DIETARY GENOMICS AS A COMPLEMENTARY TOOL IN CHILDHOOD MALNUTRITION INTERVENTION

Abstract

Malnutrition remains a critical global health challenge, especially among children. Developing effective treatment and prevention policies require accurate and large-scale dietary intake data yet traditional methods of dietary assessments rely on self-report methods and suffer from limitations of recall bias, reporting errors, and logistical constraints—particularly in resource-limited settings. Emerging omics-based approaches offer objective alternatives, with dietary genomics, specifically DNA metabarcoding, providing a non-invasive means to detect and quantify food intake from residual DNA in fecal samples. While recent studies have demonstrated feasibility for identifying dietary components and developing epidemiological metrics, the application of dietary genomics in clinical interventions for malnutrition remains unexplored. This dissertation evaluates dietary genomics as a scalable tool for monitoring dietary intervention uptake and impact in malnutrition across diverse contexts. In Chapter 2, we investigate whether food provisioning improves dietary quality in children with obesity (Durham, USA) in a randomized clinical trial using both traditional and genomic dietary assessment. Our results show comprehensive dietary improvements with food provisioning compared to usual care, with dietary genomics confirming consumption of provided foods and corroborating dietary shifts. These findings support expanding “Food-is-Medicine” interventions to pediatric populations and provide a roadmap for how dietary genomics can be integrated into clinical obesity management. In Chapter 3, we evaluate dietary genomics as a compliance biomarker in stool samples from malnourished infants from rural Pakistan receiving ready-to-use therapeutic and supplementary foods (RUTF/RUSF). Our results show significant detection of chickpea DNA (primary RUSF ingredient) coinciding with RUSF administration. Genomic analysis also uncovered unexpected dietary behaviors, such as widespread tea consumption, which may impede nutritional recovery. These findings establish dietary genomics as a novel method for compliance monitoring and highlight its potential for informing public health interventions. Collectively, the results in this thesis advance dietary genomics as a tool for enhancing interventions against childhood malnutrition and facilitating the development of effective context-specific nutritional guidelines and policies.