Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon

Insect Meal in Aquafeeds: A Sustainable Path to Enhanced Mucosal Immunity in Fish

The mucosal surfaces of fish, including their intestines, gills, and skin, are constantly exposed to various environmental threats, such as water quality fluctuations, pollutants, and pathogens. However, various cells and microbiota closely associated with these surfaces work in tandem to create a functional protective barrier against these conditions. Recent research has shown that incorporating specific feed ingredients into fish diets can significantly boost their mucosal and general immune response. Among the various ingredients being investigated, insect meal has emerged as one of the most promising options, owing to its high protein content and immunomodulatory properties. By positively influencing the structure and function of mucosal surfaces, insect meal has the potential to enhance the overall immune status of fish. This review provides a comprehensive overview of the potential benefits of incorporating insect meal into aquafeed as a feed ingredient for augmenting the mucosal immune response of fish.

The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence

The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.

The impact of diets containing Hermetia illucens meal on the growth, intestinal health, and microbiota of gilthead seabream (Sparus aurata)

The present study investigated the effect of replacing fishmeal (FM) with insect meal of Hermetia illucens (HI) in the diet of Sparus aurata farmed inshore on growth, gut health, and microbiota composition. Two isolipidic (18% as fed) and isoproteic (42% as fed) diets were tested at the farm scale: a control diet without HI meal and an experimental diet with 11% HI meal replacing FM. At the end of the 25-week feeding trial, final body weight, specific growth rate, feed conversion rate, and hepatosomatic index were not affected by the diet. Gross morphology of the gastrointestinal tract and the liver was unchanged and showed no obvious signs of inflammation. High-throughput sequencing of 16S rRNA gene amplicons (MiSeq platform, Illumina) used to characterize the gut microbial community profile showed that Proteobacteria, Fusobacteria, and Firmicutes were the dominant phyla of the gut microbiota of gilthead seabream, regardless of diet. Dietary inclusion of HI meal altered the gut microbiota by significantly decreasing the abundance of Cetobacterium and increasing the relative abundance of the Oceanobacillus and Paenibacillus genera. Our results clearly indicate that the inclusion of HI meal as an alternative animal protein source positively affects the gut microbiota of seabream by increasing the abundance of beneficial genera, thereby improving gut health and maintaining growth performance of S. aurata from coastal farms.

Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon

Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.

Exploring the effects of dietary inulin in rainbow trout fed a high-starch, 100% plant-based diet

BACKGROUND

High dietary carbohydrates can spare protein in rainbow trout (Oncorhynchus mykiss) but may affect growth and health. Inulin, a prebiotic, could have nutritional and metabolic effects, along with anti-inflammatory properties in teleosts, improving growth and welfare. We tested this hypothesis in rainbow trout by feeding them a 100% plant-based diet, which is a viable alternative to fishmeal and fish oil in aquaculture feeds. In a two-factor design, we examined the impact of inulin (2%) as well as the variation in the carbohydrates (CHO)/plant protein ratio on rainbow trout. We assessed the influence of these factors on zootechnical parameters, plasma metabolites, gut microbiota, production of short-chain fatty acids and lactic acid, as well as the expression of free-fatty acid receptor genes in the mid-intestine, intermediary liver metabolism, and immune markers in a 12-week feeding trial.

RESULTS

The use of 2% inulin did not significantly change the fish intestinal microbiota, but interestingly, the high CHO/protein ratio group showed a change in intestinal microbiota and in particular the beta diversity, with 21 bacterial genera affected, including Ralstonia, Bacillus, and 11 lactic-acid producing bacteria. There were higher levels of butyric, and valeric acid in groups fed with high CHO/protein diet but not with inulin. The high CHO/protein group showed a decrease in the expression of pro-inflammatory cytokines (il1b, il8, and tnfa) in liver and a lower expression of the genes coding for tight-junction proteins in mid-intestine (tjp1a and tjp3). However, the 2% inulin did not modify the expression of plasma immune markers. Finally, inulin induced a negative effect on rainbow trout growth performance irrespective of the dietary carbohydrates.

CONCLUSIONS

With a 100% plant-based diet, inclusion of high levels of carbohydrates could be a promising way for fish nutrition in aquaculture through a protein sparing effect whereas the supplementation of 2% inulin does not appear to improve the use of CHO when combined with a 100% plant-based diet.

Growth, Survival, and Intestinal Health Alterations in Mediterranean Yellowtail (Seriola dumerili) Due to Alternatives to Fishmeal and Fish Oil

Fishmeal and fish oil substitution in aquafeeds might have adverse effects on fish growth and health, mainly in carnivorous species, such as Mediterranean yellowtail (Seriola dumerili). Mediterranean yellowtail shows great potential as an alternative aquaculture species due to its fast growth and high price on the market, but the need for high-quality protein and fatty acid content in its diets is limiting its production. In order to improve the sustainability of its production, this study was conducted with 360 fish of 35 g to evaluate the effects on fish growth and health. Six diets were used: one control diet without replacement, three with FM replacement (FM66, FM33, and FM0) (33%, 66%, and 100% FM replacement), and two with FO replacement (FO50 and FO0) (50% and 100% FO replacement). The substitution of FM was with vegetable (VM) (corn gluten) and animal (AM) (krill and meat meal) meals. The reductions in FM and FO of up to 33 and 0%, respectively, did not affect the growth and survival of S. dumerili at the intestinal morphology level, except for the anterior intestine regarding the lower villi length and width and the posterior intestine regarding the lower width of the lamina propria. On the other hand, the substitution of fish ingredients in the diet affects liver morphology, indicating alterations in the major diameter of hepatocytes or their nuclei. Finally, diet did not affect the gut microbiota with respect to the control, but significant differences were found in alpha and beta diversity when FO and FM microbiota were compared. A 66% FM replacement and total FO replacement would be possible without causing major alterations in the fish.

Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon

Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.

Polychaete (Alitta virens) meal inclusion as a dietary strategy for modulating gut microbiota of European seabass (Dicentrarchus labrax)

Recent research has revealed the significant impact of novel feed ingredients on fish gut microbiota, affecting both the immune status and digestive performance. As a result, analyzing the microbiota modulatory capabilities may be a useful method for assessing the potential functionality of novel ingredients. Therefore, this study aimed to evaluate the effects of dietary polychaete meal (PM) from Alitta virens on the autochthonous and allochthonous gut microbiota of European seabass (Dicentrarchus labrax). Two diets were compared: a control diet with 25% fishmeal (FM) and a diet replacing 40% of fishmeal with PM, in a 13-week feeding trial with juvenile fish (initial weight of 14.5 ± 1.0 g). The feed, digesta, and mucosa-associated microbial communities in fish intestines were analyzed using high-throughput sequencing of the 16S rRNA gene on the Illumina MiSeq platform. The results of feed microbiota analyses showed that the PM10 feed exhibited a higher microbial diversity than the FM diet. However, these feed-associated microbiota differences were not mirrored in the composition of digesta and mucosal communities. Regardless of the diet, the digesta samples consistently exhibited higher species richness and diversity than the mucosa samples. Overall, digesta samples were characterized by a higher abundance of Firmicutes in PM-fed fish. In contrast, at the gut mucosa level, the relative abundances of Mycobacterium, Taeseokella and Clostridium genera were lower in the group fed the PM10 diet. Significant differences in metabolic pathways were also observed between the FM and PM10 groups in both mucosa and digesta samples. In particular, the mucosal pathways of caffeine metabolism, phenylalanine metabolism, and sulfur relay system were significantly altered by PM inclusion. The same trend was observed in the digesta valine, leucine, and isoleucine degradation and secretion pathways. These findings highlight the potential of PM as an alternative functional ingredient in aquafeeds with microbiota modulatory properties that should be further explored in the future.

Interaction between genetics and inulin affects host metabolism in rainbow trout fed a sustainable all plant-based diet

Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave.

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics

BACKGROUND

The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical composition of the gut microbiota and gut health status in Atlantic salmon and to explore possible modulatory effects of dietary prebiotics in one net-pen farm in open water. The fish with initial mean body weight of around 240 g were fed diets based on the same basal composition, either without (Ref diet) or with (Test diet) yeast cell wall based-prebiotics, during the marine production phase from December to September the following year. Sampling was conducted at three sampling time points: January, April, and September, with average water temperature of 3.9 ℃, 3.4 ℃ and 9.6 ℃, respectively.

RESULTS

As the fish progressed towards September, growth, brush border membrane enzyme activities, and the expression in the gut of most of the observed genes involved in immune (e.g., il8, cd4a, myd88, il1b, gilt, tgfb, cd8b and cd3), barrier (e.g., zo1, occludin, ecad, claudin25b and claudin15), and metabolism increased significantly. Lipid accumulation in pyloric enterocytes decreased remarkably, suggesting improvement of gut health condition. The growth of the fish did not differ between dietary treatments. Further, dietary prebiotics affected the gut health only marginally regardless of duration of administration. Regarding gut microbiota composition, a decrease in alpha diversity (Observed species, Pielou and Shannon) over time was observed, which was significantly associated with an increase in the relative abundance of genus Mycoplasma and decrease in 32 different taxa in genus level including lactic acid bacteria (LAB), such as Lactobacillus, Leuconostoc, and Lactococcus. This indicates that developmental stage of Atlantic salmon is a determinant for microbial composition. Multivariate association analysis revealed that the relative abundance of Mycoplasma was positively correlated with gut barrier gene expression, negatively correlated with plasma glucose levels, and that its relative abundance slightly increased by exposure to prebiotics. Furthermore, certain LAB (e.g., Leuconostoc), belonging to the core microbiota, showed a negative development with time, and significant associations with plasma nutrients levels (e.g., triglyceride and cholesterol) and gene expression related to gut immune and barrier function.

CONCLUSIONS

As Atlantic salmon grew older under large-scale, commercial farm settings, the Mycoplasma became more prominent with a concomitant decline in LAB. Mycoplasma abundance correlated positively with time and gut barrier genes, while LAB abundance negatively correlated to time. Dietary prebiotics affected gut health status only marginally.

Interactive Effect of Dietary Heat-Killed Lactobacillus Plantarum L-137 and Berberine Supplementation on Intestinal Mucosa and Microbiota of Juvenile Black Sea Bream (Acanthopagrus Schlegelii)

To compare the synergistic impact of dietary heat-killed Lactobacillus plantarum and berberine supplementation on intestinal health of juvenile black sea bream, the test fish (5.67 ± 0.05 g) were fed three diets: a basal control diet designated as Con; basal diet supplemented with 400 mg/kg L. plantarum, labelled LP; and basal diet supplemented with 400 mg/kg L. plantarum + 50 mg/k berberine, labelled LPBB. After 56 days of feeding, the control fish had significantly lower intestinal villus height (VH), villus surface area (VSA), and muscularis mucosae (MS) thickness than the rest of the groups (P < 0.05). The LPBB fish had significantly higher VH than the control fish, and wider MS and VSA than the rest of the groups (P < 0.05). Occludin was significantly upregulated in the LPBB fish, and heat shock protein 90 was upregulated in the control fish (P < 0.05). The abundance of Proteobacteria family was significantly higher in the intestinal microbiome of the control and LP fish, the LPBB fish had higher abundance of Cyanobacteria and Spirochaetes, and the LP group had higher Bacteroidetes abundance (P < 0.05). Potentially beneficial Delftia and Brevinema were the significantly abundant genera in the LP and LPBB fish, respectively; potentially pathogenic Elizabethkingia was abundant in the LP fish; and the control fish had higher abundance of potentially pathogenic Burkholderia-Caballeronia-Paraburkholderia (P < 0.05). According to these results, there is possible synergy between L. plantarum and berberine as dietary supplements in fostering healthy intestine for black sea bream than L. plantarum alone.

Feed Regime Slightly Modifies the Bacterial but Not the Fungal Communities in the Intestinal Mucosal Microbiota of Cobia Fish (Rachycentron canadum)

The bacterial community of the intestinal microbiota influences many host functions, and similar effects have been recently reported for the fungal community (mycobiota). Cobia is a tropical fish that has been studied for its potential in marine aquaculture. However, the study of its bacterial community has been underreported and the mycobiota has not been investigated. We analyzed the gut bacterial and fungal profile present in the intestinal mucosa of reared adult cobias fed two diets (frozen fish pieces (FFPs) and formulated feed (FF)) for 4 months by sequencing the 16S rRNA (V3-V4) and internal transcribed spacer-2 (ITS2) regions using Illumina NovaSeq 6000. No significant differences in the alpha diversity of the bacterial community were observed, which was dominated by the phyla Proteobacteria (~96%) and Firmicutes (~1%). Cobia fed FF showed higher abundance of 10 genera, mainly UCG-002 (Family Oscillospiraceae) and Faecalibacterium, compared to cobia fed FFPs, which showed higher abundance of 7 genera, mainly Methylobacterium-Methylorubrum and Cutibacterium. The inferred bacterial functions were related to metabolism, environmental information processing and cellular processes; and no differences were found between diets. In mycobiota, no differences were observed in the diversity and composition of cobia fed the two diets. The mycobiota was dominated by the phyla Ascomycota (~88%) and Basidiomycota (~11%). This is the first study to describe the gut bacterial and fungal communities in cobia reared under captive conditions and fed on different diets and to identify the genus Ascobulus as a new member of the core fish mycobiota.

Review: Effect of Experimental Diets on the Microbiome of Productive Animals

The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.

How Do Alternative Protein Resources Affect the Intestine Morphology and Microbiota of Atlantic Salmon?

The availability and cost of fishmeal constitute a bottleneck in Atlantic salmon production expansion. Fishmeal is produced from wild fish species and constitutes the major feed ingredient in carnivorous species such as the Atlantic salmon. These natural stocks are at risk of depletion and it is therefore of major importance to find alternative protein sources that meet the nutritional requirements of the Atlantic salmon, without compromising the animals' health. Terrestrial animal by-products have been used in aquaculture feed, but their use is limited by the lack of several essential amino acids and consumer acceptance. In the case of plant ingredients, it is necessary to take into account both their concentration and the extraction methodologies, since, if not dosed correctly, they can cause macro- and microscopic alterations of the structure of the gastrointestinal tract and can also negatively modulate the microbiota composition. These alterations may compromise the digestive functions, growth of the animal, and, ultimately, its well-being. An updated revision of alternative protein sources is provided, with the respective impact on the intestine health in terms of both morphology and microbiota composition. Such information may constitute the premise for the choice and development of Atlantic salmon feeds that guarantee fish health and growth performance without having a significant impact on the surrounding environment, both in terms of depletion of the fish's natural stocks and in terms of pressure on the terrestrial agriculture. The sustainability of aquaculture should be a priority when choosing next-generation ingredients.

Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides

Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.

Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater

BACKGROUND

Yeasts are gaining attention as alternative ingredients in aquafeeds. However, the impact of yeast inclusion on modulation of intestinal microbiota of fish fed plant-based ingredients is limited. Thus, the present study investigates the effects of yeast and processing on composition, diversity and predicted metabolic capacity of gut microbiota of Atlantic salmon smolt fed soybean meal (SBM)-based diet. Two yeasts, Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA), were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h, followed by spray-drying (ACJ and AWA). In a 42-day feeding experiment, fish were fed one of six diets: a fishmeal (FM)-based diet, a challenging diet with 30% SBM and four other diets containing 30% SBM and 10% of each of the four yeast products (i.e., ICJ, ACJ, IWA and AWA). Microbial profiling of digesta samples was conducted using 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models.

RESULTS

The microbial composition and predicted metabolic capacity of gut microbiota differed between fish fed FM diet and those fed SBM diet. The digesta of fish fed SBM diet was dominated by members of lactic acid bacteria, which was similar to microbial composition in the digesta of fish fed the inactivated yeasts (ICJ and IWA diets). Inclusion of autolyzed yeasts (ACJ and AWA diets) reduced the richness and diversity of gut microbiota in fish. The gut microbiota of fish fed ACJ diet was dominated by the genus Pediococcus and showed a predicted increase in mucin O-glycan degradation compared with the other diets. The gut microbiota of fish fed AWA diet was highly dominated by the family Bacillaceae.

CONCLUSIONS

The present study showed that dietary inclusion of FM and SBM differentially modulate the composition and predicted metabolic capacity of gut microbiota of fish. The inclusion of inactivated yeasts did not alter the modulation caused by SBM-based diet. Fish fed ACJ diet increased relative abundance of Pediococcus, and mucin O-glycan degradation pathway compared with the other diets.

From a cell model to a fish trial: Immunomodulatory effects of heat-killed Lactiplantibacillus plantarum as a functional ingredient in aquafeeds for salmonids

Paraprobiotics (dead/inactivated probiotics) are promising candidates in functional feeds to promote growth performance, modulate intestinal microbiota and enhance immune response of fish. During industrial production, fish are exposed to several stressful conditions such as handling, sub-optimal nutrition and diseases that can lead to reduced growth, increased mortalities and large economical losses. Such problems can be mitigated by use of functional feeds, leading to more-sustainable aquaculture and improved animal welfare. Lactiplantibacillus plantarum strain L-137 is a common bacterium found in fermented Southeast Asian dish made from fish and rice. The benefits of its heat-killed form (HK L-137) related to growth performance and immunomodulation have been studied in farmed fish such as Nile Tilapia (Oreochromis niloticus), striped catfish (Pangasianodon hypophthalmus) and bighead catfish (Clarias macrocephalus). To study if such benefits can also be observed in salmonids, we worked both at in vitro level using an intestinal epithelium cell line from rainbow trout (Oncorhynchus mykiss; RTgutGC) stimulated with HK L-137 (Feed LP20™) and at in vivo level with pre-smolt Atlantic salmon (Salmo salar) fed HK L-137 at different inclusion levels (20, 100 and 500 mg of Feed LP20™ kg-1 feed). In RTgutGC, the results showed that the barrier function of the cell monolayer was strengthened along with an increased production of IL-1β and a decreased production of Anxa1, indicating a modulation of the immune response. Interestingly, a similar trend was detected at the in vivo level in distal intestine from fish fed the highest inclusion level of HK L-137. Here, a lower production of Anxa1 was also detected (after a 61-day feeding period) in addition to an increase of total plasma IgM in the same group. Furthermore, the RNA-seq analysis showed that HK L-137 was able to modulate the gene expression of pathways related to molecular function, biological process and cellular component in distal intestine, without compromising fish performance and gut microbiota. Taken together, our study has shown that HK L-137 can modulate physiological response of Atlantic salmon, making fish more robust against stressful conditions during production.

Effects of functional ingredients on gut inflammation in Atlantic salmon (Salmo salar L)

Functional feed ingredients are frequently used in feeds for Atlantic salmon, often claimed to improve immune functions in the intestine and reduce severity of gut inflammation. However, documentation of such effects is, in most cases, only indicative. In the present study effects of two packages of functional feed ingredients commonly used in salmon production, were evaluated employing two inflammation models. One model employed soybean meal (SBM) as inducer of a severe inflammation, the other a mixture of corn gluten and pea meal (CoPea) inducing mild inflammation. The first model was used to evaluate effects of two packages of functional ingredients: P1 containing butyrate and arginine, and P2 containing β-glucan, butyrate, and nucleotides. In the second model only the P2 package was tested. A high marine diet was included in the study as a control (Contr). The six diets were fed to salmon (average weight of 177g) in saltwater tanks (57 fish per tank), in triplicate, for 69 days (754 ddg). Feed intake was recorded. The growth rate of the fish was high, highest for the Contr (TGC: 3.9), lowest for SBM fed fish (TGC: 3.4). Fish fed the SBM diet showed severe symptoms of inflammation in the distal intestine as indicated by histological, biochemical, molecular, and physiological biomarkers. The number of differently expressed genes (DEG) between the SBM and Contr fed fish was 849 and comprised genes indicating alteration in immune functions, cellular and oxidative stress, and nutrient digestion, and transport functions. Neither P1 nor P2 altered the histological and functional symptoms of inflammation in the SBM fed fish importantly. Inclusion of P1 altered expression of 81 genes, inclusion of P2 altered 121 genes. Fish fed the CoPea diet showed minor signs of inflammation. Supplementation with P2 did not change these signs. Regarding composition of the microbiota in digesta from the distal intestine, clear differences regarding beta-diversity and taxonomy between Contr, SBM, and CoPea fed fish were observed. In the mucosa the microbiota differences were less clear. The two packages of functional ingredients altered microbiota composition of fish fed the SBM and the CoPea diet towards that of fish fed the Contr diet.

Effects of dietary supplementation with prebiotics and Pediococcus acidilactici on gut health, transcriptome, microbiota, and metabolome in Atlantic salmon (Salmo salar L.) after seawater transfer

BACKGROUND

Given the importance of gut microbiota for health, growth and performance of the host, the aquaculture industry has taken measures to develop functional fish feeds aiming at modulating gut microbiota and inducing the anticipated beneficial effects. However, present understanding of the impact of such functional feeds on the fish is limited. The study reported herein was conducted to gain knowledge on performance and gut health characteristics in post-smolt Atlantic salmon fed diets varying in content of functional ingredients. Three experimental diets, a diet containing fructo-oligosaccharides (FOS), a diet with a combination of FOS and Pediococcus acidilactici (BC) and a diet containing galacto-oligosaccharides (GOS) and BC, were used in a 10-weeks feeding trial. A commercial diet without functional ingredients was also included as a control/reference. Samples of blood plasma, mucosa and digesta were subjected to microbiota, transcriptome and metabolome profiling for evaluation of the diet effects.

RESULTS

No significant growth differences were observed between fish fed the supplemented diets, but FOS-BC fed fish showed significantly faster growth than the control fed fish. The microbiota results showed that the BC was present in both the digesta, and the mucosa samples of fish fed the FOS-BC and GOS-BC diets. Digesta-associated microbiota was altered, while mucosa-associated microbiota was relatively unaffected by diet. Replacing FOS with GOS increased the level of metabolites linked to phospholipid, fatty acid, carnitine and sphingolipid metabolism. Variation in metabolite levels between the treatments closely correlated with genera mainly belonging to Firmicutes and Actinobacteria phyla. The transcriptome analyses indicated diet effects of exchanging FOS with GOS on immune functions, oxidative defense and stress responses. No significant diet effect was observed on intestinal inflammation in the pyloric caeca or in the distal intestine, or on lipid accumulation in the pyloric caeca.

CONCLUSIONS

Dietary supplementation with BC induced moderate effects on the microbiota of the digesta, while the effects of replacing FOS with GOS were more marked and was observed also for nutrient metabolism. Our data indicates therefore that the quality of a prebiotic may be of great importance for the effects of a probiotic on gut microbiota, function, and health.

Dietary Fish Meal Level and a Package of Choline, β-Glucan, and Nucleotides Modulate Gut Function, Microbiota, and Health in Atlantic Salmon (Salmo salar, L.)

Steatosis and inflammation have been common gut symptoms in Atlantic salmon fed plant rich diets. Choline has recently been identified as essential for salmon in seawater, and β-glucan and nucleotides are frequently used to prevent inflammation. The study is aimed at documenting whether increased fishmeal (FM) levels (8 levels from 0 to 40%) and supplementation (Suppl) with a mixture of choline (3.0 g/kg), β-glucan (0.5 g/kg), and nucleotides (0.5 g/kg) might reduce the symptoms. Salmon (186 g) were fed for 62 days in 16 saltwater tanks before samples were taken from 12 fish per tank for observation of biochemical, molecular, metabolome, and microbiome indicators of function and health. Steatosis but no inflammation was observed. Lipid digestibility increased and steatosis decreased with increasing FM levels and supplementation, seemingly related to choline level. Blood metabolites confirmed this picture. Genes in intestinal tissue affected by FM levels are mainly involved in metabolic and structural functions. Only a few are immune genes. The supplement reduced these FM effects. In gut digesta, increasing FM levels increased microbial richness and diversity, and changed the composition, but only for unsupplemented diets. An average choline requirement of 3.5 g/kg was indicated for Atlantic salmon at the present life stage and under the present condition.

Atlantic Salmon (Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness

The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.

Improvement of Fish Growth and Metabolism by Oligosaccharide Prebiotic Supplement

Finfish aquaculture is expected to continue to benefit from significantly improved fish diets, which are the source of energy to support the growth and health of fish. Strategies to enhance the transformation rate of dietary energy and protein to fish growth are greatly desired by fish culturists. Prebiotic compounds can be used as supplements to human, animal, and fish diets to populate beneficial bacteria in the gut. The goal of the present study is to identify low-cost prebiotic compounds with high efficacy in increasing the absorption of food nutrients by fish. Several oligosaccharides were evaluated as prebiotics in Nile tilapia (Oreochromis niloticus), one of the most widely cultured species in the world. Several parameters of the fish on different diets were evaluated, including feed conversion ratios (FCRs), enzymatic activities, expression of growth-related genes, and the gut microbiome. Two age groups of fish (30 days old and 90 days old) were used in this study. The results indicated that the addition of xylooligosaccharide (XOS), galactooligosaccharide (GOS), or XOS and GOS combination to the basic fish diet significantly decreased the feed conversion ratio (FCR) of the fish in both age groups. Both XOS and GOS decreased the FCR of 30-day-old fish by 34.4% compared to the fish on the control diet. In the 90-day-old fish group, XOS and GOS decreased the FCR by 11.9%, while the combination of the two prebiotics led to a 20.2% decrease in FCR compared to the control group. The application of XOS and GOS also elevated the production of glutathione-related enzymes and the enzymatic activity of glutathione peroxidase (GPX), indicating the enhancement of antioxidation processes in fish. These improvements were associated with significant changes in the fish gut microbiota. The abundance of Clostridium ruminantium, Brevinema andersonii, Shewanella amazonensis, Reyranella massiliensis, and Chitinilyticum aquatile were upregulated by XOS and GOS supplements. The findings of the present study suggested that the prebiotics would be more effective when they were applied to the younger fish, and the application of multiple oligosaccharide prebiotic compounds could result in a greater growth enhancement. The identified bacteria can be potentially used as probiotic supplements in the future to improve fish growth and feeding efficiency and ultimately reduce the cost of tilapia aquaculture.

Modulatory effect of Gracilaria gracilis on European seabass gut microbiota community and its functionality

Seaweeds are an important source of nutrients and bioactive compounds and have a high potential as health boosters in aquaculture. This study evaluated the effect of dietary inclusion of Gracilaria gracilis biomass or its extract on the European seabass (Dicentrarchus labrax) gut microbial community. Juvenile fish were fed a commercial-like diet with 2.5% or 5% seaweed biomass or 0.35% seaweed extract for 47 days. The gut microbiome was assessed by 16S rRNA amplicon sequencing, and its diversity was not altered by the seaweed supplementation. However, a reduction in Proteobacteria abundance was observed. Random forest analysis highlighted the genera Photobacterium, Staphylococcus, Acinetobacter, Micrococcus and Sphingomonas, and their abundances were reduced when fish were fed diets with algae. SparCC correlation network analysis suggested several mutualistic and other antagonistic relationships that could be related to the predicted altered functions. These pathways were mainly related to the metabolism and biosynthesis of protective compounds such as ectoine and were upregulated in fish fed diets supplemented with algae. This study shows the beneficial potential of Gracilaria as a functional ingredient through the modulation of the complex microbial network towards fish health improvement.

Conventional Soybean Meal as Fishmeal Alternative in Diets of Japanese Seabass (Lateolabrax japonicus): Effects of Functional Additives on Growth, Immunity, Antioxidant Capacity and Disease Resistance

Aiming to optimize soymeal-based diets for Japanese seabass (Lateolabrax japonicas), a 105-day feeding trial was conducted to evaluate the effects of functional additives, including antioxidants (ethoxyquin, thymol and carvacrol) and chelated trace elements (Cu, Mn and Zn), on the growth, immunity, antioxidant capacity and disease resistance of fish fed diets with conventional soybean meal replacing 50% of fishmeal. Three isonitrogenous (45%) and isolipidic (11%) diets were formulated: (1) standard reference diet (FM, 42% fishmeal); (2) soymeal-based diet (SBM, 21% fishmeal and 30% conventional soybean meal); (3) SBM diet supplemented 0.0665% functional additives (FAS). Each experimental diet was randomly fed to quadruplicate groups of forty feed-trained Japanese seabass (initial average body weight = 125.6 ± 0.6 g) stocked in a saltwater floating cage. Upon the conclusion of the feeding trial, lower feed intake was observed in fish fed SBM compared to those fed FM and FAS. Fish fed FM showed the highest growth performance, estimated as the weight gain rate. Notably, FAS supported faster growth of fish than those fed SBM, indicating the optimal growth performance of dietary functional additives. The feed conversion rate showed the opposite trend among dietary treatments, with the highest value in fish fed SBM. Regarding immunity, fish fed soymeal-based diets suppressed the serum alternative complement pathway activities compared to FM, whereas the respiratory burst activity in macrophages of head kidneys showed a similar picture, but no statistical differences were observed. Further, fish fed soymeal-based diets had lower serum Cu-Zn SOD, CAT and GPx activities as well as liver vitamin E levels and scavenging rates of hydroxyl radical but higher liver MDA contents compared to the FM-fed group. Fish fed FAS had higher serum Cu-Zn SOD and GPx activities and liver vitamin E levels than those fed SBM, suggesting the enhancement of antioxidant capacity of dietary functional additives. For the disease resistance against Vibrio harveyi infection, fish fed SBM had the highest cumulative mortality, followed by the FAS and FM groups. Additionally, the biomarkers related to the immune and antioxidant capacities had a positive correlation with the relative abundance of Paracoccus and Pseudomonas, while liver MDA levels had a negative correlation with the relative abundance of Pseudomonas and Psychrobacter. Collectively, soymeal replacing 50% of fishmeal suppressed the growth, immunity, antioxidant capacity and disease resistance of Japanese seabass, while dietary supplementation of antioxidants and chelated trace elements could mitigate soymeal-induced adverse effects on growth and disease resistance through the improvement in antioxidant capacity and regulation of gut microbiota.

Alternative Proteins for Fish Diets: Implications beyond Growth

Aquaculture has been challenged to find alternative ingredients to develop innovative feed formulations that foster a sustainable future growth. Given the most recent trends in fish feed formulation on the use of alternative protein sources to decrease the dependency of fishmeal, it is fundamental to evaluate the implications of this new paradigm for fish health and welfare. This work intends to comprehensively review the impacts of alternative and novel dietary protein sources on fish gut microbiota and health, stress and immune responses, disease resistance, and antioxidant capacity. The research results indicate that alternative protein sources, such as terrestrial plant proteins, rendered animal by-products, insect meals, micro- and macroalgae, and single cell proteins (e.g., yeasts), may negatively impact gut microbiota and health, thus affecting immune and stress responses. Nevertheless, some of the novel protein sources, such as insects and algae meals, have functional properties and may exert an immunostimulatory activity. Further research on the effects of novel protein sources, beyond growth, is clearly needed. The information gathered here is of utmost importance, in order to develop innovative diets that guarantee the production of healthy fish with high quality standards and optimised welfare conditions, thus contributing to a sustainable growth of the aquaculture industry.

Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host

The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections.

Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals

The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.

Feed microbiome: confounding factor affecting fish gut microbiome studies

There is an increasing interest in the impact of feed on the fish gut microbiome. Most of the studies are based on sequencing the bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well as dead bacteria. It has not been a common practice to include the feed as control, although it contains various nutritious ingredients that microorganisms can use before or after feed preparation. Thus, study designs using digesta as a proxy for the intestinal microbiome raise the concern that composition of the gut microbiome might be biased by carry-over of microbial DNA from the feed itself. Here we report analysis of 15 feeds and representative intestinal digesta of Atlantic salmon (Salmo salar) from five independent case studies. This allowed us to identify "feed microbiomes" that were microbially diverse and shared taxa with digesta microbiomes. Digesta-specific microbiomes were identified, though they were mainly enriched by a few taxa, such as Mycoplasma and Ruminococcaceae. Overall, findings are consistent with a model wherein gut microbial profiles are to a different degree influenced by bacterial DNA present in the feed itself through a "feed microbiome" carry-over effect.

Modulation of Atlantic salmon (Salmo salar) gut microbiota composition and predicted metabolic capacity by feeding diets with processed black soldier fly (Hermetia illucens) larvae meals and fractions

BACKGROUND

Black soldier fly (Hermetia illucens) is a promising insect species to use as a novel ingredient in fish feeds. Black soldier fly larvae consists of three major fractions, namely protein, lipid, and exoskeleton. These fractions contain bioactive compounds that can modulate the gut microbiota in fish such as antimicrobial peptides, lauric acid, and chitin. However, it is not certain how, or which fractions of black solider fly would affect gut microbiota in fish. In the present study, black soldier fly larvae were processed into three different meals (full-fat, defatted and de-chitinized) and two fractions (oil and exoskeleton), and included in diets for Atlantic salmon (Salmo salar). Atlantic salmon pre-smolts were fed with these diets in comparison with a commercial-like control diet for eight weeks to investigate the effects of insect meals and fractions on the composition and predicted metabolic capacity of gut microbiota. The gut microbiota was profiled by 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models.

RESULTS

The inclusion of insect meals and fractions decreased abundance of Proteobacteria and increased abundance of Firmicutes in salmon gut. The diets that contained insect chitin, i.e., insect meals or exoskeleton diets, increased abundance of chitinolytic bacteria including lactic acid bacteria and Actinomyces in salmon gut, with fish fed full-fat meal diet showing the highest abundances. The diets that contained insect lipids, i.e., insect meals and oil diets enriched Bacillaceae in fish gut. The fish fed diets containing full-fat insect meal had a unique gut microbiota composition dominated by beneficial lactic acid bacteria and Actinomyces, and showed a predicted increase in mucin degradation compared to the other diets.

CONCLUSIONS

The present results showed that the dietary inclusion of insect meals and fractions can differently modulate the composition and predicted metabolic capacity of gut microbiota in Atlantic salmon pre-smolts. The use of full-fat black soldier fly larvae meal in diets for salmon is more favorable for beneficial modulation of gut microbiota than larvae processed by separation of lipid or exoskeleton fractions.

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets

BACKGROUND

Being part of fish's natural diets, insects have become a practical alternative feed ingredient for aquaculture. While nutritional values of insects have been extensively studied in various fish species, their impact on the fish microbiota remains to be fully explored. In an 8-week freshwater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially relevant reference diet or an insect meal diet wherein black soldier fly (Hermetia illucens) larvae meal comprised 60% of total ingredients. Microbiota of digesta and mucosa origin from the proximal and distal intestine were collected and profiled along with feed and water samples.

RESULTS

The insect meal diet markedly modulated the salmon intestinal microbiota. Salmon fed the insect meal diet showed similar or lower alpha-diversity indices in the digesta but higher alpha-diversity indices in the mucosa. A group of bacterial genera, dominated by members of the Bacillaceae family, was enriched in salmon fed the insect meal diet, which confirms our previous findings in a seawater feeding trial. We also found that microbiota in the intestine closely resembled that of the feeds but was distinct from the water microbiota. Notably, bacterial genera associated with the diet effects were also present in the feeds.

CONCLUSIONS

We conclude that salmon fed the insect meal diets show consistent changes in the intestinal microbiota. The next challenge is to evaluate the extent to which these alterations are attributable to feed microbiota and dietary nutrients, and what these changes mean for fish physiology and health.

Lactococcus lactis Expressing Type I Interferon From Atlantic Salmon Enhances the Innate Antiviral Immune Response In Vivo and In Vitro

In salmon farming, viruses are responsible for outbreaks that produce significant economic losses for which there is a lack of control tools other than vaccines. Type I interferon has been successfully used for treating some chronic viral infections in humans. However, its application in salmonids depends on the proper design of a vehicle that allows its massive administration, ideally orally. In mammals, administration of recombinant probiotics capable of expressing cytokines has shown local and systemic therapeutic effects. In this work, we evaluate the use of Lactococcus lactis as a type I Interferon expression system in Atlantic salmon, and we analyze its ability to stimulate the antiviral immune response against IPNV, in vivo and in vitro. The interferon expressed in L. lactis, even though it was located mainly in the bacterial cytoplasm, was functional, stimulating Mx and PKR expression in CHSE-214 cells, and reducing the IPNV viral load in SHK-1 cells. In vivo, the oral administration of this L. lactis producer of Interferon I increases Mx and PKR expression, mainly in the spleen, and to a lesser extent, in the head kidney. The oral administration of this strain also reduces the IPNV viral load in Atlantic salmon specimens challenged with this pathogen. Our results show that oral administration of L. lactis producing Interferon I induces systemic effects in Atlantic salmon, allowing to stimulate the antiviral immune response. This probiotic could have effects against a wide variety of viruses that infect Atlantic salmon and also be effective in other salmonids due to the high identity among their type I interferons.

Different Responses of Microbiota across Intestinal Tract to Enterococcus faecium HDRsEf1 and Their Correlation with Inflammation in Weaned Piglets

Enterococcus faecium HDRsEf1 (HDRsEf1) was identified to reduce the incidence of diarrhea in weaned piglets, but the mechanism has not been elucidated yet. Based on the fact that gut microbiota plays a crucial role in regulating inflammatory responses, the effects of HDRsEf1 on microbiota across the intestinal tract in weaned piglets were investigated. Microbiota from the luminal contents and the mucosa of the ileum, cecum, and colon of HDRsEf1-treated piglets were explored by 16S rRNA sequencing and qPCR. It was demonstrated that microbiota in different gut niches responded specifically to HDRsEf1, with major alterations occurring in the ileum and cecum. The total bacterial load of microbiota in ileal luminal contents and the relative abundance of Escherichia-Shigella in the ileal mucosa was significantly down-regulated by HDRsEf1 administration, while the relative abundance of butyrate-producing bacteria (including Clostridiaceae-1, Rumencoccidae, and Erysipelotrichaceae) in cecal luminal contents was significantly up-regulated. Moreover, the utilization of HDRsEf1 improved intestinal morphological development and reduced the inflammatory response, which were negatively correlated with the relative abundance of Escherichia-Shigella in the ileal mucosa and butyrate-producing bacteria in cecal luminal contents, respectively. Collectively, this study suggests that the administration of HDRsEf1 alters gut microbiota, thereby alleviating inflammation and improving intestinal morphological development in weaned piglets.

Culture-Independent and Culture-Dependent Characterization of the Black Soldier Fly Gut Microbiome Reveals a Large Proportion of Culturable Bacteria with Potential for Industrial Applications

Black soldier fly larvae (BSFL) are fast-growing, resilient insects that can break down a variety of organic substrates and convert them into valuable proteins and lipids for applications in the feed industry. Decomposition is mediated by an abundant and versatile gut microbiome, which has been studied for more than a decade. However, little is known about the phylogeny, properties and functions of bacterial isolates from the BSFL gut. We therefore characterized the BSFL gut microbiome in detail, evaluating bacterial diversity by culture-dependent methods and amplicon sequencing of the 16S rRNA gene. Redundant strains were identified by genomic fingerprinting and 105 non-redundant isolates were then tested for their ability to inhibit pathogens. We cultivated representatives of 26 genera, covering 47% of the families and 33% of the genera detected by amplicon sequencing. Among these isolates, we found several representatives of the most abundant genera: Morganella, Enterococcus, Proteus and Providencia. We also isolated diverse members of the less-abundant phylum Actinobacteria, and a novel genus of the order Clostridiales. We found that 15 of the isolates inhibited at least one of the tested pathogens, suggesting a role in helping to prevent colonization by pathogens in the gut. The resulting culture collection of unique BSFL gut bacteria provides a promising resource for multiple industrial applications.

Processed Animal Proteins from Insect and Poultry By-Products in a Fish Meal-Free Diet for Rainbow Trout: Impact on Intestinal Microbiota and Inflammatory Markers

Sustainability of aquaculture is tied to the origin of feed ingredients. In search of sustainable fish meal-free formulations for rainbow trout, we evaluated the effect of Hermetia illucens meal (H) and poultry by-product meal (P), singly (10, 30, and 60% of either H or P) or in combination (10% H + 50% P, H10P50), as partial replacement of vegetable protein (VM) on gut microbiota (GM), inflammatory, and immune biomarkers. Fish fed the mixture H10P50 had the best growth performance. H, P, and especially the combination H10P50 partially restored α-diversity that was negatively affected by VM. Diets did not differ in the Firmicutes:Proteobacteria ratio, although the relative abundance of Gammaproteobacteria was reduced in H and was higher in P and in the fishmeal control. H had higher relative abundance of chitin-degrading Actinomyces and Bacillus, Dorea, and Enterococcus. Actinomyces was also higher in H feed, suggesting feed-chain microbiome transmission. P increased the relative abundance of protein degraders Paeniclostridium and Bacteroidales. IL-1β, IL-10, TGF-β, COX-2, and TCR-β gene expression in the midgut and head kidney and plasma lipopolysaccharide (LPS) revealed that the diets did not compromise the gut barrier function or induce inflammation. H, P, and H10P50 therefore appear valid protein sources in fishmeal-free aquafeeds.

The Use of Defatted Tenebrio molitor Larvae Meal as a Main Protein Source Is Supported in European Sea Bass (Dicentrarchus labrax) by Data on Growth Performance, Lipid Metabolism, and Flesh Quality

Objective

This study aims to determine the maximal inclusion level of defatted (d-) Tenebrio molitor larvae meal (TM) able to replace dietary fishmeal (FM) without compromising growth performance, general metabolism, and flesh quality traits in European sea bass, and to evaluate the major underlying physiological mechanisms.

Materials and Methods

Fish (55 ± 2 g) were fed with diets containing increasing levels of dTM: 0, 40, 80 and 100% (CTRL, TM40, TM80, and TM100, respectively) to replace FM. After 10 weeks of feeding, the growth performance, nutrient and energy balance, intestinal integrity, plasma metabolites and the expression of genes related to growth and nutrient metabolism, in liver and muscle were determined. The fatty acids (FA) profile, textural properties and color were also evaluated in muscle.

Results

Protein and lipids digestibility remained unaltered up to 80% dTM inclusion. Growth performance parameters were similar among dietary treatments. The dTM inclusion increased the hepatosomatic index in fish fed TM100. Muscle eicosapentaenoic acid, docosahexaenoic acid and n-3 long-chain polyunsaturated FA levels were maintained up to 80% dTM inclusion, but total cholesterol and non-esterified FA increased with dietary dTM inclusion. In liver, the expression of elongation of very long-chain FA protein 6 (elovl6) and FA desaturase 2 (fads2) did not change in fish fed TM40 and TM80, but elovl6 decreased whilst fads2 increased in fish fed TM100 when compared to those fed CTRL. The expression of cholesterol 7 alpha-monooxygenase (cyp7a1) decreased with dietary dTM inclusion. In muscle, the expression of myoblast determination protein-2 (myod2) decreased in fish fed TM80 and TM100.

Conclusion

It is feasible to substitute dietary FM by dTM up to 80% in European sea bass without detrimental effects on nutrient digestibility, growth performance and associated genetic pathways, whilst assuring fillet nutritional value for human consumption.