Open research questions in Aquaculture disease management and microbiota

What the literature leaves open

• The increasing scarcity and rising cost of fishmeal have promoted the substitution of plant-based protein sources in modern aquafeeds. High dietary inclusion of raw mulberry leaf impairs growth in carnivorous fish. The dose-dependent effects and underlying mechanisms of fermented mulberry leaf in Acipenser schrenckii remain unclear.

  Dietary Fermented Mulberry Leaf Triggers Dose-Dependent Changes in Growth, Antioxidant Immune Status and Intestinal Microecology of Amur Sturgeon (Acipenser schrenckii) · 2026 · DOI

• Further research is needed to explore the effects of FML on other fish species, - The optimal dosage of FML for other fish species needs to be determined, - The long-term effects of FML on fish health and growth need to be studied

  Dietary Fermented Mulberry Leaf Triggers Dose-Dependent Changes in Growth, Antioxidant Immune Status and Intestinal Microecology of Amur Sturgeon (Acipenser schrenckii) · 2026 · DOI

• The intestinal microbial, transcriptional, and metabolic responses of hybrid sturgeon to N. seriolae infection are not well understood. Prior studies have not investigated the mechanisms of N. seriolae infection in hybrid sturgeon using multi-omics profiling.

  Multi-omics profiling identifies intestinal microbial shifts and tissue-specific immunometabolic changes associated with experimental Nocardia seriolae challenge in hybrid sturgeon (Acipenser baerii♀ × Acipenser schrenckii♂) · 2026 · DOI

• Substantial losses from bacterial pathogens Vibrio anguillarum and Streptococcus iniae. Poor understanding of the immune mechanisms involved in fish infections by V. anguillarum and S. iniae. Need to develop targeted vaccination strategies.

  Expression and Immune Response Profiles in Nile Tilapia (Oreochromis niloticus) and European Sea Bass (Dicentrarchus labrax) During Pathogen Challenge and Infection · 2024 · DOI

• However, the extent to which aquaculture production systems restructure these communities remains poorly defined.

  Meta-analysis of gut microbiome in largemouth bass (Micropterus salmoides) under different aquaculture systems · 2026 · DOI

• However, the simultaneous responses of both microbial fractions to bacterial infection remain poorly explored in aquaculture species.

  Staphylococcus haemolyticus Infection Modifies Bacterial and Microeukaryotic Gut Communities in Nile Tilapia · 2026 · DOI

• Understanding the diversity and function of fish gut microbiomes has advanced substantially, yet many aspects remain poorly understood, particularly the interplay among microbiota, host species, and environmental factors in the context of conservation.

  Fish gut microbiome and its application in aquaculture and biological conservation · 2025 · DOI

• While adult rainbow trout are known to be sensitive, there is limited research on the response of early life stages to 6PPD-Q exposure.

  Subchronic and Acute Toxicity of 6PPD-Quinone to Early Life Stage Rainbow Trout ( Oncorhynchus mykiss ) · 2025 · DOI

• Although bony fish have CD8+ T cells, the mechanisms by which these early-evolved cytotoxic cells combat intracellular pathogens remain unclear.

  Fish requires FasL to facilitate CD8+ T-cell function and antimicrobial immunity · 2025 · DOI

• This differentiation process is scarcely characterized in teleost fish, in which B cells have been shown to share many functional and phenotypic characteristics of mammalian B1 innate subsets.

  Teleost IgM+ plasma-like cells: beyond antibody secretion · 2025 · DOI

• The function of the ILT remains elusive, and research has focused primarily on its T cell content.

  B-cell distribution and composition in the gills and the interbranchial lymphoid tissue (ILT) of the Atlantic salmon (Salmo salar L.) · 2025 · DOI

• Despite the belief that it possesses antiviral properties, the underlying mechanisms remain unclear.

  Ammonium chloride mitigates the amplification of fish virus by blocking autophagy-dependent replication · 2025 · DOI

• Although the causes for pathogen evolution and emergence were not fully elucidated, our results strongly suggest that the vapA- absent strain is responsible for a raising proportion of recent furunculosis cases, and that it may be related to a less virulent disease and a low serological response upon vaccination with the A.

  Major antigenic differences in Aeromonas salmonicida isolates correlate with the emergence of a new strain causing furunculosis in Chilean salmon farms · 2025 · DOI

• However, the changes in muscle quality and gut microbiota of shrimp in the live supply chain and their interactions are poorly understood.

  Changes in Muscle Quality and Gut Microbiota of Whiteleg Shrimp (Penaeus vannamei) Within a Live Supply Chain · 2025 · DOI

• However, the relationship between mucosal commensal microbiota, intestinal metabolites, and host environmental adaptability under heat stress remains poorly understood.

  Analysis of the Alterations in Symbiotic Microbiota and Their Correlation with Intestinal Metabolites in Rainbow Trout (Oncorhynchus mykiss) Under Heat Stress Conditions · 2025 · DOI

• Further studies are needed to fully understand the immune mechanisms involved in fish infections by V. anguillarum and S. iniae - Developing targeted vaccination strategies for N. Tilapia and E. Sea Bass - Investigating the role of Galectins in modulating leukocyte activity and apoptosis

  Expression and Immune Response Profiles in Nile Tilapia (Oreochromis niloticus) and European Sea Bass (Dicentrarchus labrax) During Pathogen Challenge and Infection · 2024 · DOI

• The CXCL12/CXCR4 axis has been extensively studied in mammals, but its regulatory mechanism in teleost fish remains unclear.

  CXCL12/CXCR4 Axis Promotes the Chemotaxis and Phagocytosis of B Cells through the PI3K-AKT Signaling Pathway in an Early Vertebrate · 2024 · DOI

• However, there remains a notable gap in knowledge concerning the infectivity of N.

  Integrated analysis of proteome and transcriptome revealed changes in multiple signaling pathways involved in immunity in the northern snakehead (Channa argus) during Nocardia seriolae infection · 2024 · DOI

• Thus, data on the duration of the humoral immune response and protection in farmed tilapia have not been reported or are poorly described.

  Duration of Protection and Humoral Immune Response in Nile Tilapia (Oreochromis niloticus L.) Vaccinated against Streptococcus agalactiae · 2024 · DOI

• Thus, Aeromonas veronii is implicated as the causative agent of the mass mortality observed in bronze gudgeon, warranting further investigations into the diagnosis, epidemiology, prevention, and treatment of this infectious disease.

  Identification of Aeromonas veronii as the Pathogen Associated with Massive Mortality in Bronze Gudgeon (Coreius heterodon) · 2024 · DOI

• These data demonstrate that while information related to clinical therapy of cancer in fish species is lacking, surgical excision of tumors in fish, when feasible for the patient and client, may improve patient outcomes.

  Retrospective Study of the Prevalence, Histopathology, Therapy, and Survival Time of Neoplastic Disease in Fish · 2024 · DOI

• The sample size was limited to 4 wild-caught and 4 captive morph individuals. The availability of samples that met the specified parameters was limited. The low occurrence of samples in the wild was a limitation.

  Comparison of Leukocyte Profiles and Cytomorphometry in Wild-Caught and Captive Morph Reticulated Pythons (Malayopython Reticulatus) · 2026 · DOI

• The comparison of immune response capabilities between wild-caught and captive morph reticulated pythons is limited. The effects of environmental conditions on the health status of reticulated pythons are not well understood.

  Comparison of Leukocyte Profiles and Cytomorphometry in Wild-Caught and Captive Morph Reticulated Pythons (Malayopython Reticulatus) · 2026 · DOI

• The study identifies a gap in the understanding of bacterial infections in goldfish. The study highlights the need for early and accurate identification of bacterial pathogens.

  Isolation and Molecular Characterization of Bacterial Pathogens Infecting Goldfish (Carassius auratus) · 2026 · DOI

• The lack of studies on the effects of dietary emodin supplementation on Pengze crucian carp fed with high plant-protein diets. The need to determine the optimal level of emodin supplementation to improve growth performance and intestinal health in carp.

  Effects of dietary emodin supplementation on the growth performance, serum biochemical parameters, and intestinal health of Pengze crucian carp (Carassius auratus var. Pengze) fed with high plant-protein diets · 2026 · DOI

Most-cited papers in Aquaculture disease management and microbiota

• Review of alternatives to antibiotic use in aquaculture · Reviews in Aquaculture · 2023 · 380 citations
• Main Components of Fish Immunity: An Overview of the Fish Immune System · Fishes · 2023 · 328 citations
• The Fish Microbiota: Research Progress and Potential Applications · Engineering · 2023 · 225 citations
• Bacterial diseases of tilapia, their zoonotic potential and risk of antimicrobial resistance · Reviews in Aquaculture · 2023 · 190 citations
• A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss) · Microbiome · 2022 · 174 citations
• Contemporary threats of bacterial infections in freshwater fish · Journal of Veterinary Research · 2018 · 111 citations
• A comparison of digestive strategies for fishes with different feeding habits: Digestive enzyme activities, intestinal morphology, and gut microbiota · Ecology and Evolution · 2023 · 106 citations
• Biology of Bony Fish Macrophages · Biology · 2015 · 98 citations
• Fish gut microbiome and its application in aquaculture and biological conservation · Frontiers in Microbiology · 2025 · 92 citations
• Impact of probiotics, prebiotics, and synbiotics on digestive enzymes, oxidative stress, and antioxidant defense in fish farming: current insights and future perspectives · Frontiers in Marine Science · 2024 · 88 citations

Most recent work

• Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Cyprinus carpio L.) to Probiotic and Prebiotic Supplementation · Animals · 2026
• Comparative Molecular and Antimicrobial Analysis of Lactococcus garvieae and Lactococcus petauri from Marine and Freshwater Fish Farms in the Mediterranean · Animals · 2026
• Effects of probiotics, prebiotics, and synbiotics on immune function, disease resistance, digestive health, and stress management in fish culture · Frontiers in Marine Science · 2026
• Antigen-displaying probiotic Bacillus subtilis spores induce subtle, strain-dependent immunomodulation in fish · Frontiers in Marine Science · 2026
• Gut microbial composition varies with host metabolic phenotype in juvenile atlantic salmon · Journal of Experimental Biology · 2026
• : A standardized bath challenge of Atlantic salmon reveals distinct infection dynamics and mortality across ten HPR-deleted infectious salmon anaemia virus isolates. · bioRxiv · 2026
• Transcriptional regulation of the rainbow trout spleen corticotropin-releasing factor system in response to inflammatory challenges: roles of NF-kB and cortisol · bioRxiv (Cold Spring Harbor Laboratory) · 2026
• Stressor- and tissue-specific regulation of the corticotropin-releasing factor system across epithelial tissues in rainbow trout · bioRxiv · 2026
• Underlying the Enhanced Ammonia Stress Resistance by Prebiotic Xylo-Oligosaccharides in Hybrid Groupers: An Integrative Analysis of Serum Physiology, Hepatic Transcriptomics, and Intestinal Health · Animals · 2026
• Microbiological and genomic surveillance of WHO critical priority pathogens along the oyster supply chain: water quality as a driver of persistence and depuration as a mitigating strategy in a One Health context · Frontiers in Bacteriology · 2026

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