Household Food Insecurity Alters Gut Microbiome Composition and Enriches Sutterella in Ethiopian Schoolchildren

Background: Household food insecurity (HFI) adversely affects child development by restricting caloric intake, dietary diversity, and food quality. Since diet is a key factor influencing the gut microbiome, HFI may negatively impact health by altering microbial communities. However, direct evidence linking HFI to changes in the gut microbiome is limited. Therefore, we investigated the effects of HFI as a composite variable and used individual HFI assessment questions as specific proxies for dietary deprivation on the gut microbiome in a group of Ethiopian schoolchildren. Methods: Fecal samples were collected from 57 school-aged children in Ethiopia, and microbial profiles were established using 16S rRNA amplicon paired-end sequencing. Food insecurity was assessed using the Household Food Insecurity Access Scale (HFIAS). Results: We observed no significant differences in alpha diversity across food security status (Wilcoxon p > 0.05). However, beta diversity analysis revealed a significant shift in microbiome composition between food-secure and food-insecure individuals (Bray–Curtis dissimilarity; PERMANOVA, p < 0.05). Further analyses of individual HFIAS questions as specific proxies for dietary deprivation showed that limited dietary variety, consumption of disliked foods, and reduced meal size were each associated with significant changes in microbial compositions (PERMANOVA; all q < 0.05). Differential abundance analyses consistently identified Sutterella as significantly more abundant among food-insecure participants (composite model q = 0.11; component-specific models q < 0.05). Additionally, a microbial feature-based machine learning model accurately predicted food security status (AUC = 0.81), with Sutterella emerging as the top predictive feature. Conclusions: Our findings suggest that food insecurity metrics are associated with alterations in gut microbial composition. The consistent enrichment of Sutterella in food-insecure children in this study suggests the need for future mechanistic studies to explore its role in mediating the effects of food insecurity.