Partial Evaluation of Autochthonous Probiotic Potential of the Gut Microbiota of Seriola lalandi

Promising Probiotic Candidates for Sustainable Aquaculture: An Updated Review

With the intensification of aquaculture to meet the rising demands of fish and shellfish, disease outbreaks during the larval and adult stages are a major challenge faced by aqua culturists. As the prophylactic use of vaccines and antibiotics has several limitations, research is now focused on sustainable alternatives to vaccines and antibiotics, e.g., medicinal plants, probiotics, postbiotics, prebiotics, and synbiotics, as promising candidates to strengthen the immune response of fish and shellfish and to control disease outbreaks. With respect to probiotics, numerous studies are available revealing their health-promoting and beneficial impacts in aquaculture. However, most studies focus on Bacillus and Lactobacillus species. Keeping in view the positive effects of probiotic lactic acid bacteria in aquaculture, researchers are now looking for other probiotic bacteria that can be used in aquaculture. Recently, many non-lactic acid bacteria (non-LAB), which are mainly host-associated, have been reported to reveal beneficial effects in fish and shellfish aquaculture. The main non-LAB probiotic genera are Bifidobacterium, Clostridium, Microbacterium, Micrococcus, Paenibacillus, Acinetobacter, Alcaligenes, Enterobacter, Phaeobacter Pseudoalteromonas, Pseudomonas, Pseudomonas, and Vibrio. Despite the promising effects of non-LAB probiotics, comparably, there is limited available information in this context. This review focuses only on probiotic strains that are non-LAB, mostly isolated from the host digestive tract or rearing water, and discusses their beneficial effects in fish and shellfish aquaculture. This review will provide detailed information on the use of various non-LAB bacteria and provide a roadmap to future studies on new probiotics for sustainable aquaculture.

Longitudinal Microbiome Investigations Reveal Core and Growth-Associated Bacteria During Early Life Stages of Scylla paramamosain

In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. In this study, we first characterized stage-specific microbiomes and shifts in the contributions of live feed and water via SourceTracker. We observed decreased microbial diversity and increased priority effects along zoea stages. Psychobacter was identified as the core genus, whereas Lactobacillus was the hub genus connecting different stages. Second, microbial correlations with various stage-specific growth traits were observed under interventions generating enhanced (probiotic mixture enrichment), normal (control), and reduced (antibiotic treatment) microbiomes. By combining machine learning regression and bioinformatics analysis, we identified four candidate growth performance-associated probiotics belonging to Rhodobacterales, Sulfitobacter, Confluentimicrobium, and Lactobacillus, respectively. Our study interpreted the dynamics and origins of the Scylla paramamosain zoea microbiome and underscored the importance of optimizing potential probiotics to increase growth performance during early life stages in marine invertebrates for effective larviculture.

A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.

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.

Trans-Anethole Alleviates DSS-Induced Ulcerative Colitis by Remodeling the Intestinal Flora to Regulate Immunity and Bile Acid Metabolism

Ulcerative colitis (UC) is the most common inflammatory bowel disease (IBD); it is incurable, and the treatment is expensive. Trans-anethole (TA), the main component of fennel, exhibits various biological activities. An increasing number of studies have demonstrated the efficacy of herbal active ingredients in the treatment of UC. This study aimed to investigate the effect and mechanism of TA in UC. In this study, we have experimented on mice with dextran sulfate sodium salt (DSS)-induced UC. The TA group was gavaged with 62.5 mg/kg TA by gavage once daily on days 8-14. To observe the effect of TA on the colon tissue, various investigations were performed, including western blot and immunohistochemistry for intestinal barrier protein expression, TUNEL staining for apoptosis, western blot, and ELISA for inflammation level, flow cytometry for Th17/Treg, LC-MS for blood bile acid content, GC-MS for blood fatty acid content, and 16s RNA for intestinal contents. TA alleviated weight loss in mice with UC; increased colon length; alleviated intestinal mucosal damage; upregulated claudin-1, occludin, and ZO-1 protein expression levels; reduced inflammatory factors in the colon and serum; and alleviated apoptosis. TA reduced fatty acid and bile acid levels by inhibiting colony abundance and reducing Th17/Treg cell differentiation in the colon. We found that TA alleviates DSS-induced UC by remodeling the intestinal flora to regulate immunity and bile acid metabolism.

Shewanella spp. from wastewater treatment plant-affected environment: isolation and characterization

Bacteria from the genus Shewanella are inhabitants of marine and freshwater ecosystems, recognized fish spoilage bacteria, but less known as fish disease agents. Shewanella spp. isolated from fish living in waters close to effluents of a wastewater treatment plant (WWTP) were not previously characterized. We have tested Shewanella isolates from WWTP-affected waters and related fish. Genotypic characterization identified most strains as S. baltica and S. oneidensis. In order to investigate the sensibility and accuracy of their MALDI-TOF MS identification, they were grown on two culture media enriched by various NaCl concentrations, incubated at different temperatures and duration. We analyzed their antimicrobial susceptibility on a panel of antimicrobial drugs and capacity for biofilm production. With a view to demonstrate their capacity to produce fatty acids, we assessed the impact of different culture media on their lipid profile. We performed zebrafish embryotoxicity tests to simulate the environmental infection of the earliest life stages in S. baltica-contaminated waters. The best MALDI-TOF MS identification scores were for strains cultivated on TSA for 24 h at 22 °C and with supplementation of 1.5% NaCl. Less than 17% of isolates demonstrated antimicrobial resistance. Most isolates were weak biofilm producers. Strain-to-strain variation of MIC and MBC was low. The major fatty acids were C15:0, C16:0, C16:1, C17:1, and iC15:0. Exposure of Danio rerio to different S. baltica concentrations induced severe effects on zebrafish development: decreased heartbeat rate, locomotor activity, and melanin pigmentation. S. baltica passed through chorionic pores of zebrafish.

Sub-lethal concentration of metamifop exposure impair gut health of zebrafish (Danio rerio)

Previous studies have demonstrated that sublethal metamifop exposures induce hepatic lipid metabolism disorder in zebrafish. Whether metamifop will cause adverse effects in zebrafish gut is unknown. In the present study, effects of metamifop on gut heath of zebrafish were investigated after sublethal concentration (0.025, 0.10 and 0.40 mg/L) exposure. Histopathology analysis showed that metamifop induced inflammation and reduction of goblet cells in the gut, indicating that gut health may be impaired. Metamifop exposure could reduce activities of digestive enzymes (lipase and alkaline phosphatase), indicating the capacity of lipid absorption were impaired. Meanwhile, the content of fatty acid-binding protein 2 (FABP2) and mRNA levels of related genes (apoa-1a, apoe-b, fatp4, lpl and fabp2) were reduced in zebrafish gut after exposure to metamifop, suggesting the lipid transportation were decreased. The transcripts of genes associated with inflammation (il-17c, tnf-α and nf-kb) were significantly increased in 0.40 mg/L metamifop treatment group, which were 1.90-, 1.53- and 2.77-fold of the control group, respectively, confirming that metamifop induced inflammatory response in zebrafish gut. Moreover, reduction of mRNA levels of cldn-15 and elevation of lipopolysaccharides (LPS) content were observed in metamifop-treated groups, which suggested that metamifop exposure increased the intestinal permeability. Furthermore, metamifop exposure decreased the relative abundance of beneficial bacteria (Psychrobacter and Aeromonas) and elevated the abundance of pathogenic bacteria (Rhodobacter and Ralstonia) in zebrafish intestine. These results indicated that metamifop exposure at sublethal concentrations would impair zebrafish gut health, via reduction of lipids absorption, inflammatory response, elevation of permeability and microbiota disorder.

Potential Role of Gastrointestinal Microbiota in Growth Regulation of Yellowtail Kingfish Seriola lalandi in Different Stocking Densities

A 90-day study was performed under three different stocking densities, including high density (10,000 fishes/cage), medium density (8000 fishes/cage), and low density (6000 fishes/cage), in a deep-sea net cage for yellowtail kingfish (Seriola lalandi). The physiological characteristics and growth performance were tested, and structural characteristics of the gastrointestinal microbiota were systematically analyzed. The results show that fishes with high density had a lower weight gain rate and a specific growth rate, as well as higher serum cortisol content. The diversity, types and numbers of dominant microbiota with significant differences, and the numbers of shared genera among the different groups all changed. Core genera in the gastrointestinal tract were obtained according to the principles of dominance, commonality, and difference. The changes in the relative abundance of the core genera might be related to the growth and physiological characteristics of the host. The ratio of Firmicutes to Bacteroidetes in the stomach and pyloric caecum, which favors the accumulation of energy by the host from the diet, was higher in the medium-density group than in the other groups. This indicates that the higher density could cause physiological stress and affect growth performance. In order to reduce the resulting growth differences, gastrointestinal microbiota might assist the host in accumulating energy, participating in the energy distribution by adjusting its structure. Based on the growth, physiology, and production practices, the medium density was the appropriate density in this study. This study provides a reference for the improvement of deep-sea culture technology and the promotion of healthy growth through the gastrointestinal microecological regulation of yellowtail kingfish.

Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment "BE" and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut "allochthonous" microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.

Lactobacillus rhamnosus GG Reduces β-conglycinin-Allergy-Induced Apoptotic Cells by Regulating Bacteroides and Bile Secretion Pathway in Intestinal Contents of BALB/c Mice

Allergy can cause intestinal damage, including through cell apoptosis. In this study, intestinal cell apoptosis was first observed in the β-conglycinin (β-CG) allergy model, and the effect of Lactobacillus rhamnosus GG (LGG) on reducing apoptosis of cells in the intestine and its underlying mechanisms were further investigated. Allergic mice received oral LGG daily, and intestinal tissue apoptotic cells, gut microbiota, and metabolites were evaluated six and nine days after intervention. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) analysis revealed that LGG intervention could reduce the incidence of cell apoptosis more effectively than natural recovery (NR). The results of 16S rRNA analysis indicated that LGG intervention led to an increase in the relative abundance of Bacteroides. Metabolite analysis of intestinal contents indicated that histamine, N-acetylhistamine, N(α)-γ-glutamylhistamine, phenylalanine, tryptophan, arachidonic acid malate, and xanthine were significantly decreased, and deoxycholic acid, lithocholic acid were significantly increased after the LGG intervention on β-CG allergy; the decreases in histamine and N(α)-γ-glutamylhistamine were significant compared with those of NR. In conclusion, LGG reduces apoptosis of cells induced by β-CG allergy, which may be related to regulation of Bacteroides and the bile secretion pathway.

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

BACKGROUND

The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery.

RESULTS

Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT.

CONCLUSION

As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish (Seriola lalandi)

Fish skin and gut microbiomes contribute to host health and growth and are often significantly different in aquaculture-reared fish compared to wild fish. Determining how factors associated with aquaculture, including altered diet and abiotic conditions, affect the microbiome will assist with optimizing farming practices and non-invasively assessing fish health. Here, juvenile yellowtail kingfish (Seriola lalandi) housed at optimal (22 °C) and non-optimal (26 °C) water temperature were fed a fishmeal control diet or the same diet substituted with 30% soy-protein concentrate (SPC) in order to investigate impacts on host health and the microbial community composition of the skin mucosa, gut mucosa and digesta. Each of these sites was observed to have a distinct microbiome composition. The combination of SPC and housing at 26 °C significantly reduced weight gain in yellowtail kingfish and affected immune parameters. The overall microbial composition and relative abundance of specific operational taxonomic units (OTUs) was also significantly altered by inclusion of SPC at 26 °C, with a notable increase in an OTU identified as Photobacterium in the skin mucosa and digesta. Increased relative abundance of Photobacterium sp. was significantly correlated with reduced levels of digesta myeloperoxidase in yellowtail kingfish; a recognized innate immunity defense mechanism. The changes in the microbial communities of yellowtail kingfish fed a diet containing 30% SPC at 26 °C highlights the importance of considering the interactive effects of diet and environmental factors on microbiome health in farmed yellowtail kingfish.