Acute diarrhea is associated with alterations in the gut microbiota, yet data from Indonesian pediatric populations remain limited. This study characterized the fecal microbiota of children and toddlers with acute diarrhea using 16S rRNA gene amplicon sequencing. A cross-sectional study was conducted on 24 pediatric patients with acute diarrhea (12 toddlers and 12 children). Fecal microbiota composition, alpha diversity, beta diversity, and functional profiles were analyzed using QIIME2 and PICRUSt2. Streptococcus thermophilus and Faecalibacterium duncaniae exhibited higher abundance in toddlers. In contrast, Fusobacterium mortiferum was relatively more abundant in children. Alpha diversity indices showed no significant differences between children and toddlers. Beta diversity analyses also demonstrated substantial overlap between groups, with no significant difference in microbial community composition. Functional prediction identified the most discriminatory pathways as those related to energy and carbohydrate metabolism, amino acid metabolism, cellular biosynthesis, and environmental adaptation. Poor nutritional status (underweight) was associated with a decrease in protective commensal bacteria (Faecalibacterium duncaniae) (p < 0.05) and an increase in dysbiosis-associated bacteria (Parabacteroides distasonis) (p < 0.05). Despite modest species-level differences with age, alpha diversity, beta diversity, and overall bacterial community composition did not differ significantly between toddlers and children, indicating that acute diarrhea itself was the dominant factor shaping gut bacterial community structure in this cohort. Further studies with larger cohorts, external validation, and shotgun metagenomic sequencing are needed to validate these findings and explore candidate microbiota-based markers for pediatric acute diarrhea.

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