Gut microbiota composition of stunted children in Banyumas Regency, Indonesia: A 16S rRNA microbiome profiling analysis

Stunting remains a major public health challenge in Indonesia and is increasingly associated with gut microbiota dysbiosis. This study examined 36 children aged 2–5 years through anthropometry, dietary assessment, and pooled fecal sampling. Full-length 16S rRNA sequencing using Oxford Nanopore Technologies revealed notable microbial alterations in the stunted group. Stunted children exhibited reduced alpha diversity and lower microbial richness, indicating a simplified gut ecosystem. Although both groups were dominated by Bacillota (>96%), stunted children showed higher proportions of Clostridia affiliated orders, including Eubacteriales, Peptostreptococcales, and Erysipelotrichaceae, along with enrichment of fermentative and dysbiosis associated genera such as Blautia, Romboutsia, and Terrisporobacter. Beneficial fiber degrading taxa, including Lachnospiraceae, were proportionally higher in normal children. Functional predictions using PICRUSt2 revealed greater microbial metabolic activity in the stunting group, particularly in carbohydrate, amino acid, and nucleotide metabolism, with elevated pathways such as starch and sucrose metabolism, glycolysis, and porphyrin and pyrimidine metabolism. Dietary assessment showed significantly lower intake of energy, protein, fat, and multiple micronutrients among stunted children, consistent with observed microbial and functional alterations. These findings indicate a distinct fermentative dysbiosis in Banyumas stunted children and highlight the need for integrated nutritional and microbiota targeted interventions. • Stunted children exhibit lower alpha diversity and reduced microbial richness • Unique Clostridia-heavy dysbiosis observed, differing from global stunting patterns • Enrichment of fermentative and mucin-degrading taxa in stunted children • Higher abundance of carbohydrate and amino acid metabolism pathways in stunting • Gut microbiota patterns correlate with significant macro- and micronutrient deficits