One challenge is the complexity

The gap

Evidence profile

Sourced from the stated research gap and stated challenges and future work and future-work section of the source papers, classified as general, drawn from work published between 2024 and 2026, spanning 4 journals. Those papers have been cited 88 times in total.

Supporting evidence — 5 representative gaps

• Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity (2026) · Microorganisms · doi

  The gap in the current understanding of nutrigenomics in cultured finfish is the lack of a comprehensive framework for analyzing the diet-microbiome-host interaction. The available evidence is concentrated on a limited range of dietary interventions and finfish species. There is a need for a more detailed understanding of the molecular and microbial responses to different dietary regulations.

  generalstated research gap
  Keywords: gap current understanding nutrigenomics cultured finfish lack comprehensive
• Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity (2026) · Microorganisms · doi

  One challenge is the complexity of the diet-microbiome-host interaction in cultured finfish. Another challenge is the limited range of dietary interventions and finfish species studied. The paper also highlights the challenge of interpreting gene-expression findings in the context of tissue-specific responses and microbial niche.

  generalstated challenges
  Keywords: one challenge complexity diet-microbiome-host interaction cultured finfish another
• Impact of probiotics, prebiotics, and synbiotics on digestive enzymes, oxidative stress, and antioxidant defense in fish farming: current insights and future perspectives (2024) · Frontiers in Marine Science · cited 88× · doi

  The specific role of probiotics, prebiotics, and synbiotics in modulating digestive enzymes, oxidative stress, and antioxidant defense systems is not well understood. There is a lack of standardized methodologies for studying the impact of these interventions on fish health. The variations in experimental design, species-specific responses, and lack of standardized methodologies contribute to the complexity of the field.

  generalstated research gap
  Keywords: specific role probiotics prebiotics synbiotics modulating digestive enzymes
• Fish microbiota and its role in fish physiology and diseases regulation (2026) · Environmental Biology of Fishes · 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.

  generalfuture workevidence 5/5
  Keywords: fish microbiota health microbiome functional microbial host microbes provide approaches dysbiosis actions multi omics aquaculture
• Fish microbiome as a mediator of xenobiotic toxicity: mechanistic insights, ecological implications and future directions (2026) · The Journal of Basic and Applied Zoology · doi

  Further research is needed to elucidate the molecular mechanisms of microbiome-xenobiotic interactions. Studies should investigate the relevance of these mechanisms across different fish species. The paper suggests exploring the potential of manipulating the fish microbiome as a strategy to mitigate xenobiotic toxicity and improve host health.

  generalfuture-work sectionevidence 4/5
  Keywords: further research needed elucidate molecular mechanisms microbiome-xenobiotic interactions

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