Decoding the Microbiome: Advancing Aquaculture with Precision Analysis

Scientific advancements have revealed that our world is shaped by far more than what meets the eye. Microbial communities colonize nearly every surface at astonishing concentrations, including plants, animals, and their environments. In fact, bacteria outnumber host cells by at least a 10-to-1 ratio. These bacterial communities, collectively known as the microbiome, play a vital role in the development, health, and survival of all living organisms. As a result, microbiome analysis and manipulation have become critical topics in food production—particularly in aquaculture, the world’s fastest-growing food sector. 

However, translating microbiome data into practical applications remains a challenge for both service providers and farmers. While it is widely accepted that microbial balance, diversity, and functionality are key to maintaining fish and environmental health, specific guidelines are still lacking. For example, what bacterial composition and concentrations create the most effective biofilter? How should producers define gut dysbiosis? Which analytical services provide the most relevant data, and how do they compare? 

Recent research has underscored the need for high-resolution data when categorizing bacteria as “beneficial” or “detrimental.” Answering these complex questions requires species-level identification. While hypervariable region sequencing (e.g., V3/V4) is fast and cost-effective, it has trade-offs—one of the most significant being reduced species-level accuracy. 

To address this, Onda and the Center for Aquaculture Technologies have partnered to offer full-length 16S sequencing and analysis, enabling precise species identification. Our advanced pipeline supports the accurate detection of pathogens, probiotics, nitrifying bacteria, off-flavour compounds, and more. Additionally, we provide expert consultation on study design and result interpretation to help producers and researchers make informed decisions.