Microbial Diversity, Functional Genomics and Antimicrobial Resistance in Integrated Fish Farming System in Bangladesh

The Integrated Fish Farming (IFF) system, combining fish farming with poultry and livestock rearing, is a sustainable agricultural practice prevalent in Bangladesh due to its economic and resource efficiency. This system's complex microbial ecosystems are critical to its health and productivity. Understanding microbial diversity, functional genomics, and antimicrobial resistance (AMR) within IFF systems is essential for optimizing efficiency and sustainability.Microbial communities are vital for nutrient cycling, disease suppression, and overall environmental health. Beneficial bacteria like Firmicutes are crucial for fermentation and nutrient absorption in poultry and livestock, enhancing animal growth and health. Diverse microbial populations in sediments and water significantly impact fish health and water quality. Despite their importance, comprehensive studies on microbial diversity and functional roles in IFF systems are limited.The widespread use of antibiotics in agriculture has led to the emergence of AMR, posing significant threats to animal and human health. Antibiotic-resistant bacteria can spread through environmental pathways, leading to zoonotic diseases. This research aims to analyze microbial diversity, functional genomics, and AMR in an Integrated Fish and Chicken Farming system in Bangladesh using high-throughput sequencing and advanced bioinformatics tools. Identifying antimicrobial resistance genes (ARGs) prevalence will help develop strategies to mitigate AMR risks, providing insights into IFF systems' ecological dynamics and informing sustainable management practices.