Scientists decode diet from stool DNA – no questions asked

SEATTLE – 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?" said Dr. Christian Diener, lead author of the study. "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."

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

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.

The full study is published in Nature Metabolism and can be accessed here. For media inquiries or interview requests, please contact ISB’s media team at communications@isbscience.org.

About ISB

Institute for Systems Biology (ISB) is a collaborative and cross-disciplinary non-profit biomedical research organization based in Seattle. We focus on some of the most pressing issues in human health, including aging, brain health, cancer, chronic illness, infectious disease, and more. Our science is translational, and we champion sound scientific research that results in real-world clinical impacts. ISB is an affiliate of Providence, one of the largest not-for-profit healthcare systems in the United States. Follow us online at isbscience.org, and on YouTube, Facebook, LinkedIn, X, Bluesky, and Instagram.