What Scientists Learn from Fecal DNA
Tracking DNA in digested food can provide valuable data to researchers — information that could have a major impact on nutritional guidance for people with obesity and digestive diseases and other gastrointestinal and nutrition-related issues.
David and Petrone’s 2023 study analyzing DNA in stool samples, published in the Proceedings of the National Academy of Sciences (PNAS), showed what — and roughly how much — people ate.
They noticed that kids with obesity had a higher diversity of plants in them than kids without obesity. Sounds backward — wouldn’t a child who eats more plants be a healthier weight? “The more I dug into it, it turns out that foods that are more processed often tend to have more ingredients. So, a Big Mac and fries and a coffee have 19 different plant species,” said David.
Going forward, he said, researchers may have to be “more specific about how we think about dietary diversity. Maybe not all plant species count toward health in the same way.”
David’s work provides an innovative way to conduct nutrition research, said Jotham Suez, PhD, an assistant professor in the department of molecular microbiology and immunology at Johns Hopkins Bloomberg School of Public Health.
“We need to have some means of tracking what people actually ate during a study, whether it’s an intervention where we provide them with the food or an observational study where we let people eat their habitual diet and track it themselves,” said Suez, who studies the gut microbiome.
“Recall bias” makes food questionnaires and apps unreliable. And research suggests that some participants may underreport food intake, possibly because they don’t want to be judged or they misestimate how much they actually consumed.
“There’s huge promise” with a tool like the one described in the PNAS study for making connections between diet and disease, Suez said. But access may be an issue for many researchers. He expects techniques to improve and costs to go down, but there will be challenges. “This method is also almost exclusively looking at plant DNA material, Suez added, “and our diets contain multiple components that are not plants.”
And even if a person just eats an apple or a single cucumber, that food may be degraded somewhere else in the gut, and it may be digested differently in different people’s guts. “Metabolism, of course, can be different between people,” Suez said, so the amounts of data will vary. “In their study, the qualitative data is convincing. The quantitative is TBD [to be determined].”
But he said it might be “a perfect tool” for scientists who want to study indigestible fiber, which is an important area of science, too.
“I totally buy it as a potentially better way to do dietary analytics for disease associations,” said Stollman, an expert in fecal transplant and diverticulitis and a trustee of the American College of Gastroenterology. Stollman sees many patients with diverticular disease who could benefit.
“One of the core questions in the diverticular world is, what causes diverticular disease, so we can ideally prevent it? For decades, the theory has been that a low fiber diet contributes to it,” said Stollman, but testing DNA in patients’ stools could help researchers explore the question in a new and potentially more nuanced and accurate way. Findings might allow scientists to learn, “Do people who eat X get polyps? Is this diet a risk factor for X, Y, or Z disease?” said Stollman.