Irina Viktorovna Sukhovskaya

The gut microbiome of rainbow trout plays a crucial role in fish nutrition, immune function and stress resistance, making it a key factor in aquaculture sustainability. This review systematizes metagenomic data that enable the distinction between resident and transient microbial communities and the identification of a core microbiome. At the phylum level, the core is predominantly composed of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Mycoplasmatota, with additional phyla detected depending on the gut region and methodological approach. Diet-induced changes are often rapid and reversible: insect meal and certain probiotics increase the abundance of beneficial Bacillota and suppress opportunists. Unlike dietary shifts, chronic stressors—particularly elevated temperatures and antibiotic treatment—can override these benefits, causing a persistent alpha diversity reduction, overgrowth of Pseudomonadata, and depletion of key commensals. The autochthonous mucosal microbial community is more resilient to short-term fluctuations but can be irreversibly altered by prolonged stress or antimicrobial therapy, leading to dysbiosis and reduced colonization resistance. A holistic understanding of host–microbe–environment interactions is essential for establishing dynamic reference ranges for a “healthy” microbiome. Such knowledge would enable early detection of dysbiosis and support the rational development of functional feeds and probiotics in commercial trout farming.

The present study investigated the effect of Ligula intestinalis L. infection on several components of the antioxidant system and on protein oxidation in the host fish, common bream Abramis brama L. In ligulosed bream, the hepatopancreatic antioxidant system response included a decrease in catalase (CAT) activity, an increase in glutathione S-transferase (GST) activity, and no change in superoxide dismutase (SOD) activity. The contents of molecular antioxidants in the organs of infected bream were inconsistent; for instance, hepatopancreatic α-tocopherol content was significantly lower, whereas retinol content was significantly higher than in uninfected individuals. In contrast, no significant differences were found in the α-tocopherol or retinol content in the skeletal muscles of infected and uninfected fish. The protein oxidation, estimated via protein carbonyl content, was unaffected by ligulosis, as was the activity of proteasomes. However, the activity of calpain, another protease, was significantly higher in the skeletal muscle of infected fish. Overall, the data reveal moderate and tissue-specific alterations in oxidative stress markers in A. brama infected with L. intestinalis, suggesting a complex host–parasite interaction that does not result in severe systemic oxidative damage under the studied conditions.

The lipopolysaccharide (LPS)-induced inflammation model is widely used in mammalian studies but remains poorly investigated in a variety of fish species. We reproduce this model in rainbow trout, Oncorhynchus mykiss, a species of high economic value, to validate specific inflammatory biomarkers for reliably assessing the health and immune status of farmed fish. The inflammatory process, together with the effect of preconditioning, was modeled using two consecutive intraperitoneal injections of 300 and 600 µg LPS. We assessed innate immunity biomarkers, including the expression of inflammation-related genes (il1ß, il8), peripheral blood leukocyte profiles, serum bactericidal activity (SBA), and various serum and hepatic biochemical parameters. These parameters comprised the concentration of C-reactive protein (CRP, an acute phase protein), and the activities of antioxidant enzymes (superoxide dismutase, catalase, glutathione-S-transferase) measured at 24 and 96 h post-injection. In trout, LPS-induced effects involved the overexpression of pro-inflammatory interleukins (il1ß, il8), a left shift in white blood cells (characterized by a prevalence of immature neutrophils), and enhanced SBA. In contrast to warm-blooded animals, LPS challenge in trout did not appear to significantly elevate CRP levels or antioxidant enzyme activity. Further investigations in other fish species are needed to determine whether these are traits specific to trout or common to bony fish. Our findings provide a foundation for developing a biomarker panel suitable for the routine assessment of welfare, early detection of infection-associated inflammation in cultured fish, and the screening of the anti-inflammatory and immunostimulant activities of drugs and feed additives.

Background Ligula intestinalisis a parasitic tapeworm with a complex life cycle. During the procercoid stage, they parasitize copepods. Later, the cestodes develop into plerocercoids in the body cavity of plankton-feeding fish before finally maturing within the intestines of piscivorous birds. The impact of plerocercoid infection on hosts may be dramatic, including organ compression, disrupted maturation and reproduction, and alter behavior. These effects, which are mediated by neuroendocrine and immunomodulatory mechanisms, can also lead to a mass fish kill. L. intestinalis and their host fish serve as a major model system for parasitological studies due to the substantial impact of these parasites on the ecology, behavior, and physiology of the fish. However, the molecular mechanisms underlying this host-parasite relationship are not well understood, in part due to limited omics data. Here, we present de novo transcriptome assembly, proteome prediction and functional annotation of the L. intestinalis plerocercoids and various tissues from infected and uninfected breams Abramis brama from Lake Syamozero (Karelia). Methods and results A total of three transcriptomes were generated using 132 M paired-end Illumina reads from L. intestinalis plerocercoids, 170 M reads from pooled tissue samples isolated from uninfected bream individuals, and 240 M from infected breams, and were assembled de novo. Additionally, we generated and annotated the predicted proteomes of both species. The transcriptome assemblies were deposited in the NCBI database (BioProject PRJNA1222162), while the translated protein sequences and functional annotations are available in a public repository. Conclusions These data will be valuable for studying molecular adaptations of cestodes to the parasitic lifestyle, as well as host-parasite relationships.

The tapeworm Ligula intestinalis (Linnaeus, 1758) is a broadly distributed parasite with high epidemiological significance. Its first intermediate hosts are crustaceans, its second intermediate hosts are fish, while the definitive hosts are various fish-eating birds and, as recently shown, ringed seals. The stages of Ligula intestinalis in fish are called plerocercoids. In this study we obtained new data on the occurrence of plerocercoids of L. intestinalis in freshwater bream Abramis brama in six lakes in Karelia (Northwestern Russia). Infection of freshwater bream with L. intestinalis in Lakes Onego, Ladoga, Svyatozero and Konchezero was found for the first time. In Lake Syamozero, where long-term parasitological monitoring has been conducted, infection indices of bream with L. intestinalis were similar to those recorded in 1975. Using two mitochondrial genes (cytb and COI), we examined the genetic structure of L. intestinalis from different localities. Phylogenetic analysis showed that all specimens of of L. intestinalis examined in our study belonged to “Lineage A” identified by Nazarizadeh et al. (2023). We found 40 haplotypes of concatenated cox1+ cytb in freshwater bream from different water bodies in Northwestern Russia and Europe. Plerocercoids from Karelian lakes were represented by 22 haplotypes, of which 21 were unique. Our molecular analysis of L. intestinalis from freshwater bream in European part of the Palearctic shows that this parasite lineage is genetically diverse and rapidly expanding.

Reared rainbow trout are vulnerable to environmental stressors, in particular seasonal water warming, which affects fish welfare and growth and induces a temperature response, which involves modifications in tissue lipid profiles. Dietary supplements of plant origin, including the studied mix of a flavonoid, dihydroquercetin and a polysaccharide, arabinogalactan (25 and 50 mg per 1 kg of feed, respectively), extracted from larch wood waste, were shown to facilitate stress tolerance in fish and also to be beneficial for the safety of natural ecosystems and the sustainability of aquaculture production. This four-month feeding trial aimed to determine the effects of the supplement on liver and muscle lipid accumulation and the composition in rainbow trout reared under environmental variables. During periods of environmental optimum for trout, a consistent increase in energy lipid stores, particularly triacylglycerols (2.18 vs. 1.49-fold over a growing season), and an overall increase in lipid saturation due to lower levels of PUFAs, such as eicosapentaenoic (20:5n-3), docosahexaenoic (22:6n-3) and arachidonic (20:4n-6) acids, were observed in both control and supplement-fed fish, respectively. However, in fish stressed by an increase in ambient temperature, dietary supplementation with dihydroquercetin and arabinogalactan reduced mortality (3.65 in control vs. 2.88% in supplement-fed fish, p < 0.05) and alleviated the high-temperature-induced inhibition of lipid accumulation. It also stabilised the membrane phospholipid ratio and moderated the fatty acid composition of fish muscle and liver, resulting in higher levels of n-3 PUFAs and their precursors. Thus, the natural compounds tested are beneficial in accelerating fish tolerance to environmental stressors, reducing mortality and thermal response, and moderately improving fillet quality attributes by increasing the protein/lipid ratio and the abundance of fatty acids essential for human nutrition.

The objective of this study was to investigate the bactericidal activity of blood plasma from cultured rainbow trout obtained from two different fish farms. Plasma from trout naturally infected with the bacterial pathogen Flavobacterium psychrophilum was found to inhibit the growth of Aeromonas hydrophila in vitro. Incubation of A. hydrophila in bacteriostatic trout plasma resulted in agglutination and growth retardation, without causing massive damage to the cell membrane. The proteome of the plasma with high antimicrobial activity revealed an abundance of high-density apolipoproteins, some isoforms of immunoglobulins, complement components C1q and C4, coagulation factors, lectins, periostin, and hemoglobin. Analysis of trout proteins retained on A. hydrophila cells revealed the presence of fish immunoglobulins, lectins, and complement components on bacteria whose growth was inhibited, although the native membrane attack complex of immunised trout plasma did not assemble effectively, resulting in a weak bactericidal effect. Furthermore, this study examined the bacterial response to trout plasma and suggested that the protein synthesis pathway was the target of antimicrobial proteins from fish blood. Taken together, these findings illustrate the advantages of the affinity approach for understanding the role of plasma proteins in host defence against pathogens.

The implantation of optical sensors is a promising method for monitoring physiological parameters of organisms in vivo. For this, suitable hydrogels are required that can provide a biocompatible interface with the organism’s tissues. Amorphous hydrogel is advantageous for administration in animal organs due to its ease of injection compared to resilient analogs. In this study, we investigated the applicability of a semi-liquid 2.5% polyacrylamide hydrogel (PAAH) as a scaffold for fluorescent polyelectrolyte microcapsules (PMs) in rainbow trout. The hydrogel was injected subcutaneously into the adipose fin, which is a small, highly translucent fold of skin in salmonids that is convenient for implanting optical sensors. Using histological methods, we compared tissue organization and in vivo stability of the applied hydrogel at the injection site after administration of uncoated PMs or PMs coated with 2.5% PAAH (PMs-PAAH) for a period of 3 to 14 days. Our results showed that the introduction of PMs into the gel did not have a masking effect, as they were recognized, engulfed, and carried away by phagocytes from the injection site. However, both PMs and PMs-PAAH were found to provoke chronic inflammation at the injection site, although according to cytokine expression in the fish spleen, the irritating effect was local and did not affect the systemic immunity of the fish. Therefore, our study suggests low applicability of 2.5% polyacrylamide as a scaffold for injectable sensors within a timeframe of days.

Natural feed supplements have been shown to improve fish viability, health, and growth, and the ability to withstand multiple stressors related to intensive cultivation. We assumed that a dietary mix of plant-origin substances, such as dihydroquercetin, a flavonoid with antioxidative, anti-inflammatory, and antimicrobial properties, and arabinogalactan, a polysaccharide with immunomodulating activity, would promote fish stress resistance and expected it to have a protective effect against infectious diseases. Farmed rainbow trout fish, Oncorhynchus mykiss, received either a standard diet or a diet supplemented with 25 mg/kg of dihydroquercetin and 50 mg/kg of arabinogalactan during a feeding season, from June to November. The fish in the control and experimental groups were sampled twice a month (eight samplings in total) for growth variable estimations and tissue sampling. The hepatic antioxidant status was assessed via the quantification of molecular antioxidants, such as reduced glutathione and alpha-tocopherol rates, as well as the enzyme activity rates of peroxidase, catalase, and glutathione-S-transferase. The lipid and fatty acid compositions of the feed and fish liver were analyzed using thin-layer and high-performance liquid chromatography. The viability, size, and biochemical indices of the fish responded to the growth physiology, environmental variables such as the dissolved oxygen content and water temperature, and sporadic factors. Due to an outbreak of a natural bacterial infection in the fish stock followed by antibiotic treatment, a higher mortality rate was observed in the fish that received a standard diet compared to those fed supplemented feed. In the postinfection period, reduced dietary 18:2n-6 and 18:3n-3 fatty acid assimilation contents were detected in the fish that received the standard diet in contrast to the supplemented diet. By the end of the feeding season, an impaired antioxidant response, including reduced glutathione S-transferase activity and glutathione content, and a shift in the composition of membrane lipids, such as sterols, 18:1n-7 fatty acid, and phospholipids, were also revealed in fish fed the standard diet. Dietary supplementation with plant-origin substances, such as dihydroquercetin and arabinogalactan, decreases lethality in fish stocks, presumably though the stimulation of natural resistance in farmed fish, thereby increasing the economic efficacy during fish production. From the sustainable aquaculture perspective, natural additives also diminish the anthropogenic transformation of aquaculture-bearing water bodies and their ecosystems.