Despite the widespread implementation of sanitation, immunization and appropriate treatment, infectious diarrheal diseases still inflict a great health burden to children living in low resource settings. Conventional microbiology research in diarrhea have focused on the pathogen's biology and pathogenesis, but initial enteric infections could trigger subsequent perturbations in the gut microbiome, leading to short-term or long-term health effects. Conversely, such pre-existing perturbations could render children more vulnerable to enteropathogen colonization and diarrhea. Recent advances in DNA sequencing and bioinformatic analyses have been integrated in well-designed clinical and epidemiological studies, which allow us to track how the gut microbiome changes from disease onset to recovery. Here, we aim to summarize the current understanding on the diarrheal gut microbiome, stratified into different disease stages. Furthermore, we discuss how such perturbations could have impacts beyond an acute diarrhea episode, specifically on the child's nutritional status and the facilitation of antimicrobial resistance.