Gut Microbes Reveal Pseudomonas Medicates Ingestion Preference via Protein Utilization and Cellular Homeostasis Under Feed Domestication in Freshwater Drum, Aplodinotus grunniens

Gut Microbe Rikenellaceae_RC9_gut_group and Knoellia-Mediated Acetic Acid Regulates Glucose and Lipid Metabolism in the Muscle of Freshwater Drum (Aplodinotus grunniens) Under High-Fat Diets

Metabolic disorders and complications induced by high-fat diets (HFDs) are a hot research topic in aquatic animal nutrition and health, but the mechanism of gut microbes and their metabolites on muscle homeostasis is not yet clear. In this study, a 16-week HFD (Con, 6% fat and HFD, 12% fat) rearing experiment was conducted with a freshwater drum (20.88 ± 2.75 g, about 20,000 fish per pond) to investigate the underlying regulation of gut microbes on muscle nutrient and metabolism. Results revealed that HFD had no remarkable effect on proximate nutrients (moisture, ash, crude protein, and crude fat), total amino acids, and fatty acids contents in muscle. Moreover, decreased acetic acid content by HFD in the gut and muscle was confirmed to regulate lipid metabolism, as evidenced by the activation of fatty acid synthesis (acetyl-CoA carboxylase alpha [ACC1] and sterol regulatory element binding protein-1 [SREBP1]) and inhibition of fatty acid lipolysis (AMP-activated protein kinase [AMPK], adipose triglyceride lipase [ATGL], and carnitine palmitoyl transferase 2 [CPT2]). Interestingly, RNA-seq revealed glycolytic metabolism (glycolysis/gluconeogenesis and pyruvate metabolism) was active in the muscle under HFD, which was further confirmed to be the intermediate for acetic acid to regulate lipid metabolism. Strikingly, gut microbe Rikenellaceae_RC9_gut_group and Knoellia regulate muscle lipid and glucose metabolism through their derived metabolite acetic acid, which is the key target for gut microbe to regulate muscle. Taken together, these results reveal the regulatory mechanism of gut microbes and derived metabolites on muscle metabolism and development, providing a theoretical basis for the healthy regulation of HFD in aquatic animals.

Transcriptome Sequencing Reveals Effects of Artificial Feed Domestication on Intestinal Performance and Gene Expression of Carnivorous Mandarin Fish (Siniperca chuatsi) and Related Mechanisms

Mandarin fish (Siniperca chuatsi) is a voracious carnivorous species, usually consuming only live bait fish, but dietary acclimation enables it to accept artificial feed. However, the effects of dietary acclimation on intestinal performance and gene expression in mandarin fish and related mechanisms remain largely unknown. Therefore, this study investigated the effects of artificial feed on intestinal physicochemical and biochemical performance and gene expression in mandarin fish. Mandarin fish were sampled on day 10 after feeding with live dace (LD), at day 40 after subsequent feeding with dead dace plus artificial feed (DD + AF) from day 11 to day 40, and at day 90 after continuous feeding with artificial feed (AF) alone from day 41 to day 90 for transcriptome sequencing. The biochemical analysis results indicated that artificial feed significantly increased the activity of antioxidant enzymes glutathione peroxidase and superoxide dismutase in the intestine, liver, and stomach. Histological analysis demonstrated intestinal damage in mandarin fish fed with artificial feed. The GO and KEGG enrichment analyses indicated that the DEGs in AF vs. DD + AF were significantly enriched in the pentose phosphate pathway, and the DEGs in AF vs. LD were mainly significantly enriched in glycolysis/gluconeogenesis and PPAR signaling pathways. Nineteen feed acclimation-related key genes such as gene pfkfb4a and scd were identified in the intestine and found to exhibit upregulated expressions. These results revealed that artificial feed domestication enhanced the antioxidant capacity of the mandarin fish intestine and reduced hepatic lipid deposition by upregulating the related gene expression of mandarin fish and that the regulation of carbon metabolisms, including sugar, lipid, and steroid metabolisms, might be fundamental mechanisms for mandarin fish to acclimatize to dietary changes. These findings provide novel insights into the feed acclimation mechanism of mandarin fish, holding implications for promoting large-scale artificial feed aquaculture of mandarin fish and improving economic efficiency.

Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome

Habitual dietary changes have the potential to induce alterations in the host's gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.

Effects of Fishmeal Substitution with Mealworm Meals (Tenebrio molitor and Alphitobius diaperinus) on the Growth, Physiobiochemical Response, Digesta Microbiome, and Immune Genes Expression of Atlantic Salmon (Salmo salar)

A 12-week growth trial was conducted to assess the effects of mealworm meals, as a substitution for fishmeal, on the growth, physiobiochemical responses, digesta microbiome, and immune-related genes expression of Atlantic salmon (Salmo salar). Twenty Atlantic salmon parr (38.5 ± 0.1 g, initial weight) were stocked into each of 16 tanks in a recirculating aquaculture system. A fishmeal-based diet (100% FM) was used as the control treatment and was compared with three test diets where: (1) fishmeal was partially (50%) replaced with defatted mealworm meal, Tenebrio molitor (50% DMM), (2) fishmeal was fully replaced with defatted mealworm meal (100% DMM), and (3) fishmeal was partially replaced with whole lesser mealworm meal, Alphitobius diaperinus (50% WMM). All substitutions were done on a crude protein basis. Each of the four experimental diets was evaluated in quadruplicate tanks as part of randomized design. The results indicated that Atlantic salmon showed high survival (greater or equal to 98.8%), and no significant difference in final growth, feed efficiency, feces stability and condition indices. Hepatosomatic index was lower in fish fed 100% DMM and 50% WMM when compared to fish fed the control diet (100% FM). Whole-body proximate and amino acid compositions were not statistically different between treatments, while essential fatty acids, including linolenic, eicosapentaenoic acid, and homo-a-linolenic, were lower in fish fed 100% DMM. Plasma parameters (total protein, alanine aminotransferase, alkaline phosphatase, and total iron-binding capacity), hepatic peroxide, and antioxidant enzymes were not significantly affected by dietary substitutions, whereas plasma immunoglobulin M showed significantly higher levels in fish fed 50% DMM and 100% DMM when compared to fish fed the control diet (100% FM). The inclusion of mealworm meals significantly impacted the overall microbiome composition but not the richness and evenness of the salmon digesta microbiomes compared to control. The most common genus in all treatments was Pseudomonas, which has been previously shown to have both commensal and pathogenic members. The relative expressions of growth (IGF-I) and protein synthesis (TIPRL) were not significantly different between the treatments, whereas immunoglobulin genes (IgM, IgD, and IgT) were significantly upregulated in fish fed the DMM diets when compared to fish fed the control diet. Overall, this study suggests that the mealworm meals tested could be suitable alternatives to fishmeal in the diet of Atlantic salmon.

Combined Dietary Administration of Chlorella fusca and Ethanol-Inactivated Vibrio proteolyticus Modulates Intestinal Microbiota and Gene Expression in Chelon labrosus

The use of functional feeds in aquaculture is currently increasing. This study aimed to assess the combined impact of dietary green microalgae Chlorella fusca and ethanol-inactivated Vibrio proteolyticus DCF12.2 (CVP diet) on thick-lipped grey mullet (Chelon labrosus) juvenile fish. The effects on intestinal microbiota and the transcription of genes related to metabolism, stress, and the immune system were investigated after 90 days of feeding. Additionally, the fish were challenged with Aeromonas hydrophila and polyinosinic-polycytidylic acid (poly I:C) to evaluate the immune response. Microbiota analysis revealed no significant differences in alpha and beta diversity between the anterior and posterior intestinal sections of fish fed the control (CT) and CVP diets. The dominant genera varied between the groups; Pseudomonas and Brevinema were most abundant in the CVP group, whereas Brevinema, Cetobacterium, and Pseudomonas were predominant in the CT group. However, microbial functionality remained unaltered. Gene expression analysis indicated notable changes in hif3α, mhcII, abcb1, mx, and tnfα genes in different fish organs on the CVP diet. In the head kidney, gene expression variations were observed following challenges with A. hydrophila or poly I:C, with higher peak values seen in fish injected with poly I:C. Moreover, c3 mRNA levels were significantly up-regulated in the CVP group 72 h post-A. hydrophila challenge. To conclude, incorporating C. fusca with V. proteolyticus in C. labrosus diet affected the microbial species composition in the intestine while preserving its functionality. In terms of gene expression, the combined diet effectively regulated the transcription of stress and immune-related genes, suggesting potential enhancement of fish resistance against stress and infections.

Peroxisome Proliferator-Activated Receptor Signaling-Mediated 13-S-Hydroxyoctadecenoic Acid Is Involved in Lipid Metabolic Disorder and Oxidative Stress in the Liver of Freshwater Drum, Aplodinotus grunniens

The appropriate level of dietary lipids is essential for the nutrient requirements, rapid growth, and health maintenance of aquatic animals, while excessive dietary lipid intake will lead to lipid deposition and affect fish health. However, the symptoms of excessive lipid deposition in the liver of freshwater drums (Aplodinotus grunniens) remain unclear. In this study, a 4-month rearing experiment feeding with high-fat diets and a 6-week starvation stress experiment were conducted to evaluate the physiological alteration and underlying mechanism associated with lipid deposition in the liver of A. grunniens. From the results, high-fat-diet-induced lipid deposition was associated with increased condition factor (CF), viscerosomatic index (VSI), and hepatosomatic index (HSI). Meanwhile, lipid deposition led to physiological and metabolic disorders, inhibited antioxidant capacity, and exacerbated the burden of lipid metabolism. Lipid deposition promoted fatty acid synthesis but suppressed catabolism. Specifically, the transcriptome and metabolome showed significant enrichment of lipid metabolism and antioxidant pathways. In addition, the interaction analysis suggested that peroxisome proliferator-activated receptor (PPAR)-mediated 13-S-hydroxyoctadecenoic acid (13 (s)-HODE) could serve as the key target in regulating lipid metabolism and oxidative stress during lipid deposition in A. grunniens. Inversely, with a lipid intake restriction experiment, PPARs were confirmed to regulate lipid expenditure and physiological homeostasis in A. grunniens. These results uncover the molecular basis of and provide specific molecular targets for fatty liver control and prevention, which are of great importance for the sustainable development of A. grunniens.

Validation and Functional Analysis of Reference and Tissue-Specific Genes in Adipose Tissue of Freshwater Drum, Aplodinotus grunniens, under Starvation and Hypothermia Stress

Adipose tissue is critical to the growth, development, and physiological health of animals. Reference genes play an essential role in normalizing the expression of mRNAs. Tissue-specific genes are preferred for their function and expression in specific tissues or cell types. Identification of these genes contributes to understanding the tissue-gene relationship and the etiology and discovery of new tissue-specific targets. Therefore, reference genes and tissue-specific genes in the adipose tissue of Aplodinotus grunniens were identified to explore their function under exogenous starvation (1 d, 2 w, 6 w) and hypothermic stress (18 °C and 10 °C for 2 d and 8 d) in this study. Results suggest that 60SRP was the most stable reference gene in adipose tissue. Meanwhile, eight genes were validated as tissue-specific candidates from the high-throughput sequencing database, while seven of them (ADM2, β₂GP1, CAMK1G, CIDE3, FAM213A, HSL, KRT222, and NCEH1) were confirmed in adipose tissue. Additionally, these seven tissue-specific genes were active in response to starvation and hypothermic stress in a time- or temperature-dependent manner. These results demonstrate that adipose-specific genes can be identified using stable internal reference genes, thereby identifying specific important functions under starvation and hypothermic stress, which provides tissue-specific targets for adipose regulation in A. grunniens.

Hypothermia-Mediated Apoptosis and Inflammation Contribute to Antioxidant and Immune Adaption in Freshwater Drum, Aplodinotus grunniens

Hypothermia-exposure-induced oxidative stress dysregulates cell fate and perturbs cellular homeostasis and function, thereby disturbing fish health. To evaluate the impact of hypothermia on the freshwater drum (Aplodinotus grunniens), an 8-day experiment was conducted at 25 °C (control group, Con), 18 °C (LT18), and 10 °C (LT10) for 0 h, 8 h, 1 d, 2 d, and 8 d. Antioxidant and non-specific immune parameters reveal hypothermia induced oxidative stress and immunosuppression. Liver ultrastructure alterations indicate hypothermia induced mitochondrial enlargement, nucleoli aggregation, and lipid droplet accumulation under hypothermia exposure. With the analysis of the transcriptome, differentially expressed genes (DEGs) induced by hypothermia were mainly involved in metabolism, immunity and inflammation, programmed cell death, and disease. Furthermore, the inflammatory response and apoptosis were evoked by hypothermia exposure in different immune organs. Interactively, apoptosis and inflammation in immune organs were correlated with antioxidation and immunity suppression induced by hypothermia exposure. In conclusion, these results suggest hypothermia-induced inflammation and apoptosis, which might be the adaptive mechanism of antioxidation and immunity in the freshwater drum. These findings contribute to helping us better understand how freshwater drum adjust to hypothermia stress.

miR-1/AMPK-Mediated Glucose and Lipid Metabolism under Chronic Hypothermia in the Liver of Freshwater Drum, Aplodinotus grunniens

Our previous study demonstrated that low temperature could induce hepatic inflammation and suppress the immune and oxidation resistance of freshwater drum. However, the metabolism, especially the glucose and lipid metabolism involved, is poorly studied. To further explore the chronic hypothermia response of freshwater drum, an 8-day hypothermia experiment was conducted at 10 °C to investigate the effect of chronic hypothermia on glucose and lipid metabolism via biochemical and physiological indexes, and metabolic enzyme activities, miRNAs and mRNA-miRNA integrate analysis in the liver. Plasma and hepatic biochemical parameters reveal chronic hypothermia-promoted energy expenditure. Metabolic enzyme levels uncover that glycolysis was enhanced but lipid metabolism was suppressed. Differentially expressed miRNAs induced by hypothermia were mainly involved in glucose and lipid metabolism, programmed cell death, disease, and cancerization. Specifically, KEGG enrichment indicates that AMPK signaling was dysregulated. mRNA-miRNA integrated analysis manifests miR-1 and AMPK, which were actively co-related in the regulatory network. Furthermore, transcriptional expression of key genes demonstrates hypothermia-activated AMPK signaling by miR-1 and subsequently inhibited the downstream glucogenic and glycogenic gene expression and gene expression of fatty acid synthesis. However, glycogenesis was alleviated to the control level while fatty acid synthesis was still suppressed at 8 d. Meanwhile, the gene expressions of glycolysis and fatty acid oxidation were augmented under hypothermia. In conclusion, these results suggest that miR-1/AMPK is an important target for chronic hypothermia control. It provides a theoretical basis for hypothermia resistance on freshwater drum.