News Release

Microbiome Sequencing as a Precursor to Adaptive Production Management in PondsĀ 

Microbiome sequencing provides valuable insights, enabling pond producers to understand the advantages and risks associated with microorganisms.

Microbiome pond
Shrimp ponds in the countryside of Thailand.

Published in Hatchery Feed & Management Vol 11 Issue 2 2023

Pond culture is a proven production model. By rearing organisms in a more controlled section of what amounts to their natural habitat, one can harness the ability of nature to meet many of their environmental needs. While this openness to nature is the strongest asset of pond production, it is, ironically, also the greatest weakness. By being open to environmental inputs such as rain, sun, and bacterial introduction, key water quality and biological conditions that directly impact the health and yields of one’s stock are only partially within the control of aquaculture producers. This lack of control can create situations where stock are stressed, which affects feed utilization, organism wellbeing, and opens the door for opportunistic pathogens to flourish, causing disease and further impacting organism health and efficiency. 

One effective defense against these opportunistic pathogens is an adaptive production management strategy. To be effective, the strategy must rely on actionable insights derived from best practices and tailored to one’s situation, enabling efficient and targeted efforts. When considering opportunistic pathogens, conducting a comprehensive analysis of the microbiological composition of the pond through microbiome analysis provides valuable insights, enabling pond producers to better understand and address the benefits and risks posed by these microbes in an actionable way. 

In the realm of microbiome analysis, high-throughput sequencing stands as the gold standard, offering a timely and cost-effective method to explore the microbial composition of the pond. Dr. Adriana Artiles, Business Development Manager for Genetics at the Center for Aquaculture Technologies (CAT), says, “Through the evolution of high-throughput sequencing, we can gather information more quickly and at a lower cost than traditional microbiological sampling. The regular use of this technology enhances our knowledge of pond microbiomes and allows us to become proactive, rather than reactive.” 

Microbiome Balance and Stock Health

The microbiome of a pond ideally consists of a full suite of beneficial microorganisms in balance with their environment. A healthy microbiome is one in equilibrium, with microbes growing alongside one another, and populations of unwanted bacteria kept in check by balanced populations of beneficial bacteria and environmental factors. Such a microbiome is a key driver of stock health. A shift in environmental conditions can disrupt the balance of a pond’s microbial community, leading to stress in organisms, compromised immune capacity, proliferation of unwanted bacteria, and an increased risk of disease. 

Controlling the growth of unwanted bacteria is essential but challenging. While antibiotics have commonly been used for disease control, their use comes with financial costs, and there is increasing public concern about their use in animal protein production. However, adaptive management tools such as probiotics, symbiotics, bacteriophages, and immune-boosting feed additives are garnering great attention from the aquaculture industry. Although these tools show promise as effective solutions by balancing the pond microbiome, they are still in the early stages of implementation. In such cases, the use of microbiome sequencing can assess the suitability and effectiveness of these approaches in specific pond applications, facilitating their optimized utilization. 

Actionable Insights from Microbiome Analysis

“Microbiome analysis can be used to detect unwanted bacteria threatening production through time, quantify the diversity, and describe the function of microbes in your animal’s environment, and custom design of a monitoring program for species of interest,” adds Jordan Poley, Manager of Laboratory Services at CAT. He further emphasizes the information generation capabilities of microbiome sequencing, stating, “Microbiome data can also be applied as bioindicators for the effects of manipulating feeds (e.g., probiotics), altering stocking density, responses and recovery in shifting environments, disease challenge monitoring, among other important events in the production cycle.” 

Once the information has been produced, the manner in which it is presented becomes crucial in determining whether it is actionable or not. This does not mean documentation should be colorful or presentations should be flashy. A good microbiome report encompasses clear and comprehensive data analysis and interpretation. It presents the findings in an understandable manner, including information on microbial composition, diversity, and abundance. The report offers context through comparisons to reference datasets, allowing for contextual understanding and benchmarking. Importantly, the report provides practical recommendations based on the results, supporting informed decision-making and potential interventions. Customization options ensure the report addresses specific needs and objectives, enabling a deeper understanding of the microbial ecosystem. 

This comprehensive reporting becomes especially valuable for aquaculture producers who have the need to address the unpredictable nature of the environment, ensuring stability and productivity in aquaculture operations. By leveraging actionable microbiome insights, producers can effectively safeguard their stock, promote microbial balance, and optimize pond performance. 


The Center for Aquaculture Technologies (CAT) drives breakthroughs in aquaculture and its allied sectors through specialized expertise in genetics, health, and nutrition. CAT’s international capabilities combine deep expertise in aquaculture and fisheries, molecular research, and tank-based testing, enabling them to provide innovative, research-driven solutions that enhance productivity, efficiency, and sustainability in aquaculture.