Feed Composition and Antibiotic Supplements Modulate Digestive Enzyme Activities and Alter Gut Microbiome of Pacific White Shrimp

Abstract The transition from fishmeal to sustainable alternatives in aquaculture is essential, however the physiological and microbial impacts of alternative diets in shrimp remain poorly understood. Here, we examine how substituting fishmeal with plant-based proteins such as guar and soybean meals, the inclusion of feather meal, and the use of a commonly used antibiotic (gentamicin) influence digestive enzyme function, protein digestibility, and gut microbial assemblages in Litopenaeus vannamei (Pacific white shrimp). The guar-based diet notably altered gut microbiota composition and decreased leucine aminopeptidase activity while maintaining high protein digestibility (>90%). In contrast, the soya/feather diet caused greater disruption to enzyme activity and microbial communities, resulting in reduced digestibility (∼75%). The gent/guar diet showed comparable digestibility and microbial stability to the guar diet, with only minor shifts at the genus level. Although digestibility data for the acclimation diet were unavailable, these findings highlight diet-specific physiological and microbial responses to fishmeal substitutes. This emphasizes the need to consider dietary formulation, digestive function, and microbiome dynamics when developing sustainable aquafeeds for shrimp farming. Importance The Pacific white shrimp (Litopenaeus vannamei) is a cornerstone of global aquaculture, yet optimizing its diet remains challenging. Current shrimp farming heavily depends on fishmeal, an unsustainable protein source, and antibiotic use to maintain shrimp health raises concerns about antimicrobial resistance and environmental impacts. This study highlights how alternative dietary formulations, including plant-based proteins and antibiotic supplements, influence shrimp digestive physiology and reshape gut microbiomes. Understanding these interactions is crucial to developing feed formulations that support robust shrimp growth and health without excessive reliance on antibiotics or fishmeal. By demonstrating how specific dietary ingredients affect both shrimp digestion and beneficial gut bacteria, this research provides valuable insights that can inform sustainable and responsible shrimp aquaculture practices globally.