Monitoring Freshwater Quality in Egypt and the Suez Canal Region: The Critical Role of Metagenomics and Integrated Assessment

Freshwater quality plays a critical role in ensuring safe drinking water, highlighting the need for continuous and comprehensive monitoring. In Egypt, the Nile River serves as the main freshwater source, contributing over 90% of the nation’s water supply. The Ismailia Canal and its branches, vital freshwater sources for the Suez Canal region, face significant degradation due to different sources of pollution. Despite its importance, limited information exists on the bacterial composition of these freshwater systems. Traditional culture-based methods are commonly employed to detect indicator bacteria, identify dominant species, and evaluate antibiotic resistance. While these methods are useful, they fail to capture the full microbial diversity. To address this limitation, metagenomic approaches, particularly high-throughput 16S rRNA gene sequencing, provide a more comprehensive characterization of the water microbiome. This integrated approach, combined with physico-chemical assessments, offers deeper insights into bacterial community dynamics and pollution impacts, supporting improved water resource management and drinking water safety.