway, decreased the lipolysis and increased the lipogenesis, and subsequently increased the lipid accumulation in fish. These results revealed the positive roles of FXR in triggering immune responses and improving lipid metabolism and accumulation in hybrid grouper.

Dynamics impacts of oxytetracycline on growth performance, intestinal health and antibiotic residue of grouper in exposure and withdrawal treatment

Little is known about the effects of oxytetracycline (OTC) on marine fish. Using juvenile pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), we investigated the effects of 56 days dietary oxytetracycline (OTC; OTCD) exposure (80 mg/kg body weight/day) on fish growth performance, intestinal health and antibiotic residue. Meanwhile, the alteration of intestinal health status and antibiotic residue after 7 (O7) or 14 days (O14) OTC withdrawal treatment were explored. We also assessed the potential human health risks based on target hazard quotient (THQ). The results showed that OTC exposure had no effects on growth rate parameters but caused liver and intestine atrophy. OTC exposure impaired the intestinal health by distorting intestinal morphological features, inducing oxidative stress, repressing immune function, triggering NF-κB-mediated inflammatory response and apoptosis, while 7 days OTC withdrawal treatment improved intestinal health status and 14 days OTC withdrawal treatment further improved it. In addition, the order of OTC residue in tested tissues after OTC exposure was: liver > kidney > spleen > muscle > intestine. OTC residue was significantly decreased in all tissues along with the increasing of withdrawal treatment period. Adults and children consuming the edible tissues (muscle) of OTC-treated or withdrawal-treated pearl gentian grouper would not experience any previous health risk as the THQ < 1 in all group.

Effects of Different Viscous Guar Gums on Growth, Apparent Nutrient Digestibility, Intestinal Development and Morphology in Juvenile Largemouth Bass, Micropterus salmoides

An 8-week feeding trial was conducted to investigate the effects of different viscous guar gums on the growth performance, apparent nutrient digestibility, intestinal development and morphology of juvenile largemouth bass. Four isoproteic and isolipidic diets (crude protein 42.5%, crude lipid 13.7%) were formulated to contain 8% cellulose (Control group), 8% low viscous guar gum with 2,500 mPa s (Lvs-GG group), 8% medium viscous guar gum with 5,200 mPa s (Mvs-GG group) and 8% high viscous guar gum with 6,000 mPa s (Hvs-GG group), respectively. Each diet was fed to quadruplicate groups of 40 fish (6.00 ± 0.01 g) per repetition. Dietary guar gum inclusion significantly decreased the weight gain rate, specific growth rate, protein efficiency ratio, protein productive value and lipid deposition rate, and these parameters decreased considerably with increasing guar gum viscous and were lowest in the Hvs-GG group. Dietary guar gum inclusion significantly decreased the apparent digestibility of dry matter, crude protein and crude lipid, and these parameters decreased considerably with increasing guar gum viscous and were lowest in the Hvs-GG group. Intestinal protease, lipase and creatine kinase activities in the guar gum groups were significantly lower than those in the control group, and intestinal protease and lipase activities decreased considerably with increased guar gum viscous. Intestinal alkaline phosphatase activity in the Hvs-GG group and intestinal Na⁺/K⁺-ATPase activity in the Mvs-GG and Hvs-GG groups were significantly lower than those in the Lvs-GG and control groups. Serum high-density lipoprotein, total cholesterol and triglyceride concentrations and superoxide dismutase activity in the guar gum groups were significantly lower than those in the control group. Intestinal villus height and muscular thickness in the guar gum groups were considerably higher than those in the control group, whereas the goblet cell relative number in the Mvs-GG and Hvs-GG groups and the microvillus height in the Lvs-GG and Hvs-GG groups were significantly lower than those in the control group. The expression level of IGF-1 in the guar gum groups and the expression level of GLP-2 in the Mvs-GG and Hvs-GG groups were significantly higher than those in the control group. These results indicated that guar gum diets adversely affected intestinal morphology, decreased intestinal digestive and absorptive enzyme activities, and caused poor nutrient digestibility and growth performance in juvenile largemouth bass. Moreover, the adverse effects of guar gum are closely related to its viscous, and high viscous guar gum produces more extreme negative impacts on juvenile largemouth bass.

Intestinal flora and immunity response to different viscous diets in juvenile largemouth bass, Micropterus salmoides

An 8-weeks feeding trial was conducted to estimate the effects of different viscous cellulose on the intestinal flora and health in juvenile largemouth bass (Micropterus salmoides). Four isoproteic and isolipidic experimental diets were formulated (crude protein 42.50%, crude lipid 13.70%) to contain 8% cellulose (control group; 5.14 mPa s), 8% low viscous carboxymethyl cellulose (CMC) with 800 mPa s (Lvs-CMC group; 182.15 mPa s), 8% middle viscous CMC with 2000 mPa s (Mvs-CMC group; 320.48 mPa s) and 8% high viscous CMC with 5000 mPa s (Hvs-CMC group; 440.65 mPa s), respectively. The weight gain rate, specific growth rate, protein efficiency ratio, protein and lipid deposition rate in the CMC groups were dramatically lower than those in the control group, while feed conversion rate showed an opposite result. Plasma diamine oxidase activity, endothelin-1 and lipopolysaccharide concentrations in the Mvs-CMC and Hvs-CMC groups were significantly higher than in the control group, accompanied by a significant down-regulation of Occludin, Caludin-1 and Caludin-4. Intestinal glutathione concentration, superoxide dismutase and catalase activities in the CMC groups were significantly lower than in the control group, accompanied by a significant up-regulation of Keap1 and down-regulation of Nrf2. Moreover, CMC diets dramatically down-regulated the expression levels of IL-10 and TGF-β1. Digesta total short chain fatty acid and acetate concentrations in the CMC groups were dramatically higher than in the control group, while butyrate concentration showed an opposite result. The OTU, Sobs, Shannon and Simpson indices of intestinal flora in the CMC groups were dramatically lower than in the control group. Notably, structural analysis showed that dietary CMC dramatically increased the abundance of C. somerae and P. shigelloides, but reduced the abundance of C. colicanis and C. perfringens. In summary, increasing dietary viscosity adversely affects the intestinal flora structure and diversity, increases acetate/butyrate-producing bacterial ratio and the abundance of pathogenic microorganisms, disrupting intestinal flora homeostasis, impairs mucosa barrier function, induces intestinal inflammation and epithelial cell apoptosis in juvenile largemouth bass. Our findings demonstrate that soluble cellulose is more detrimental to intestinal health and growth in juvenile largemouth bass compared to insoluble cellulose, and the adverse effects of soluble cellulose are mainly caused by its viscosity. Importantly, this study demonstrate that viscosity is the main characteristic of non-starch polysaccharides that are detrimental to the intestinal health of fish.

Soybean β-conglycinin and glycinin reduced growth performance and the intestinal immune defense and altered microbiome in juvenile pearl gentian groupers Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂

The utilization efficiency of soy protein is affected by its 2 anti-nutritional substances-the antigens β-conglycinin and glycinin. This study investigated their effects on the growth performance, intestinal immune defense, and microbiome in juvenile pearl gentian groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂). Three isonitrogenous and isolipidic diets were formulated containing fishmeal supplemented with 70 g/kg β-conglycinin or 100 g/kg glycinin, or no supplementation (control). Each experimental diet was fed to quadruplicate groups with 30 fish in each tank for 8 weeks. Dietary inclusion of either β-conglycinin or glycinin significantly reduced weight gain and specific growth rates, and cell proliferation of the distal intestine. Histological evaluation of the intestine tract revealed the inflammation signs, characterized by reducing of plica height and width as well as the number of the goblet cells, and widening of the lamina propria. The group fed the β-conglycinin diet had reduced lysozyme activity, contents of immunoglobulin M and complements 3 and 4. Increased activities of caspase-3 and -9 were observed in the group fed the β-conglycinin diet compared to the other 2 groups. In the intestinal microbiota, the relative abundances of the potentially pathogenic genera Photobacterium and Vibrio were significantly higher in the glycinin group than those in others. Therefore, the existence of soybean antigens (β-conglycinin or glycinin) could damage the structural integrity of the intestine, reduce immune defense, reshape the intestinal microbiome and, ultimately, impair growth in fish.

Transcriptome analysis reveals the mechanism of alkalinity exposure on spleen oxidative stress, inflammation and immune function of Luciobarbus capito

Saline-alkali land is distributed all over the world, and it affects the economic development of fisheries. The alkalinity in water is related to the accumulation of carbonate, so the is generally higher. To understand how alkalinity impacts the immune response in Luciobarbus capito, we performed transcriptomic profiles for spleen, the immune organ of Luciobarbus capito which were underwent alkalinity exposure. Totally there are 47,727,954, 53,987,820 and 51,398,546 high quality clean reads obtained from the control groups, and 46,996,982, 49,650,460 and 45,964,986 clean reads from the alkalinity exposure groups. Among them, 611 genes were differently expressed, including 534 upregulated and 77 down-regulated genes. The identified genes were enriched using databases of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). It was found that differentially expressed genes in Luciobarbus capito spleen tissue were enriched into 14 GO pathways, and differentially expressed genes in Luciobarbus capito spleen were enriched into 25 corresponding KEGG pathways under alkalinity stress. Inflammation and immune function genes and pathways were identified and validated by quantitative real-time RT-PCR. Our results showed that alkalinity exposure leads to inflammation and immunoregulation in spleen of Luciobarbus capito. These results provide new insights for unveiling the biological effects of alkalinity in Luciobarbus capito.