Are biopesticides really safe? Impacts on gut microbiota and intestinal health in freshwater fish

The growing use of biopesticides as eco-friendly alternatives to chemical pesticides is reshaping pest control in agriculture and aquaculture. However, their potential effects on non-target aquatic species, particularly freshwater fish, remain underexplored. This review investigates how different biopesticides, such as microbial agents, biochemical compounds, and plant-incorporated protectants, affect the gut microbiota and intestinal health of freshwater fish. The gut microbiome plays a vital role in digestion, nutrient absorption, immunity, and overall fish health. Biopesticide exposure may disrupt microbial balance, leading to reduced diversity, changes in community composition, inflammation, and dysbiosis. These alterations can impair digestive efficiency, immune function, growth, and reproduction. Promising mitigation strategies include the use of probiotics, prebiotics, symbiotics, insect-based feeds and other non-bacterial dietary interventions to restore gut homeostasis and improve fish resilience. In addition, advanced techniques like metagenomics and metabolomics are enhancing our understanding of host–microbiome interactions under biopesticide exposure. This review emphasizes the importance of including gut microbiota health in environmental risk assessments for biopesticide use in aquaculture. Future studies should adopt a multidisciplinary approach combining toxicology, microbiology, nutrition, and environmental science to develop species-specific, long-term strategies that safeguard fish health in increasingly pesticide-influenced aquatic environments.