Microbial Diversity, Functional Genomics and Antibiotic Resistance in Integrated Chicken and Fish Farming Systems in Bangladesh

Abstract

The Integrated Fish Farming (IFF) system, practiced in Bangladesh for its economic benefits and resource efficiency, requires an understanding of microbial diversity, functional genomics, and antimicrobial resistance to optimize efficiency and sustainability. This study delves into the microbial compositions, diversity, and antibiotic resistance within diverse environmental samples using 16S rRNA sequencing and KEGG pathway analysis. The taxonomic analysis revealed a microbial community comprising 2838 OTUs, with Bacteria (99.81%) dominating over Archaea (0.19%). Sediment samples exhibited the highest archaeal diversity, primarily consisting of Euryarchaeota, Parvarchaeota, and Crenarchaeota. Bacterial diversity encompassed 70 phyla, with Firmicutes being predominant, particularly in chicken gut samples. Notable bacterial genera included Lactobacillus and Weissella. Alpha diversity analysis highlighted significant microbial richness in sediment and fish intestine samples, while beta diversity analysis using Bray-Curtis PCoA indicated distinct microbial community compositions across sample types. Functional genomic analysis revealed metabolic genes as the most predominant across all samples, focusing on amino acid, carbohydrate, and energy metabolism. Noteworthy pathways included ribosome biogenesis and ABC transporters, particularly abundant in sediment and feed samples. Antibiotic susceptibility testing of 55 isolates demonstrated high resistance rates, notably against Tetracyclines and Fluoroquinolones, with Escherichia coli and Proteus mirabilis exhibiting the highest resistance. Antibiotic resistance genes identified through KEGG pathways, such as bcrC and vanX, were abundant in sediment and chicken gut samples, indicating significant resistance profiles. This comprehensive profiling underscores the diverse and complex microbial ecosystems in various samples, the metabolic dominance in these environments, and the concerning levels of antibiotic resistance among common bacterial pathogens. These findings emphasize the need for ongoing surveillance and targeted interventions to mitigate the spread of antibiotic resistance in microbial communities. This is the first study in the country to reveal microbial diversity, antimicrobial resistance and functional genomics in Integrated Chicken and Fish Farming settings.