Gut microbiome diversity analysis of Indonesian healthy and stunted children

Stunting is an impaired growth condition in children caused by poor nutrition, recurrent inflammation, and socioeconomic factors. It continues to be a global health problem in children, especially in developing countries. The gut microbiome is important in supporting children's health by increasing defense against pathogens and assisting the absorption of nutrients in the digestive system. This study explored microbiome diversity between healthy and stunted children in Tasikmalaya district, Indonesia. This cohort study included 118 children aged 0-24 months, with 34 stunted and 84 healthy children. Secondary measures such as identity, nutrition, and history of diarrhea in children were also taken. Characterization of the bacterial community was carried out with a shotgun metagenomic approach followed by alpha diversity analysis, correlation analysis, and principal component analysis to describe variations in microbiome composition. The results of this study show that stunted children have a higher Shannon index value compared to healthy children, indicating greater microbiota diversity. PCA results show the separation of stunted and healthy groups based on breastfeeding status values, where the healthy group tended to have more exclusive breastfeeding status than the stunted group. Exclusive breastfeeding creates a favorable environment for the growth of beneficial microorganisms such as Bifidobacterium and Lactobacillus. This is confirmed by results showing that Bifidobacterium and Lactobacillus is higher in healthy children than stunted children. However, in the stunting group, pro-inflammatory genera such as Eggerthella, Haemophilus, and Bilophila were found higher. Correlation analysis found that Haemophilus were negatively correlated with height-for-age z-score while positively correlated with weight-for-length/height z-score. This suggests that Haemophilus colonization is associated with the risk of stunting severity in children. These results suggest that the pattern of the gut microbiome in stunted children reflects a gut condition affected by chronic inflammation and adaptation to complex food intake. Findings from this study may suggest potential microbiota-based interventions for early detection and prevention of stunting.