Metagenomic Insights into the Viral and Bacterial Communities of a Shrimp Farm Ecosystem: Diversity and Ecological Significance

Environmental stressors such as poor water quality, overstocking, and temperature spikes force shrimp to divert energy from growth and immunity to maintain homeostasis, increasing their susceptibility to opportunistic pathogens. Despite this risk, information on how these conditions affect viral and bacterial abundance, diversity, and community structure in shrimp farms remains scarce. To address this gap, this study offers a broad metagenomic analysis of the viral and bacterial communities in a shrimp farm, uncovering their diversity and ecological significance. In total, 13,572 viral operational taxonomic units (vOTUs) were recovered. Most viruses belonged to the realm Duplodnaviria, with Caudoviricetes dominating the libraries. Additionally, some contigs were linked to the Iridoviridae, a family that can affect fish and shrimp. Taken together, these findings highlight the critical role of virus–host interactions in marine environments and underscore the utility of metagenomic analysis for monitoring and safeguarding aquaculture health.