Infectious gastroenteritis is a diagnosis that depends greatly on traditional culture, which has a slow turnaround time and is unable to detect viruses, parasites, or fastidious bacteria, thus creating a serious ethiological gap in knowledge. The goal of the study was to determine the impact of shotgun metagenomic next -generation sequencing (mNGS) on the detection and analysis of intestinal microbes comparatively to its diagnostic capability, rapidity, and overall yield against the standard of care. A prospective, lab-based study where 200 stool samples were subjected to a conventional culture and a standardized mNGS workflow and compared statistically in terms of sensitivity, specificity and turnaround time, was conducted on patients with acute gastroenteritis. Findings indicated that mNGS was far better than culture, having a sensitivity of 96.7 -1 (95 CI: 88.7-99.1-1) and a 33.2 -hour improvement in average time-to-result (35.2 vs. 68.4-1 hours, p = 0.001). Moreover, mNGS added significant diagnostic information to the other tests by detecting viral and parasitic pathogens in 29.4% of culture-negative samples and antimicrobial resistance genes in 44.5% of all samples. We conclude that contemporary metagenomic technology is a revolutionary, more holistic method of detecting intestinal pathogens with the potential to provide rapid, true, and comprehensive diagnosis which is essential in enhancing the management and antimicrobial stewardship of patients.