Association of Gut Microbiota Composition with Stunting Incidence in Children under Five in Jakarta Slums

Background: Stunting can be linked to various factors, one of which is dysbiosis. This study aims to analyze the microbiota composition and related contributing factors of stunted and non-stunted children in the slum areas of Jakarta. Methods: The subjects in this study included 21 stunted (HAZ ≤ −2SD) and 21 non-stunted children (−2SD ≤ HAZ ≤ 3SD) aged 2–5 years. Microbiota analysis was performed by extracting DNA from the subjects’ feces and then via 16S rRNA sequencing using next-generation sequencing (NGS). Results: The results of this study showed that in stunted children, the abundance of Mitsuokella (24,469 OTUs), Alloprevotella (23,952 OTUs), and Providencia alcalifaciens (861 OTUs) was higher, while in non-stunted children, that of Blautia (29,755 OTUs), Lachnospiraceae (6134 OTUs), Bilophila (12,417 OTUs), Monoglobus (484 OTUs), Akkermansia muciniphila (1116 OTUs), Odoribacter splanchnicus (42,993 OTUs), and Bacteroides clarus (8900 OTUs) was higher. Differences in microbiota composition in the two groups were influenced by nutrient intake, birth history, breastfeeding history, handwashing habits before eating, drinking water sources, and water sources for other activities. Conclusions: This study highlights that stunted children have a significantly different gut microbiota composition compared to non-stunted children, with higher levels of pathogenic bacteria and lower levels of beneficial bacteria. Future research should focus on interventions that can improve the gut microbiota composition to prevent stunting in children.