Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6–24 Months with Persistent Diarrhea of Unknown Etiology

Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (<i>p</i> < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log₂FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as <i>Bifidobacterium longum</i>, <i>Faecalibacterium</i>, <i>Lactobacillus</i>, and <i>Eubacterium</i>, alongside an enrichment of opportunistic taxa including <i>Klebsiella</i>, <i>Enterococcus lactis</i>, and <i>Streptococcus</i> spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.