Over the past decade, public awareness and concern for the welfare of farmed fish have continued to grow. In response, the aquaculture sector has made significant strides in improving welfare standards, guided by a robust body of scientific research. These advances have been supported by interdisciplinary collaboration and EU-funded projects such as AQUAEXCEL, which have deepened our understanding of fish health, physiology and behaviour. They have also raised important ethical questions, particularly when research involves exposing animals to potentially stressful conditions in order to identify adverse effects and devise strategies for their mitigation.

Ensuring that such research is conducted responsibly and ethically has been a cornerstone of the AQUAEXCEL initiatives. Since the early days of AQUAEXCEL, Professor Felicity Huntingford has served as the project’s independent Ethics Advisor. A leading authority on fish behaviour and welfare, Professor Huntingford brought decades of experience to this role, helping researchers navigate the ethical dimensions of their work while maintaining scientific integrity. Over the course of AQUAEXCEL, AQUAEXCEL2020 and AQUAEXCEL3.0, she has reviewed more than 500 research projects, not only helping to ensure compliance with ethical standards but also fostering a culture of continuous improvement. This legacy has contributed to the development of tools and practices that have raised the bar for future research, enabling deeper scientific insights while reducing the impact on experimental fish. Central to this progress has been the integration of the 3Rs principle – Replacement, Reduction, and Refinement – into the core of AQUAEXCEL’s research activities.

Five years after our first interview for AQUAEXCEL2020, we spoke again with Professor Felicity Huntingford to reflect on how the ethical landscape in aquaculture research has developed. Looking back across the programme, she highlighted the impressive body of work carried out under AQUAEXCEL and noted that, by the end of the project, the community is now better equipped to apply the 3Rs, with stronger ethical standards and more effective tools to support them.

Interviewer: Could you please remind us of what the 3Rs principle is and why it’s important in aquaculture research?

Felicity: The 3Rs—Replacement, Reduction, and Refinement are foundational ethical principles in animal research, aimed at ensuring that legitimate scientific goals are achieved with minimal cost to the animals concerned. Thus they encourage researchers to:

  • Replace animals with alternatives wherever possible,
  • Reduce the number of animals used to the minimum necessary for valid results, and
  • Refine procedures to minimise pain, suffering, and distress.

Applying the 3Rs is both a scientific and moral imperative where live animals are used in research, as is often the case for aquaculture science.

Interviewer: How has the AQUAEXCEL contributed to better compliance with the 3Rs?

Felicity: During programme we reviewed many TransNational Accessapplications and Joint Research Activities ethical returns. What stood out was that not only were the great majority of projects designed in accordance with the 3Rs principal, but many also produced tools and insights that could improve compliance in future research. In other words, the benefits extended beyond the individual studies, potentially shifting the balance between scientific gain and animal cost in a positive direction.

Interviewer: Could you give us some examples of these tools?

Felicity: Absolutely. We identified several research projects that developed new research tools, often building on work carried out in the earlier stages of the AQUAEXCEL programme. These tools help researchers gain more knowledge, while at the same time offering new ways of reducing the impact on experimental fish. Let me highlight some examples:

  • AEFishBIT Bio-Logger (Publication: Calduch-Giner et al., 2022)

This small, lightweight tag is attached gently to the fish’s gill cover. The tag records 3D acceleration data, allowing scientists to monitor swimming and breathing patterns in real time, without needing to touch or disturb the fish. One fitted, the tag, which was tested successfully in four major aquaculture species, allows behaviour and physiology of individual fish to be recorded non-invasively. This is an excellent example of how cutting-edge technical innovation can make research both more precise and more humane, fully in line with the 3Rs.

  • Photo-Based fish identification (Publication: Bekkozhayeva & Cisar, 2022)

This system uses automated image analysis to identify individual fish based on their scale patterns, even in species without obvious markings. Proven to be 100% accurate in tests with carp and seabass, it eliminates the need for tagging or invasive marking, representing a clear Refinement. Beyond that, by allowing researchers to follow the same individual before and after a stressor, for example, it potentially produces more statistically powerful results, which on turn allows fewer fish to be used (Reduction).

  • Microbiome Network Analysis Tool (Publication: Soriano et al., 2023)

This computational tool models the complex interactions within fish gut microbiomes and their environments. It helps researchers predict outcomes without needing to run as many live experiments, thussupporting Replacement and Reduction, especially in early-stage hypothesis testing.

  • Virtual Aquaculture Simulation Platform (Publication: Saad et al., 2023)

This web-based platform simulates fish performance in different aquaculture systems using intelligent agents. It allows researchers and farm managers to test scenarios virtually before conducting real-world trials. This is a powerful example of Replacement and Reduction, as it minimises the need for live testing.

  • In vitro gut epithelium used to test functional feeds (Publication: Fosse et. al 2025)

This study (mainly funded by Nutrimar, with synergistic funding from AQUAEXCEL3.0) used state of the art tissue culture technology to produce a monolayer of rainbow trout cells that behaves like an in vitro gut epithelium. This system was used to test a battery of potential functional feeds for their effects on gut health and immune responsiveness, identifying those (brown algal extract, for example) that might promote effective immune responsiveness and protect fish during stressful events. This is an excellent illustration of a powerful, cost-effective research tool and an excellent example of replacement.

Interviewer: That’s very impressive! So, these tools don’t just help researchers, they also protect animal welfare?

Felicity: Exactly. They accelerate knowledge gain while reducing the ethical cost, an ideal outcome. The AQUAEXCEL progbramme has shown that with the right investment in innovation, we can make aquaculture research both more effective and more humane.

Interviewer: Would you have any final thoughts you would like to share, Felicity?

Felicity: I think AQUAEXCEL has been an extraordinary programme, incredibly productive in terms of gaining knowledge to promote sustainable aquaculture, its main and important goal. What stands out to me is that concern for welfare has been there right from the start. The 3Rs weren’t just something to tick off, they were built into the heart of the research and actually helped drive innovation. That’s real added value, these findings have pushed the field forward and helped tackle some of the more difficult challenges in aquaculture.

Interviewer: Those are compelling final thoughts, Felicity. Thank you again for your time and for highlighting the significant role of the 3Rs in driving innovation within AQUAEXCEL.