Background: Undernutrition and stunting are significant public health concerns globally, particularly in low- and middle-income countries. Nutritional intervention is the cornerstone of the management and prevention of these conditions. However, the gut microbiome has recently emerged as an essential modulator of the effects of nutritional interventions in undernutrition and stunting. This scoping review aims to examine the impact of nutrition intake (including if there is any intervention) over time on gut microbiome changes in infants and children under the age of 2 who experience undernutrition and stunting. Methods: A literature search was conducted in PubMed and Cochrane Library, including studies from 2013 to 2023, using terms related to malnutrition, stunting, failure to thrive, and gut microbiome. Inclusion criteria were applied to select eligible studies for review. Five studies were chosen to be included in this review. Results: The findings indicate that nutrition intake over time, including dietary supplementation and prebiotics, can influence the gut microbiome composition, diversity, and functionality in undernutrition and stunting infants and children. These may promote the growth of beneficial bacteria while reducing the abundance of harmful pathogens. Moreover, improvements in nutritional status, growth parameters, and immune function were observed in association with positive changes in the gut microbiota. Conclusion: Nutrition intake can positively modulate the gut microbiome in undernutrition and stunting infants by supporting the growth of beneficial gut bacteria such as Actinobacteria, Bacteroides, Streptococcus, Bifidobacterium, Prevotella sp, and other bacterial taxa that vary with age, ultimately contributing to enhanced growth and development outcomes. Further studies are needed to better understand the mechanisms underlying these effects and to develop targeted nutritional interventions that optimize the gut microbiome in undernutrition and stunting infants and children under 2 years.

Weight faltering (WF) has been associated with stunting and with long-term adverse consequences for health and development. Nutritional care for managing WF may consist of giving nutritional advice (NA) and/or provision of oral nutrition supplements (ONSs). In this study, we aimed to evaluate practical management options in the community for infants with WF aged 6–12 months. This nonrandomized clinical trial was conducted in the community of Makassar, South Sulawesi, from March 2022 to March 2023. A total of 1013 infants were enrolled for screening. Anthropometric measures were performed in 913 infants, of which 170 showed WF below the 15th percentile of the WHO weight increment table without stunting. Infants with a weight increment below P5th were assigned to receive NA plus ONS, while infants between P5th and below P15th were assigned to receive only NA. At the second and third months, ONSs were administered to WF infants who were below P15th. One month after the intervention, 87/105 infants in the NA-plus-ONS group (82.8%) and 52/65 infants in the NA-only group (80%) were no longer WF. After 3 months, infants in the NA-plus-ONS group achieved greater weight gain than infants in the NA group (264.1 g vs. 137.4 g, p < 0.001) as well as greater length gain (2.35 cm vs. 2.14 cm, p < 0.001). WF management should be started at below P15th to achieve a better result. Infants with greater nutritional deficits should be assigned to receive the combination of NA plus ONSs to achieve a higher rate of resolution of growth.

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.