Microbiome determinants of productivity in aquaculture of whiteleg shrimp.

Aquaculture holds immense promise for addressing the food needs of our growing global population. Yet, a quantitative understanding of the factors that control its efficiency and productivity has remained elusive. In this study, we address this knowledge gap by focusing on the microbiome determinants of productivity, more specifically animal survival and growth, for one of the most predominant animal species in global aquaculture, whiteleg shrimp ( IMPORTANCE: Aquaculture is a rapidly growing industry essential for global food security, yet its productivity is often constrained by high mortality rates and inefficient growth. While the microbiome is known to influence host health and nutrient assimilation, its broader role in animal production remains poorly understood. Here, we take a data-driven approach to address this gap by systematically analyzing shrimp-associated microbiomes across hatcheries and farms. By integrating microbiome data with machine learning, we demonstrate that microbial communities are powerful predictors of key production outcomes, shaping shrimp survival and growth. Our findings suggest that the microbiome could serve as a diagnostic tool for assessing production conditions and optimizing management strategies. In addition, machine learning techniques offer a promising avenue for identifying beneficial microbes and developing targeted microbiome therapies to enhance aquaculture sustainability and efficiency.