Rainbow Trout Research Articles

Differences in diacylglycerol acyltransferases expression patterns and regulation cause distinct hepatic triglyceride deposition in fish

Triglyceride (TAG) deposition in the liver is associated with metabolic disorders. In lower vertebrate, the propensity to accumulate hepatic TAG varies widely among fish species. Diacylglycerol acyltransferases (DGAT1 and DGAT2) are major enzymes for TAG synthesis. Here we show that large yellow croaker (Larimichthys crocea) has significantly higher hepatic TAG level than that in rainbow trout (Oncorhynchus mykiss) fed with same diet. Hepatic expression of DGATs genes in croaker is markedly higher compared with trout under physiological condition. Meanwhile, DGAT1 and DGAT2 in both croaker and trout are required for TAG synthesis and lipid droplet formation in vitro. Furthermore, oleic acid treatment increases DGAT1 expression in croaker hepatocytes rather than in trout and has no significant difference in DGAT2 expression in two fish species. Finally, effects of various transcription factors on croaker and trout DGAT1 promoter are studied. We find that DGAT1 is a target gene of the transcription factor CREBH in croaker rather than in trout. Overall, hepatic expression and transcriptional regulation of DGATs display significant species differences between croaker and trout with distinct hepatic triglyceride deposition, which bring new perspectives on the use of fish models for studying hepatic TAG deposition.

Effect of three unsaturated fatty acids on the protein oxidation and structure of myofibrillar proteins from rainbow trout (Oncorhynchus mykiss)

In this study, the impact of three unsaturated fatty acids (Oleic acid: OA, Eicosapentaenoic acid: EPA, Docosahexaenoic acid: DHA) on the oxidation and structure of rainbow trout myofibrillar protein (MP) was explored. The findings revealed a notable increase in carbonyl content (P < 0.05) and a significant decrease in total sulfhydryl content (P < 0.05) of MP with the concentration increase of the three unsaturated fatty acids. Endogenous fluorescence spectroscopy and surface hydrophobicity analyses showed that unsaturated fatty acids can cause unfolding and exposure of hydrophobic groups in MP. In addition, SDS-PAGE showed that disulfide bonds were associated with MP cross-linking and aggregate size induced by unsaturated fatty acids. Overall, three unsaturated fatty acid treatments facilitated the oxidation of myofibrillar proteins, and the extent of protein oxidation was closely associated with the concentration of unsaturated fatty acids.

Development of polymorphic simple sequences repeats markers from whole gene resequencing data comparison of 68 Oncorhynchus mykiss

Rainbow trout (Oncorhynchus mykiss) is a significant cold-water fish farmed in China. Currently, most molecular marker-assisted breeding applications in rainbow trout rely on SSR markers. Although many rainbow trout SSR markers have been developed, methods for mining many polymorphic SSR markers from the genome and identifying them efficiently and rapidly are still lacking. For this reason, this study used in silico simulation method to rapidly develop a large number of polymorphic SSR markers quickly. A total of 354,613 SSR loci with two to six nucleotide repeat motifs were mined from 32 chromosomes of the rainbow trout reference genome using GMATA. The chromosome sequences of the reference genome were then aligned to the whole genome sequencing data (10×) of 68 rainbow trout samples. In silico genotyping was performed using the HipSTR programme to compare and count the variation in the number of repeats of the motifs of the SSR loci in the samples. The loci with high deletion rates and monomorphism were discarded, while those with more than one non-reference allele were kept. The final set of polymorphic SSR loci screened was 78,828. Finally, 4,821 SSR loci were selected with more than 3 alleles and no deletion in all rainbow trout samples and were physically mapped. The average polymorphic information content of these loci was 0.692, indicating high levels of polymorphism. These SSRs were utilized to analyse the genetic diversity and population structure of the 68 rainbow trout samples. The results showed that these 68 samples were divided into two groups. These newly discovered polymorphic SSR markers will provide valuable information for evaluating the construction of rainbow trout family lines for genetic diversity and improvement.

Gut physiology of rainbow trout (Oncorhynchus mykiss) is influenced more by short-term fasting followed by refeeding than by feeding fishmeal-free diets.

Supplementing a fishmeal-free diet with yeast extract improves rainbow trout (Oncorhynchus mykiss) growth performance and modulates the hepatic and intestinal transcriptomic response. These effects are often observed in the long term but are not well documented after short periods of fasting. Fasting for a few days is a common practice in fish farming, especially before handling the fish, such as for short sorting, tank transfers, and vaccinations. In the present study, rainbow trout were subjected to a 4-day fast and then refed, for 8days, a conventional diet containing fishmeal (control diet) or alternative diets composed of terrestrial animal by-products supplemented or not with a yeast extract. During the refeeding period alone, most of the parameters considered did not differ significantly in response to the different feeds. Only the expression of claudin-15 was upregulated in fish fed the yeast-supplemented diet compared to the control diet. Conversely, fasting followed by refeeding significantly influenced most of the parameters analyzed. In the proximal intestine, the surface area of villi significantly increased, and the density of goblet cell tended to decrease during refeeding. Although no distinct plasma immune response or major signs of gut inflammation were observed, some genes involved in the structure, complement pathway, antiviral functions, coagulation, and endoplasmic reticulum stress response of the liver and intestine were significantly regulated by refeeding after fasting. These results indicate that short-term fasting, as commonly practiced in fish farming, significantly alters the physiology of the liver and intestine regardless of the composition of the diet.

Unveiling climatic niches for deeper insights into invasion potential and enhanced distribution models of freshwater fishes

AbstractIntroduced species may exhibit variations in their preferred climatic niches between their native and introduced ranges, which can have important implications for the transferability of distribution models. In the Himalayan ecoregion, little is known about the geographic distribution and climatic niche overlap between native and introduced cold‐water species. Here, we used the COUE (centroid shift, overlap, unfilling, and expansion) framework to explore the invasive potential of rainbow (Oncorhynchus mykiss) and brown (Salmo trutta fario) trout and corresponding climatic niche overlap with native snow trout (Schizothorax plagiostomus and Schizothorax richardsonii) in the Indus and Ganges River basins. Although we found more stability in the climatic niche for O. mykiss (93%) than S. trutta (58%), both species do not conserve their climatic niches in this region (p &gt; 0.05). S. trutta has expanded more toward new environmental conditions (42%) compared to O. mykiss (7%). However, there are still available environmental gaps that O. mykiss and S. trutta can potentially occupy in the future. There was a higher overlap in climatic niches between S. plagiostomus and O. mykiss and between S. richardsonii and S. trutta. Observed shifts in climatic niches of these introduced species can negatively affect the transferability of distribution models, which may underestimate the assessments of habitat suitability for introduced trout in the Himalayas. Our study demonstrates that the information on climatic niche dynamics can inform the model‐building process and improve the transferability and predictive performance to better assess vulnerability of sensitive habitats to introduced species in the Himalayas and elsewhere.

Niche overlap by invasion of Oncorhynchus mykiss on the habitat of its amphibian prey in central Mexico

Niche overlap by invasion of Oncorhynchus mykiss on the habitat of its amphibian prey in central Mexico

Effects of Chronic Stress from High Stocking Density in Mariculture: Evaluations of Growth Performance and Lipid Metabolism of Rainbow Trout (Oncorhychus mykiss).

(1) Background: In aquaculture, chronic stress due to high stocking density impairs animals' welfare and results in declined fishery production with low protein quality. However, most previous studies evaluated the effects of high stocking density on trout in freshwater rather than seawater. (2) Methods: Juvenile trout were reared for 84 days in circular tanks under three stocking densities, including low density ("LD", 9.15 kg/m3), moderate density ("MD", 13.65 kg/m3), and high density ("HD", 27.31 kg/m3) in seawater. The final densities of LD, MD, and HD were 22.00, 32.05 and 52.24 kg/m3, respectively. Growth performance and lipid metabolism were evaluated. (3) Results: Growth performance and feeding efficiency were significantly reduced due to chronic stress under high density in mariculture. The digestive activity of lipids was promoted in the gut of HD fish, while the concentration of triglycerides was decreased in the blood. Furthermore, decreased acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS), increased hormone-sensitive lipase (HSL) concentrations, and activated hepatic β-oxidation processes were observed in trout under HD. Redundancy analysis showed that glycerol and HSL can be used as potential markers to evaluate the growth performance of trout in mariculture. (4) Conclusions: We showed that chronic high stocking density led to negative effects on growth performance, reduced de novo synthesis of fatty acids, and enhanced lipolysis.

At-sea application of the comet assay to a deep-sea fish

Given the go ahead, deep-sea mining operations are likely to continue for decades on a substantial spatial scale and the resulting sediment plumes combined, are likely to extend beyond the licenced mining areas, and could lead to the chronic exposure of deep-sea organisms to a mixture of metals, even mobile species, such as fish, that could conceivably display avoidance behaviour. The metal concentrations, often substantially below lethal doses, mean that individual mortality is too blunt a measure to allow assessment of “serious harm”. Commonly used cellular biomarkers of exposure in ecotoxicology include DNA damage using the Comet assay. True deep-sea ecotoxicological studies with fish are rare and to our knowledge, there are no published data or method optimizations for deep-sea fish. Coryphaenoides ssp. were collected during SMARTEX expedition 1 (Feb/Mar, 2023) to the Clarion Clipperton Zone (CCZ) in the Eastern Pacific Ocean using a baited trap deployed between 4580–4,732m depth for 24–48 h. Blood and gill tissue were removed and processed for the Comet assay. In order to reduce artefactual DNA damage from cryopreservation observed previously, two sets of samples were prepared: a cryopreservative (10% DMSO) was added to one set of samples and stored at −80 °C; the second set was used to perform a Comet assay within hours of collection. A custom-built gimble table enabled horizontal electrophoresis at sea after which Comet assay slides were dried and stored at room temperature until further analysis. The Comet assay was also assessed in freshly sampled and frozen rainbow trout cells as a proxy control in order to evaluate potential artefacts from the collection and sampling procedure of the deep-sea fish. The blood samples processed at sea had a significantly reduced level of DNA damage compared to the frozen samples. There was no significant difference between the fresh deep-sea and rainbow trout samples. However, the freshly prepared gill samples in Coryphaenoides ssp. showed substantial artefacts, possibly as a consequence of barotrauma. These results represent the first effort at establishing baseline DNA damage data for deep-sea fish, an essential component in understating and quantifying the impact of deep-sea mining.

The Species Composition and Prevalence of Thorny-Headed Worms (Acanthocephala: Echinorhynchidae, Neoechinorhynchidae and Pomphorhynchidae) in Trouts, Complex Measures to Control Them in Fish Farms in the Territory of Azerbaijan Republic

During period 2015-2020 spreading of acanthocephaliasis in the rainbow and brown trout in the fish breeding farms of Azerbaijan Republic was studied. Totally, from 668 fish examined specimens 430 (64.37%) were infected. Correlation of data on the extensiveness and intensity of invasion by thorny-headed worms (Acanthocephala) in trout farms is ventured to make an assumption about unfavorable epidemiological situation in trout breeding farms of the Republic of Azerbaijan. For the purpose of control acanthocephaliasis in trout, a number of drugs were used. The most effective drug was Tetramizole-20%, which was adopted in the trout farms.

Exploring the Effects of Graphene-Based Nanoparticles on Early Salmonids Cardiorespiratory Responses, Swimming and Nesting Behavior.

Graphene-based nanomaterials are exceptionally attractive for a wide range of applications, raising the likelihood of the release of graphene-containing nanoparticles into aquatic environments. The growing use of these carbon nanomaterials in different industries highlights the crucial need to investigate their environmental impact and evaluate potential risks to living organisms. The current investigation evaluated the nanotoxicity of graphene (nanoflakes) and graphene oxide (GO) nanoparticles on the cardiorespiratory responses (heart rate, gill ventilation frequency), as well as the swimming and nesting behavioral parameters of early stage larvae and juvenile salmonids. Both short-term (96 h) and long-term (23 days) exposure experiments were conducted using two common species: brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). The findings demonstrated notable alterations in fish nesting behavior, swimming performance, and cardiorespiratory functions, indicating the potential toxicity of nanoparticles. This impact was observed at both physiological and whole-organismal levels in salmonids at early stages. Future investigations should explore different types of nanocarbons and their potential enduring effects on fish population structure, considering not only individual survival but also broader aspects of development, including feeding, reproductive, and other social dynamics.

Metabolic, neurotoxic and immunotoxic effects of PFAAs and their mixtures on the proteome of the head kidney and plasma from rainbow trout (Oncorhynchus mykiss)

PFAAs (Perfluoroalkyl acids) are a class of bioaccumulative, persistent and ubiquitous environmental contaminants which primarily occupy the hydrosphere and its sediments. Currently, a paucity of toxicological information exists for short chain PFAAs and complex mixtures. In order to address these knowledge gaps, we performed a 3-week, aqueous exposure of rainbow trout to 3 different concentrations of a PFAA mixture (50, 100 and 500 ng/L) modeled after the composition determined in Lake Ontario. We conducted an additional set of exposures to individual PFAAs (25 nM each of PFOS (12,500 ng/L), PFOA (10,300 ng/L), PFBS (7500 ng/L) or PFBA (5300 ng/L) to evaluate differences in biological response across PFAA congeners. Untargeted proteomics and phosphorylated metabolomics were conducted on the blood plasma and head kidney tissue to evaluate biological response. Plasma proteomic responses to the mixtures revealed several unexpected outcomes including Similar proteomic profiles and biological processes as the PFOS exposure regime while being orders of magnitude lower in concentration and an atypical dose response in terms of the number of significantly altered proteins (FDR < 0.1). Biological pathway analysis revealed the low mixture, medium mixture and PFOS to significantly alter (FDR < 0.05) a number of processes including those involved in lipid metabolism, oxidative stress and the nervous system. We implicate plasma increases in PPARD and PPARG as being directly related to these biological processes as they are known to be important regulators in all 3 processes. In contrast to the blood plasma, the high mixture and PFOA exposure regimes caused the greatest change to the head kidney proteome, altering many proteins being involved in lipid metabolism, oxidative stress and inflammation. Our findings support the pleiotropic effect PFAAs have on aquatic organisms at environmentally relevant doses including those on PPAR signaling, metabolic dysregulation, immunotoxicity and neurotoxicity.

Shotgun proteomic analyses of Pseudomonas species isolated from fish products

Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens.

Tomato seed mucilage-whey protein isolate coating enriched with shallot essential oil: Effect on quality changes of the trout fish fillet during cold storage

The current study assessed the effect of tomato seed mucilage (TSM) active coating on rainbow trout's physical, chemical, visual, and microbial characteristics during cold storage. This research also investigated the effect of replacing TSM with whey protein isolate (WPI) and adding shallot essential oil (SEO) at varying concentrations (0%, 1%, and 2%). Ultimately, the correlation between the characteristics and their modeling was examined by applying zero order, first order, and Weibull kinetic models. According to the findings, the application of TSM-WPI coating, particularly when combined with SEO, and substituting 50% of TSM with WPI resulted in a significantly reduction (p˂0.05) in the rate of alterations in weight loss (WL), textural attributes (Hardness, Chewiness, Springiness, Cohesiveness, and Gumminess), pH, TBA, TVB-N, visual characteristics (L*, and ΔE), as well as total viable count (TVC) and psychrotrophic bacteria count (PTC). Furthermore, a significant decrease (p˂0.05) in the rate of changes for all qualitative variables was observed when the ratio of WPI to TSM and SEO concentration were increased. Generally, the coating consisting of 50% TSM and 50% WPI containing 2% SEO exhibited the most effective performance in delaying unfavorable quality changes. Pearson's analysis indicated a notable correlation between the physical, color, chemical, and microbial characteristics. The kinetic models successfully and accurately predicted the physical, chemical, and visual changes in trout fillets during storage with various treatments. The Weibull model performed the best.

Growth performance, health status, gut microbiome, and expression of immune and growth-related genes of rainbow trout (Oncorhynchus mykiss) fed diets with pea protein replacement of fish meal

The need for fish meal constrains fish farming and significantly impacts sustainability of the aquaculture industry. Hence, it is important to investigate the use of plant-based protein sources in fish diets. The present study was conducted to determine the effects of different levels of fish meal (FM) replacement by pea protein (PP) in a 60-day feeding experiment in rainbow trout, Oncorhynchus mykiss. Effects on growth performance, body composition, hematology, serum biochemistry and immunology, and immune (TNF-α, IL1-ß and Il-8) and growth-related (GH and IGFI) gene expression were investigated. Five experimental diets (45% protein and 20% lipid) differed in replacement level of FM by PP at rates of 0% (control (PP0)), 25% (PP25), 50%(PP50), 75%(PP75) and 100%(PP100). Fish were fed with experimental diets in triplicate twice daily. The best growth performance was obtained in PP0 and PP25 groups. While fat ratios of fish fillets significantly differed (p < 0.05), there was no significant effects on protein ratios (p < 0.05). There was no significant change in the hematological values of fish, except those fed the PP100 diets, which displayed a reduction in eyrthocyte counts, hemoglobin content and hematocrit. As PP supplementation increased fish showed elevated serum glucose, total protein, cholesterol and myeloperoxidase activity and decreased glutamic pyruvic transaminase and alkaline phosphatase activity. Fish fed diets with between 25 and 75% replacement showed a decline in lactic acid bacteria in the gut. Significant increases in expression were observed in the liver of the PP25 fish relative to the 0% control for all immune and growth-related genes except for IL1-ß. These data suggest that up to 25% of FM can be replaced by PP without any adverse effects on rainbow trout.

Pelagic fish spared from ocean catch by integrating Black Soldier Fly Larvae in U.S. aquaculture production

The sustainability challenges associated with utilizing forage fish sourced from ocean catch as fish meal and fish oil in the aquaculture industry has increased the demand for alternative feeds. Previous research indicates that Black Soldier Fly Larvae (BSFL; Hermetia illucens) can partially replace fish meal and/or fish oil in the diets of farmed aquaculture species without compromising fish growth or efficiency. The objective of our study was to identify the amount of pelagic fish from ocean catch that could be spared from fish meal and fish oil production by integrating BSFL in the diets of three aquaculture species, Atlantic Salmon (Salmo salar), Rainbow Trout (Oncorhynchus mykiss), and Whiteleg Shrimp (Litopenaeus vannamei) in the United States. Annual output for these aquaculture species was collected for 2017–2019. For each specie, we calculated the total metric tons (MT) of spared pelagic fish, by taxa, from fish meal and fish oil production based on total lifetime food intake and dietary replacement rates of fish meal and fish oil by BSFL as established in previous literature. At the highest level of dietary BSFL substitution for fish meal and/or fish oil that did not sacrifice performance of the three aquaculture species, 40,843 MT of pelagic fish could be spared from ocean catch in the U.S. per year. Therefore, integrating BSFL in the diets of aquaculture species could reduce the demand for pelagic fish sourced from ocean catch and positively contribute to the sustainability of aquaculture production.

A new paradigm for smart packaging: A dual-channel freshness monitoring platform based on aerogels of sodium alginate-anthocyanin complex with high colorimetric sensitivity and stability

Global seafood consumption is estimated at 156 million tons annually, with an economic loss of >25 billion euros annually due to marine fish spoilage. In contrast to traditional smart packaging which can only roughly estimate food freshness, an intelligent platform integrating machine learning and smart aerogel can accurately predict remaining shelf life in food products, reducing economic losses and food waste. In this study, we prepared aerogels based on anthocyanin complexes that exhibited excellent environmental responsiveness, high porosity, high color-rendering properties, high biocompatibility, high stability, and irreversibility. The aerogel showed excellent indication properties for rainbow trout and proved suitable for fish storage environments. Among the four machine learning models, the radial basis function neural network and backpropagation network optimized by genetic algorithm demonstrated excellent monitoring performance. Also, the two-channel dataset provided more comprehensive information and superior descriptive capability. The three-layer structure of the monitoring platform provided a new paradigm for intelligent and sophisticated food packaging. The results of the study might be of great significance to the food industry and sustainable development.

Rainbow trout (Oncorhynchus mykiss, Walbaum 1792) adenocarcinoma investigation with various diagnostic imaging techniques.

Diagnostic imaging techniques provide a new aspect of the ante-mortem and post-mortem diagnostics in fish medicine. Ultrasonography, computed tomography (CT) and magnetic resonance imaging (MRI) can provide more information about the internal organs and pathognomic lesions. The authors used diagnostic imaging techniques to evaluate and describe the neoplastic malformation in a 3-year-old female rainbow trout (Oncorhynchus mykiss). The fish was examined with Siemens Somatom Definition AS + CT scanner and Siemens Biograph mMR scanner. The animal was lethargic and showed anorectic signs and muscular dystrophy. During the post-mortem investigation, histopathology and immunohistochemistry were also performed allowing us to identify the neoplasms. The results showed a large soft tissue mass in the first mid-intestine segment, which proved to be an adenocarcinoma. This subsequently led to digestion problems and absorption disorders. Immunohistochemically, neoplastic cells of carcinoma revealed E-cadherin and pancytokeratin positivity. This is the first study to report the use of MRI and CT for studying gastrointestinal adenocarcinoma in rainbow trout.

Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes.

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.

Dietary Supplementation of Chromium Picolinate does not affect Growth Performance and Feed Conversion Ratio of Rainbow Trout (Oncorhynchus mykiss)

Aims: A growth experiment was conducted to explore the impact of dietary chromium on the growth performance and feed conversion ratio of rainbow trout (Oncorhynchus mykiss).&#x0D; Study Design: Original Research Article&#x0D; Place and Duration of Study: Fisheries Research Station (FRS), Trishuli Nepal, between November 1 to January 29, 2023.&#x0D; Methodology: A total of 270 healthy and equal sized- O. mykiss (initial weight: 27g) were fed on a non-supplemented basal diet (Cr-Pic0), or a basal diet supplemented with 0.4g/kg Cr-Pic (Cr-Pic0.4), or a basal diet supplemented with 1.2g/kg Cr-Pic (Cr-Pic1.2) for 90 days. Each diet was randomly assigned to three replicate groups of 30 fish per flowthrough raceway tanks for 90 days and fed to apparent satiation twice daily.&#x0D; Results: Upon conclusion of the feeding trial, the results showed no significant differences in final weight, weight gain, specific growth rate, or condition factor among treatments (P&gt;0.05). There were also no significant differences in the survival rate and feed conversion ratio of the rainbow trout fed various experimental diets (P&gt;0.05).&#x0D; Conclusion: The results suggest that growth performance, food conversion, and survival of rainbow trout fingerlings are not affected by 0.4 or 1.2 mg/kg supplementation of Cr-Pic in diet.

A meta‐analysis revealing the technical, environmental, and host‐associated factors that shape the gut microbiota of Atlantic salmon and rainbow trout

AbstractSalmonids, specifically Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), are commonly farmed and their gut microbiota plays important roles for optimal growth, health, and physiology. However, differences in experimental design, technical factors and bioinformatics make it challenging to compare the results from different studies and draw general conclusions about their influence on the fish gut microbiota. For a more comprehensive understanding of the gut microbiota, we collected all the publicly accessible 16S rRNA gene sequencing data with clearly stated sample metadata from freshwater Atlantic salmon and rainbow trout intestinal contents and mucosa sequenced on the Illumina MiSeq platform. A total of 783 samples from 19 published studies were included in this meta‐analysis to test the impact of the technical, environmental, and host‐accociated factors. This meta‐analysis revealed that all the tested factors significantly influenced the alpha and beta diversities of the gut microbiota of salmon and trout. Technical factors, especially target region and DNA extraction kit, affected the beta diversity to a larger extent, while host‐associated and environmental factors, especially diet and initial fish weight, had a higher impact on the alpha diversity. Salmon had a higher alpha diversity and higher abundance of Enterococcus and Staphylococcus than trout, which had higher abundance of Weissella and Mycoplasma. The results of this meta‐analysis fill in a critical knowledge gap that demonstrate technical methodologies must be standardized and factors associated with host and environment need to be accounted for in the future design of salmonid gut microbiota experiments.