The research examined the changes in the gut microbiome in relation to acute diarrhea in Al-Qadisiyah Province, Iraq, which is the subject of a high public health burden in low- and middle-income communities where the regional patterns of the microbiome are scarcely known. The proposed cross-sectional case-control study was to be conducted at three hospitals in Al-Diwaniyah between March and November 2025, including 100 acutely diarrhea hospitalized patients and 100 controls who perfectly matched them in terms of age, sex, and residency. Analysis of fecal samples was conducted with the 16S rRNA V3-V4 sequencing on the Illumina MiSeq platform and bioinformatics analysis with QIIME2 2023.11. The findings showed that the microbial alpha diversity of cases relative to controls was significantly reduced and the Shannon index was significantly lower, which reveals a breakdown in microbial richness and evenness. Beta diversity analysis also showed distinct patterns of separation in compositions between groups. At the phylum level, patients showed a strong increase in Proteobacteria and a decrease in Firmicutes and Bacteroidetes, which indicates a change in microbiome towards a dysbiotic and inflammation-related one. Differential abundance analysis revealed the enriched presence of the important bacterial genera in patients, including Escherichia-Shigella and Streptococcus, and the positive taxa such as Faecalibacterium were more abundant in controls. It is noteworthy that microbial diversity was negatively correlated with the severity of dehydration and therefore the clinical implications of microbial diversity. The diagnostic potential of microbiome profiles was supported by the high accuracy in classification by a Random Forest model. Also, the presence of urban-rural gradients in the abundance of Proteobacteria suggests environmental factors, especially water quality, as the potential cause of dysbiosis. On the whole, these results have created a specific microbial profile of acute diarrhea in this area and have justified the creation of microbiome-based diagnostics and specific therapeutic interventions like probiotics.