Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices

Abstract

Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.