New method uses stool DNA to track diet and health

Scientists have developed a breakthrough method to track diet using stool metagenomic data.

Developed by researchers at the Institute for Systems Biology (ISB), the new method, called MEDI (Metagenomic Estimation of Dietary Intake), detects food-derived DNA in stool samples to estimate dietary intake. MEDI leverages stool metagenomics, which refers to sequencing all the DNA present in fecal samples (including microbial, human, and food-derived DNA). This non-invasive, data-driven approach offers an objective alternative to traditional food diaries and questionnaires, which are still the gold standard in dietary assessment but can suffer from misreporting and compliance issues.

For decades, nutrition research has depended on self-reported diaries and questionnaires – approaches that require a high degree of effort and compliance from research participants. How many strawberries did I eat two days ago? Did I have one glass of orange juice with breakfast, or two? MEDI provides a solution by analyzing food-derived DNA in gut metagenomic samples, offering a convenient alternative that shows good agreement with known dietary and nutritional intake patterns."

Dr. Christian Diener, lead author of the study

Key findings:

• An Alternative to Questionnaire-Based Diet Tracking: Leveraging a database of more than 400 food items and over 300 billion base pairs of genomic information, MEDI accurately detected food intake patterns in infants and adults, and across two controlled feeding studies. MEDI 
• Connecting Dietary Intake to Nutrition: MEDI converts the relative abundance profile of specific food items into nutrient profiles, assuming a 100 gram portion. These nutrient profiles show good agreement with data from controlled feeding studies.
• Identified Diet-Related Health Risks: Without food logs, MEDI pinpointed dietary features linked to metabolic syndrome in a large clinical cohort.

Our study represents a major leap forward in how we track diet and its impacts on human health. With food-derived DNA signatures in stool, we now have a powerful way to measure diet and microbiome composition from the same sample, which will expand our understanding of the forces shaping the human gut microbiome, personalized nutritional responses, and disease risk."

Dr. Sean Gibbons, senior author of the study, ISB Associate Professor

With further development, MEDI could transform nutrition science, epidemiological studies, and clinical trials, allowing researchers, doctors, and individuals to track diet-related health risks with unprecedented ease.