Longitudinal Microbiome and Metabolome Shifts After Successful Intervention in Impending Stunting in Indonesian Infants

Abstract

Background/Objectives: Stunting and weight faltering (WF) remain pressing public health challenges in low- and middle-income countries, with long-term consequences for child growth, development, and survival. While the role of gut health in early growth is increasingly recognized, evidence on how the gut microbiome and metabolome respond to nutritional interventions in WF infants is scarce. This study explored gut microbiome and metabolome changes in Indonesian infants aged 6-12 months who overcame WF following a one-month intervention. Methods: Infants were assigned to either a Nutritional Advice (NA) group or a Nutritional Advice plus Oral Nutritional Supplements (NAONS) group. Stool samples were collected before and after the intervention for microbiome (16S rRNA sequencing) and metabolome (LC-MS) analysis. Results: Significant shifts in gut microbial composition (beta diversity) and species richness (Chao1 index) were observed in both groups, suggesting enhanced microbial diversity and gut resilience. Within-group analysis revealed increases in beneficial genera such as Faecalibacterium and Peptostreptococcus, and a reduction in pro-inflammatory Fusobacterium in the NA group. The NAONS group showed a notable decrease in Proteus, a potentially pathogenic genus. Between-group comparisons indicated higher abundances of Lactococcus and Leuconostoc in the NAONS group, likely reflecting the influence of milk protein-rich supplements on microbial colonization, favoring lactic acid bacteria over SCFA-producing taxa, leading to better gut health. Metabolome analysis revealed significant changes in the NA group, increases in metabolites like Threonine, Tryptophan, and Xylose pointed to improved energy metabolism and gut health, while a decrease in Oxalic Acid suggested better metabolic efficiency. In contrast, the NAONS group, while benefiting from rapid weight gain, displayed a distinct metabolic profile influenced by high milk protein intake. No significant correlations were found between microbiome and metabolome changes, highlighting the complexity of gut-host interactions, suggesting that the interventions led to independent shifts in the aforementioned profiles. Conclusions: Overall, the findings suggest that nutritional interventions may enhance gut health and support recovery from weight faltering, providing insights into strategies that may contribute to restoring healthy growth trajectories and preventing stunting by modulating gut health.

Keywords: Indonesian infants; metabolome; microbiome; stool sample analysis; weight faltering.

Figure 1

Beta diversity analysis of the microbiome of the 2 groups before and after 1–month of intervention. ***: statistically significant; PCoA: Principal Coordinate Analysis.

Figure 2

Alpha diversity analysis of the microbiome of the 2 groups before and after 1-month intervention. *** and ****: statistically significant; ns: statistically not significant; #: paired t test; and ##: Wilcoxon Signed-Rank test.

Figure 2

Alpha diversity analysis of the microbiome of the 2 groups before and after 1-month intervention. *** and ****: statistically significant; ns: statistically not significant; #: paired t test; and ##: Wilcoxon Signed-Rank test.

Figure 3

Pairwise comparison taxonomy of the 2 groups in the microbiome analysis before and after 1-month intervention. * and **: statistically significant; p.adj: adjusted p-values using Wilcoxon Signed-rank test and FDR correction.

Figure 4

Beta diversity analysis of the microbiome of the 2 groups after 1–month intervention. ns: not statistically significant; PCoA: Principal Coordinate Analysis.

Figure 5

Alpha diversity analysis of the microbiome of the 2 groups after 1-month intervention. *: statistically significant; ns: statistically not significant; #: Independent t test; ##: Wilcoxon Signed-Rank test.

Figure 6

Pairwise taxonomy comparison of the 2 groups in the microbiome analysis after 1-month intervention. * and **: statistically significant; p.adj: adjusted p values using Wilcoxon Signed-rank test and FDR correction.

Figure 7

Beta diversity analysis of the metabolome of the 2 groups. *: statistically significant; ns: not statistically significant; PCoA: Principal Coordinate Analysis.

Figure 8

Pairwise metabolome comparison of the 2 groups in the metabolome analysis. * and **: statistically significant; p.adj: adjusted p-values using Wilcoxon Signed-rank test and FDR correction.

Figure 8

Pairwise metabolome comparison of the 2 groups in the metabolome analysis. * and **: statistically significant; p.adj: adjusted p-values using Wilcoxon Signed-rank test and FDR correction.

Figure 9

Beta diversity analysis of the metabolome of the 2 groups after 1–month intervention. ns: not statistically significant; PCoA: Principal Coordinate Analysis.

Figure 10

Pairwise comparison of the 2 groups in the metabolome analysis after 1–month intervention. * and **: statistically significant; p.adj: adjusted p-values using Wilcoxon Signed-rank test and FDR correction.