Science AI Journal
Immunology and Microbiology · Research topic

Open research questions in Aquaculture disease management and microbiota

42 unresolved questions extracted from the limitations and future-work sections of 270 Aquaculture disease management and microbiota papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • We acknowledge that the use of shrimp with different clinical outcomes for viral load and histopathological analyses represents a limitation of the present study, as moribund shrimp from the challenged control group were included as a pathological reference to confirm successful WSSV infection rather than as direct comparators to the surviving shrimp in the treatment groups.

    Non-GMO surface display of VP28 on Pediococcus pentosaceus for oral protection against white spot syndrome virus in shrimp · 2026 · DOI

  • While they demonstrated notable resilience over the 30-day period, the long-term physiological consequences and potential cumulative effects of these adaptations warrant further investigation.

    Intestinal transcriptomic responses to chronic carbonate alkalinity stress in grass carp (Ctenopharyngodon idella) · 2026 · DOI

  • This inferred connection is based solely on correlation and remains to be experimentally tested. Overall, this study reveals correlations among gut microbiota, metabolism, and antimicrobial immunity, providing a preliminary basis for subsequent mechanistic studies, but the causal relationships among them remain to be fur- ther validated.

    Emodin treatment is associated with enhanced resistance to Aeromonas hydrophila and correlates with gut microbiota–immune–metabolic modulation in Yellow River Carp: a multi−omics study · 2026 · DOI

  • Previous studies have reported that peracetic acid (PAA) is an effective disinfectant, but its application in shrimp aquaculture remains underexplored.

    The Effects of Peracetic Acid on Post‐Larvae and Juvenile Pacific White Shrimp ( <i>Litopenaeus vannamei</i> ) and Seven <i>Vibrio</i> Species Isolates at Two Salinities · 2026 · DOI

  • While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation.

    Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish <i>Kyphosus cinerascens</i> · 2026 · DOI

  • For spring viremia of carp virus (SVCV), a notifiable rhabdovirus of global concern, it remains unclear whether host entry pathways in fish are realistically “druggable” and how small molecules can be integrated into practical farm interventions.

    A novel host-targeted inhibitor of clathrin-mediated endocytosis limits spring viremia of carp virus infection · 2026 · DOI

  • This study outlined several notable strengths. To our knowl- edge, this current study represents the first report of two noble autochthonous probiotic bacteria E. mori ASP8 and B. stercoris ASP10 from the gut of wild-type stinging cat- fish, H. fossilis. The rigorous multifaceted bio-safety assess- ment including in vitro and in vivo concluded both strains are non-pathogenic. Furthermore, this study demonstrated that both strains showed exceptional resilience to stimulated gastrointestinal conditions. Another notable strength of this study is that a broad spectrum of antimicrobial activity, with the ability to produce bacteriocin and siderophore, and to co-aggregate with pathogens, was identified in both strains. Despite promising findings, this study also acknowledged certain limitations such as finding of in vivo effectiveness of probiotic strains on gut microbiome modification, the immu- nity of the host, and whole genome sequencing–based strain identification, and these portions will be considered in our future studies.

    Probiotic potential of autochthonous Enterobacter mori ASP8 and Bacillus stercoris ASP10 isolated from gut microbiota of healthy stinging catfish, Heteropneustes fossilis (Bloch) · 2026 · DOI

  • The results presented demon- strated that local secondary responses are present in the gills upon re-infection, yet whether this is due to responses organized in remote tissues such as the spleen, or is a result of memory B and T cell populations retained in the mucosa should be further investigated.

    Transcriptomic profiling and IgM and IgT repertoire dynamics in rainbow trout gills following primary and secondary challenge with Lactococcus petauri · 2026 · DOI

  • In recent years, research focused on fish intestinal microbiota has increased dramatically; however, most of the studies conducted utilize 16S rRNA sequenc- ing and provide merely descriptive data as opposed to functional data. Even though functional studies that examine microbiota are on the rise, these studies are still not as widespread as previous methods. The current gnotobiotic fish models need further refine- ment before being an adequate model for examin- ing host-microbiota interactions. Establishing causal links between specific bacterial species and their Vol.: (0123456789) 80 Page 14 of 21 Environ Biol Fish (2026) 109:80 functions in fish gut microbiota requires culturing these microbes; adopting culturomics approaches, as applied in humans and other mammals, could signifi- cantly advance this research. The gut microbiota has potential as a health indica- tor in fish. Knowledge of gut microbiome homeosta- sis will inform possibilities for modulating intestinal microbiota to enhance growth, immunity, and per- formance. In zebrafish, a high Fusobacteria-to-Pro- teobacteria ratio reflects microbiota homeostasis and is associated with liver health, whereas deviations indicate dysbiosis. Similarly, studies in economically important fish suggest that higher ratios of Fusobac- teria, Firmicutes, and Bacteroidetes to Proteobacte- ria are predictive of improved health. Despite these promising avenues of research, there is still consider- able knowledge gaps in understanding structural and functional aspects of gut microbiome homeostasis and dysbiosis in fish. It is important to engage in com- prehensive studies on ecological interactions among the gut microbiome, as well as to establish microbial profiles as standard approaches. Both actions would minimize confounding factors and allow for conclu- sions and the status of regulation of the gut microbi- ome to be made in more generalizable ways. Although most present-day researches are mainly based on the 16S rRNA gene sequencing and metagenomics to characterize the taxonomic com- position, this technique offers minimal information about microbial functionality and host-microbe inter- actions. Multi-omics technologies, such as metatran- scriptomics, metaproteomics, and metabolomics, can provide a powerful framework to close this gap by connecting the potential of microbial genome with the actual expression of genes, synthesis of pro- teins as well as the production of metabolites. Such methods can be used to clarify functional pathways that regulate nutrient metabolism, immune regula- tion, responses to stress, and resistance to disease in fish and thus can be used to have a more mechanis- tic comprehension of how the microbiome mediates health outcomes. Moreover, integrating multi-omics with environmental, physiological, and host-genomic data will contribute to the unraveling of the context- specific microbial functions and the identification of functional biomarkers of health and dysbiosis. With the decreasing costs of sequencing and the matura- tion of bioinformatics tools, the use of integrative multi-omics approaches to microbiome studies will bring fish microbiome studies beyond descriptive profiling into predictive and translational research outcomes useful to aquaculture, conservation biology and fish health management. Studies on fish gut microbiota can introduce new, sustainable, ecological protocols in aquaculture. Iso- lating and culturing gut microbes may lead to novel probiotics, and former probiotics may serve as post- biotics and/or paraprobiotics. In addition, investigat- ing natural compounds and ingredients that selec- tively promote beneficial microbes or inhibit harmful microbes will help maintain microbial balance. In summary, fish microbiota research will not only help build a better understanding of host-microbiota inter- actions but also provide new mechanisms to improve fish health and build sustainability in aquaculture. Author contributions SM IK and RAM conceived the idea. SM and MA collected the literature and participated in writing. SM, MA RAM, IAN and IK proofread and edited the final ver- sion. All authors have read and approved the final version of the manuscript.

    Fish microbiota and its role in fish physiology and diseases regulation · 2026 · DOI

  • Group II interferons in zebrafish display antiviral activities (reference 72), but their specific role in macrophage activation and the cross-talk between group II IFN signaling and TNF-α or IFN-γ pathways in bony fish macrophages has not been investigated.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • The functional characterization of TNF-α in grass carp head kidney leukocytes identified NF-κB signaling involvement (reference 83), but the complete signaling cascade from TNF receptor binding through NF-κB activation in fish macrophages across different infection stimuli has not been mapped.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • Interferon-gamma (IFN-γ) signaling has been shown to activate nitric oxide production in grass carp monocytes/macrophages (reference 68), but the downstream IFN-γ receptor isoforms (reference 70) and their differential signaling outcomes across diverse teleost species remain uncharacterized at the functional level.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • The NADPH oxidase assembly pathway and p47phox phosphorylation mechanisms are well-characterized in mammalian neutrophils (references 93-94, 100), but the equivalent phosphorylation sites and mobilization kinetics of NOX2 components in fish macrophages have not been systematically mapped across species.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • While TNF-α gene duplication and multiple TNF isoforms have been documented in teleosts (references 82, 84), the functional differences between TNF-α1, TNF-α3, and other TNF variants in bony fish macrophage activation and antimicrobial responses remain unexplored across different fish species and infection contexts.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • M1 and M2 macrophage polarization has been identified in zebrafish (reference 85), but the specific molecular markers distinguishing these polarized macrophage subsets in other teleost fish species (carp, goldfish, rainbow trout) have not been characterized, limiting understanding of macrophage functional heterogeneity across fish models.

    Biology of Bony Fish Macrophages · 2015 · DOI

  • The use of phytogenic feed additives in aquaculture has gained attention as a sustainable strategy to enhance fish growth and health; however, optimal inclusion levels and mechanistic responses remain insufficiently defined.

    Optimal lemongrass (Cymbopogon citratus) supplementation improves growth, feed efficiency, and digestive development without altering hematological status in red tilapia (Oreochromis spp.) · 2026 · DOI

  • These findings underscore the importance of further research into external factors affecting microbial growth in aquaculture environments and suggest the need for systematic monitoring and control measures to enhance hygiene standards in fish farming operations.

    Monitoring the Microbial Prevalence in Farmed Trout Species from an Aquaculture Facility in Kosovo · 2026 · DOI

  • However, most genome-editing studies have been conducted under laboratory or conventional aquaculture conditions, with limited information available regarding the long-term performance, ecological interactions, microbial dynamics, and biosafety of genome-edited fish in aquaponic environments.

    CRISPR/Cas9-Mediated Genetic Optimization of Nile Tilapia (Oreochromis niloticus) for Sustainable Aquaponic Systems · 2026 · DOI

  • Silver Pomfret is increasingly threatened by many diseases under intensive artificial culturing conditions, yet conserved host biomarkers across different infections remain poorly defined.

    Transcriptomic Analysis and Machine Learning Identify Cross-Pathogen Biomarkers for Bacterial and Parasitic Infections in Silver Pomfret (Pampus argenteus) · 2026 · DOI

  • Abstract Although Flammulina velutipes residues are increasingly used in fish feeds, their mode of action in the gut is poorly defined.

    Comprehensive analysis of microbiome and transcriptome revealed the mechanisms of <i>Flammulina velutipes</i> stem‐base enhance intestinal health in <i>Gymnocypris eckloni</i> · 2026 · DOI

  • Hence, it is reasonable to imagine that the efficacy of the solu- tions may vary depending on the microorganism tested, and future research should explore this aspect and simulate mixed biofilms representative of the microorgan- isms commonly found in endodontic infections.

    Disinfection of gutta-percha cones contaminated with Enterococcus faecalis using calcium hypochlorite, sodium hypochlorite and chlorhexidine · 2026 · DOI

  • Thus, it is still valid to conclude that the effect of β-glucan on the growth of fish is not fully understood, and possible factors responsible for this effect include the concentration of β-glucan in the diet and species-specific responses (6).

    Correlation of duration of β-1,3/1,6-glucan administration with the effectiveness of immune stimulation in juvenile vimba bream <i>(Vimba vimba)</i> · 2026 · DOI

  • Therefore, the in silico findings should be interpreted with appropriate caution, and future studies are needed to experimentally verify the proposed molecular mechanisms underlying praziquantel activity against P.

    Evaluation of the antiparasitic efficacy of praziquantel against Prohemistomum vivax (Cyathocotylidae) metacercariae in naturally infected African catfish (Clarias gariepinus) · 2026 · DOI

  • The study isolated bacterial pathogens from only one aquarium location (Chackai, Thiruvananthapuram district), limiting the geographical scope and generalizability of findings to other regions or goldfish populations.

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

  • Further research examining variations in leukocyte profiles, leukocyte cytomorphometry, and genetic traits across different morphs of M. reticulatus is strongly advised.

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

Most-cited papers in Aquaculture disease management and microbiota

Most recent work

Find a gap in your own Aquaculture disease management and microbiota sub-topic

This page shows what the Aquaculture disease management and microbiota literature already flags as unresolved. To narrow it to your specific question, run the guided finder — it searches the gap library on demand and checks candidates against 250M+ OpenAlex works.

Open the Research Gap Finder →

Related topics in Immunology and Microbiology

Immune cells in cancer
82 open questions
T-cell and B-cell Immunology
75 open questions
Psoriasis: Treatment and Pathogenesis
70 open questions
Antibiotic Use and Resistance
68 open questions
Reproductive tract infections research
66 open questions
interferon and immune responses
58 open questions
HIV Research and Treatment
56 open questions
Immune Cell Function and Interaction
54 open questions
42 open questions have been extracted from the limitations and future-work passages of 270 Aquaculture disease management and microbiota papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

Tools for your next paper

Gaps & Literature SearchFind open questions in any field — 120,000+ open gaps mined from our own library.Pre-CheckIs your paper ready? A Tier 1–5 acceptance probability in seconds.Journal FinderA ranked shortlist of target journals from a 17,500-venue index.Duplicate Publication CheckerCheck prior-publication & salami-slicing risk across 8 sources.Citation GeneratorFreeA DOI or title → APA, MLA, Vancouver, Chicago, BibTeX, RIS. No signup.Graphical Abstract MakerFreeTurn your findings into a colorblind-safe graphical abstract.

Compare the category — Honest roundups of the AI research tools, ours listed alongside the alternatives.

Command palette

Jump anywhere, run any action.