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Open research questions in Aquaculture disease management and microbiota

1,021 gap statements mined from Aquaculture disease management and microbiota papers in our 7.9M-paper local library, which holds 4,390 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.

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What the literature leaves open

  • Second, vaccine efficacy must be evaluated not only through survival metrics but also through comprehensive immune profiling, including gene expression analysis, antibody responses, and mucosal immunity. Third, innovative vaccine delivery systems, such as feed-based oral vaccines, offer practical advantages for large-scale aquaculture operations.

    Fish Disease Occurrence and Immune Prevention and Control · 2026 · DOI

  • Genomic characteristics alone, however, are insufficient to establish LG2 as a vaccine candidate, and its suitability must be assessed through antigenic profiling, immunogenicity testing and controlled challenge experiments.

    Phenotypic and phylogenomic characterization of Lactococcus garvieae isolates from rainbow trout (Oncorhynchus mykiss) in Türkiye · 2026 · DOI

  • Not all phases were completed due to logistical constraints. For case B, phases P1, P3, and P5 were omitted. The study had a limited number of monitored deliveries.

    Dynamics of infectious salmon anemia virus in biofouling on well-boat hulls · 2026 · DOI

  • To the best of our knowledge, only a few studies have specifically examined the effects of S. In our research, feed supplements containing probiotics and prebiotics for common carp produced promising results that could serve as a basis for further research into enhancing growth, gut integrity, and intestinal microbiota.

    Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Cyprinus carpio L.) to Probiotic and Prebiotic Supplementation · 2026 · DOI

  • The paper identifies technical challenges in the analysis of proteomic data, including the need for suitable m/z precursor ions. The study also identifies challenges in the interpretation of biomarker data, including the need to integrate multiple biomarkers. The paper does not explicitly state other specific technical or domain challenges.

    Integrating non-lethal and oxidative stress biomarkers to evaluate the effects of the probiotic Bacillus subtilis FI99 supplementation in plant-based diets for meagre · 2026 · DOI

  • The lack of knowledge on the use of coffee pulp as a dietary supplement for Nile tilapia. The need for safe and sustainable dietary strategies to enhance fish health and performance. The gap in understanding the effects of coffee pulp on growth performance, immunity, gene expression, and gut microbiota of Nile tilapia.

    Effects of coffee pulp (Coffea arabica) on growth performance, immunity, gene expression, and gut microbiota of Nile tilapia (Oreochromis niloticus) raised in biofloc system · 2026 · DOI

  • Environmental data were limited to discrete sampling measurements, so the observed associations with glacial melt, turbidity, seasonality, and oxygen remain contextual correlates rather than confirmed drivers of the outbreak; hence, continuous monitoring would be needed to establish causality.

    Hematological and biochemical alterations in rainbow trout Oncorhynchus mykiss during a natural Aeromonas sp. outbreak in high-altitude Ladakh, trans-Himalayas · 2026 · DOI

  • Despite the advances reported to date in natural compound–antibiotic combination therapies, several challenges remain. One of the major obstacles is the limited in vivo validation of these strategies.

    Joining Forces Against Antibiotic Resistance in Aquaculture: The Synergism Between Natural Compounds and Antibiotics · 2026 · DOI

  • Currently available commercial probiotics have limited efficacy in aquaculture. There is a need to identify indigenous probiotics from the midgut of gibel carp as effective and host-specific probiotics.

    Evaluation of novel probiotic Bacillus candidates from the midgut of gibel carp (Carassius auratus gibelio): effects on fish growth, immunity, and resistance to CyHV-2 infection · 2026 · DOI

  • It notes that previous research has focused on the effects of acute heat stress, but the impacts of chronic heat stress are not well understood.

    Chronic heat stress attenuates innate immunity and increases susceptibility to Aeromonas hydrophila in Siberian sturgeon (Acipenser baerii) · 2026 · DOI

  • The molecular mechanisms underlying LMBV pathogenesis are not well understood. The host immune evasion strategies and viral replication dynamics of LMBV are not well understood.

    Characterization of a novel isolated largemouth bass virus (LMBV) strain: genomic insights, host transcriptional responses, and lipid droplet-dependent viral replication · 2026 · DOI

  • The virus can be transmitted vertically and horizontally, making it difficult to control. Current methods for controlling the virus are limited. The disinfection treatment must be effective in reducing the detectable viral load in fertilized eggs, rotifers, and copepods.

    Effect of povidone-iodine and chlorine dioxide disinfection on reducing transmission of carp herpesvirus type II in Carassius gibelio · 2026 · DOI

  • Further studies are needed to investigate the long-term effects of disinfection treatment on the health of Carassius gibelio. Further studies are needed to investigate the potential environmental impacts of using PVP-iodine and ClO₂ as disinfectants. Further studies are needed to investigate the efficacy of PVP-iodine and ClO₂ in preventing the transmission of other diseases in Carassius gibelio.

    Effect of povidone-iodine and chlorine dioxide disinfection on reducing transmission of carp herpesvirus type II in Carassius gibelio · 2026 · DOI

  • The lack of sustainable seed production methods for Etroplus suratensis. The need for integrated ecological, social, and economic considerations in aquaculture. The gap in the development of effective tools for transforming degraded culture systems.

    Application of bioaugmentors as Immobilized Microbial Consortia (IMC) for sustainable seed production of Etroplus suratensis in semi-intensive brackish-water earthen ponds under an Ecosystem-based Approach to Aquaculture (EAA): A pilot-scale field validation · 2026 · DOI

  • The need to find an effective and eco-friendly control measure for scuticociliatosis. The risk of drug residues and pathogen resistance associated with chemotherapy. The potential side effects of UV light on farmed organisms.

    Blue-violet light (405 nm): a non-chemical intervention for Metanophrys sp. infection in large yellow croaker (Larimichthys crocea) · 2026 · DOI

  • Dietary CHM shows potential as a sustainable functional ingredient for koi carp cultured under biofloc conditions. The 10 g/kg diet produced the most consistent improvements in growth, feed efficiency, digestive enzyme activity, intestinal morphology, immune- and antioxidant-related gene expression, and ammonia-stress tolerance.

    Corn husk meal as a sustainable dietary additive in biofloc-cultured koi carp (Cyprinus carpio var. koi): Integrative effects on growth performance, immune response, histology, gene expression, and ammonia-stress resilience · 2026 · DOI

  • Chemotherapeutants have limited efficacy against dactylogyrideans. The use of phytotherapeutics as an alternative to chemotherapeutants is a relatively new area of research.

    Astrocaryum aculeatum fixed oil is effective against dactylogyrideans without compromising gill structure in Colossoma macropomum · 2026 · DOI

  • The paper identifies a gap in the understanding of E. ictaluri and its impact on fish farming. The study aims to fill this gap by providing genetic insights into virulence and resistance.

    Whole-genome sequencing analysis of three Edwardsiella ictaluri isolates from Indonesia: genetic insights into virulence and resistance in pangasius farming · 2026 · DOI

  • Further mapping and research on viral viability and infectivity in biofouling environments. Investigation into the role of exterior biofouling as a reservoir for ISAV. Study of the effects of antifouling measures on ISAV transmission.

    Dynamics of infectious salmon anemia virus in biofouling on well-boat hulls · 2026 · DOI

  • Finally, the associations drawn between the XRD/FTIR structural characterization and functional outcomes (digestive enzyme activity, growth) are correlative rather than mechanistically demonstrated, and the trial was conducted at laboratory scale over 45 days, so extrapolation to commercial hatchery conditions or later developmental stages requires further validation; moreover, the feed intake efficiency should be…

    Effect of Nano- and Microparticulate Fermented Fish Protein Hydrolysate Diets on Growth, Digestive Function, Intestinal Development, and Gene Expression in Common Carp (Cyprinus carpio) Larvae · 2026 · DOI

  • Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

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

  • Investigate the effects of CPP on other fish species, - Examine the long-term effects of CPP supplementation, - Determine the optimal level of CPP inclusion for different growth…

    Effects of coffee pulp (Coffea arabica) on growth performance, immunity, gene expression, and gut microbiota of Nile tilapia (Oreochromis niloticus) raised in biofloc system · 2026 · DOI

  • The study used a controlled feeding experiment with a limited number of fish - The experiment was conducted over a 60-day feeding period - The study did not investigate the long-term effects of nutraceuticals on Labeo…

    Complementary effects of polyphenolic nutraceuticals in enhancing antioxidant defense and immunity of Labeo rohita · 2026 · DOI

  • Investigate the long-term effects of nutraceuticals on Labeo rohita - Examine the effects of different concentrations of nutraceuticals on antioxidant defense and immunity - Study the potential applications of polyphenolic nutraceuticals in other fish…

    Complementary effects of polyphenolic nutraceuticals in enhancing antioxidant defense and immunity of Labeo rohita · 2026 · DOI

  • The study was conducted in a controlled environment, - The sample size was 360 Nile tilapia, - The experiment was limited to a 60-day feeding…

    Effects of dietary Reishi mushroom (Ganoderma lucidum) supplementation on immune response, antioxidant status, and disease resistance in Nile tilapia (Oreochromis niloticus) · 2026 · DOI

Most-cited papers in Aquaculture disease management and microbiota

Most recent work

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Open questions raised by papers listed on this page include: (1) The lack of knowledge on the use of coffee pulp as a dietary supplement for Nile tilapia (“Effects of coffee pulp (Coffea arabica) on growth performance, immunity, gene…”, 2026); (2) There is a need to identify indigenous probiotics from the midgut of gibel carp as effective and host-specific probiotics (“Evaluation of novel probiotic Bacillus candidates from the midgut of gibel carp…”, 2026); (3) It notes that previous research has focused on the effects of acute heat stress, but the impacts of chronic heat stress are not well understood (“Chronic heat stress attenuates innate immunity and increases susceptibility to…”, 2026); (4) The molecular mechanisms underlying LMBV pathogenesis are not well understood (“Characterization of a novel isolated largemouth bass virus (LMBV) strain:…”, 2026); (5) Further studies are needed to investigate the long-term effects of disinfection treatment on the health of Carassius gibelio (“Effect of povidone-iodine and chlorine dioxide disinfection on reducing…”, 2026). 1,021 gap statements have been mined from Aquaculture disease management and microbiota papers in our 7.9M-paper local library, which holds 4,390 papers on the topic; the gaps come from whichever of those papers state one. They are mostly the research gaps the authors state and the papers' abstracts, plus future-work, limitations and challenges passages. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one, so you can read the original claim in context.

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