Harnessing the power of Sequencing and AI to Advance Aquaculture Monitoring Technologies[

Aquaculture health management is increasingly reliant on continuous, data-driven surveillance of bacterial microbiomes rather than reactive diagnosis. KOA Biotech's platform, KOA Lens, applies 16S rRNA gene sequencing and Oxford Nanopore sequencing alongside AI-based analysis to characterize microbial community shifts, offering the potential to flag signs of dysbiosis before clinical symptoms appear in fish populations. In this interview, KOA Biotech Scientist Miquel Rozas Belmonte discusses how the sequencing partnership with GENEWIZ from Azenta Life Sciences improved data quality and consistency across their reference datasets.

Aquaculture is a cornerstone of global food production, with over 50% of fish for human consumption coming from fish farms.

Modern aquaculture has made remarkable advances in efficiency and sustainability, but like all livestock systems, it faces challenges from infectious diseases, particularly under intensive production. Addressing these challenges through improved health management, vaccination, biosecurity, and innovative disease prevention strategies can enhance productivity, support fish welfare, and promote the long-term sustainability of the aquaculture industry.

In this interview, Miquel Rozas Belmonte, Scientist at KOA Biotech, shares how their team is transforming aquaculture through continuous microbiological monitoring using AI, supported by GENEWIZ from Azenta Life Sciences.

Overall, KOA Biotech’s work demonstrates the value of longitudinal microbiome monitoring and the power of combining sequencing with AI-driven analysis to advance applied microbiology and generate more accurate, actionable insights.

Q: Can you give a short overview of KOA Biotech and the core problem you are solving?

KOA Biotech provides bacterial monitoring services for aquaculture farms, with a focus on tracking bacterial populations over time. By monitoring changes in bacterial communities, the platform identifies emerging health risks before fish develop clinical signs, enabling farmers to implement timely preventive interventions that support fish health and optimize productivity.

Q: What are the key biological or microbiological questions you are addressing?

We focus on how bacterial populations evolve over time, identifying when communities shift toward an “unhealthy” state. Instead of reacting to infections, we aim to detect early signals of dysbiosis, an imbalance in the healthy microbiome.

Q: Why is early pathogen detection important for fish farming operations?

Traditional health monitoring workflows typically begin once fish show clinical signs or following the first mortality events. At that stage, diagnostic methods such as multiplex PCR or classical microbiology are used to identify the bacteria involved by analysing targeted tissues or organs. While these methods are essential for confirming the cause of a health event, the process of sample collection, shipment, and laboratory analysis can take several days before results are available. During this time, the condition of the stock may continue to evolve, making timely management decisions more challenging. By contrast, continuous monitoring of microbial populations provides early insight into changes in the farm microbiome, enabling farmers to detect emerging health risks sooner and implement preventive measures before clinical signs become widespread. This proactive approach supports healthier stocks, improves production outcomes, and helps farmers make faster, more informed management decisions.

Q: Can you explain how KOA Biotech’s technology works?

KOA Biotech currently offers an image-based microbiology system called KOA Lens to help identify critical contamination points within farming operations. KOA Lens uses AI to identify critical bacterial populations from samples collected throughout the aquaculture environment, for example water, fish, feed, and tank surfaces. KOA Lens has been developed and validated using 16S rRNA gene sequencing data. The 16S rRNA gene is a widely accepted genetic marker for bacterial classification because it contains both highly conserved and species-specific variable regions, enabling precise taxonomic assignments using existing reference genomes.

The results of bacterial colony identification via sequencing of 16S rRNA gene PCR are used to train the KOA Lens system and validate bacterial identification, ensuring a high level of accuracy and reliability.

KOA Biotech is also developing a next-generation, biosensor-based platform (K-Gen) using genetically modified bacteria to enable continuous, automated water monitoring.

Oxford Nanopore sequencing technology from GENEWIZ is being used to further develop both technologies. Microbiome sequencing enables comprehensive characterisation of the microbial communities present in aquaculture samples, allowing comparisons between healthy and compromised fish environments and improving our understanding of microbiome dynamics. These data are used to identify microbial signatures associated with changes in fish health and to further train, calibrate, and validate KOA Biotech’s predictive monitoring tools.

Q: How did partnering with GENEWIZ support your research and analytical workflows?

When building our bacterial detection assays from scratch, we needed to ensure reliable sequencing and understand quality parameters. GENEWIZ provided both sequencing and technical support. When we encountered inconsistent sequence quality from certain environmental isolates, the team made recommendations and helped us optimise our workflows. Their guidance helped us improve sequencing success rates and data consistency, enabling us to build a more robust reference dataset. GENEWIZ has become an essential partner for our sequencing needs, providing quick, high-quality data critical for training our datasets and enabling automation.

Q: Based on your experience, what key insights should a scientific audience, particularly those working with sequencing technologies, take away from your work?

Sanger sequencing remains the gold-standard for accurate bacterial identification and taxonomic classification of individual microbial colonies. In contrast, Oxford Nanopore Technologies (ONT) sequencing provides a broader view of the microbial communities present in aquaculture samples, enabling characterization of the overall microbiome rather than isolated colonies. This broader perspective allows us to identify microbial signatures associated with healthy and compromised fish environments, improving the training and calibration of our predictive monitoring technologies.

For me, the key is to understand the strengths, limitations, and potential biases of each sequencing approach and to use them in a complementary way. By combining the accuracy of Sanger sequencing with the comprehensive microbiome profiling provided by ONT, we can obtain a more complete and biologically meaningful picture of what is happening within complex environmental samples.

BIOGRAPHY

Miquel Rozas holds an industrial PhD in biotechnology and is a Scientist at KOA Biotech. Driven by a passion for innovation and the potential of biotechnology to address societal challenges, he specializes in the applied fields of molecular biology and microbiology. At KOA Biotech, he combines his expertise and motivation to develop systems for monitoring bacterial microbiomes, helping to make the aquaculture industry more efficient and sustainable.

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