Rahmat Apipi

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.

Diarrhea remains a major global health issue and is one of the leading causes of morbidity and mortality, especially in children. Changes in the composition of gut microbiota are strongly associated with the occurrence of diarrhea, particularly due to infections caused by pathogenic microorganisms. Conventional diagnostic techniques, such as culture, still have limitations in detecting diverse and unculturable microbes. Metagenomics offers a comprehensive diagnostic solution by analyzing the entire genetic material directly from stool samples using sequencing-based approaches. This review discusses two metagenomic strategies—16S rRNA sequencing and whole-genome shotgun metagenomic sequencing—based on studies conducted in India and Peru. The 16S rRNA approach enables the identification of bacterial community structure and dysbiosis in diarrhea cases, while shotgun metagenomics provides higher resolution for detecting pathogenic species, including Campylobacter spp., and co-infections that are often missed by standard methods. Both techniques demonstrate significant advantages in detecting microbiota diversity, identifying novel pathogens, and uncovering antimicrobial resistance profiles. Therefore, metagenomics represents a promising diagnostic tool for improving the accuracy of diarrhea detection and supporting public health interventions in endemic regions.