Bacterial diversity associated with the different shrimp farming systems in Bangladesh

Microbial community inhabiting in the gut and surrounding environments is a key driver in the health and disease status of cultured shrimp. Arbitrarily application of antibiotics in aquaculture is a promising concern due the emergence of antibiotic resistant genes (ARGs). The present study investigates the microbiome composition and 19 ARGs of the cluster, extensive, semi-intensive, and improved extensive shrimp farming systems in the southwest coastal region of Bangladesh using 16S rRNA metagenomic sequencing and traditional PCR method. Proteobacteria was the dominant phyla observed in sediment, water and shrimp gut samples (n=12). The predominant phyla over different farming systems except Proteobacteria were Firmicutes, Actinobacteria, Bacteroidetes, and Cyanobacteria. Firmicutes was the predominant phyla (relative abundance 53.33%) in the gut of shrimp cultured in the cluster and semi-intensive (relative abundance 59.2%) culture system. The results indicated that bacterial community structure was significantly distinct among gut, sediment, and water samples as well as over the different farming systems. The shared operational taxonomic unit (OTU) in the sediment sample (16495) was nearly double than the gut (7931) and water (8513) bacterial communities. The cluster farming system showed 768 shared OTUs among gut, sediment and water groups followed by improved extensive system. Sul1, cat, gyrA(C), tetA, tetC, tetX, ere(A), vanR, and dfrA1 were predominantly detected in water and sediment samples. Semi-intensive farming system had the highest prevalence of ARGs (21.05%) followed by cluster (15.79%), improved extensive (7.02%), and extensive (5.26%) farming system. Therefore, the production strategy might focus on the alternatives of antibiotic to for shaping the shrimp cultivation more sustainable.