April 8, 2024 – A glowing moment got here when Lawrence David chatted sooner or later with an ecologist who studies the microbiomes and diets of huge herbivores within the African savanna. David was jealous. He had studied the human microbiome and this ecologist had tons of animal statistics that were rather more specific than what David had obtained about humans.
“How on earth do you get all this nutritional data?” David remembered asking. “Obviously he didn’t ask the animals what they ate.”
All of those specific statistics come from DNA sequencing of animal feces collected from the savanna.
As a matter of fact.
Depending on if you read this, you could have the DNA of greater than a dozen plant species and one other three or 4 animal species gurgling through your stomach. This is the pure poop that comes straight from the poop.
David and colleagues are analyzing DNA in human feces to higher understand digestion and the links between weight loss program and health, potentially paving the best way for treatments for diet-related diseases.
Diet, DNA and feces
Everything we eat (except vitamins, minerals, and salt) comes from something living, and all living things have genomes.
“A significant portion of this DNA” stays undigested and is then excreted, said David, a graduate student and associate professor of molecular genetics and microbiology at Duke University in Durham, North Carolina.
“We use DNA sequencing to reconstruct what people eat,” said David. “We're trying to figure out if there are patterns in people's diets and how we can measure those using DNA or some kind of genetic forensics.” Then they link that data to health outcomes like obesity.
A typical human's excrement probably incorporates the DNA of 10-20 plant species and three or 4 forms of animal DNA. “And that’s the average person. Some people may have more than 40 types at a time,” David said.
The study of DNA in human feces has potential applications in research and clinical settings. For example, it could help develop personalized nutrition strategies for patients, which is already being tested. He hopes DNA information will help “link patterns in people’s diets to their microbiome.”
An enormous advantage: poop doesn't lie. When reconstructing an individual's weight loss program, people either forget what they ate, distort the reality, or don't feel like keeping track.
“Patients report the fruit they ate yesterday, but not the M&Ms,” said Dr. Neil Stollman, chief of gastroenterology at Alta Bates Summit Medical Center in Oakland, California.
Some people can't write every thing down because they're too old or too young – the very people at highest risk for diet-related diseases, David said.
Get poop and discover
For ethical, legal and logistical reasons, collecting and analyzing feces is a whole lot of work. “And then there’s a certain ick factor to this type of work,” said David.
To collect samples, place a plastic cup under the bathroom seat to catch the stool. The person then wipes or scoops some right into a tube, closes the lid, and either brings it with them or mails it to the lab.
In the lab, David said: “If the DNA is still in the plant cells, we break the cells open using different methods. We use what we call a “stomaker,” which is 2 large paddles, and cargo the feces into it.” [which is in a plastic bag] put in after which mash – mash. Sometimes we also load in small particles of glass after which shake them really hard – that is one other option to physically break down the plant cells. This may also be done with chemicals. “It’s like a chemistry lab,” he said, noting that the method takes about half a day.
“There is a lot more bacterial DNA in stool than dietary DNA and even a little bit of human DNA and sometimes fungi,” David said. “The concentration of bacteria in stool is among the highest concentrations of bacteria on the planet,” he said, but his lab is concentrated on the plant DNA it found.
They use a molecular process called polymerase chain response (PCR) that amplifies and selectively copies DNA from plants. (The scientists who invented this “genius” process won Nobel Prize, noted David.) Like a COVID-19 PCR test, the method only matches certain forms of DNA and could be made kind of specific. In David's lab, they’re searching for a middle ground of specificity where the PCR process targets chloroplasts in plants.
Once they’ve discovered all different sequences of the food types, they have to find the DNA code, a time-consuming step. His colleague Briana Petrone has compiled a reference database of specific DNA sequences corresponding to different plant species. That work took greater than a 12 months, David said, noting that only a handful of other labs across the country sequence DNA in feces, with most of them studying it in animals reasonably than humans.
There are estimated to be 200,000 to 300,000 edible plant species on the planet, he said. “I think historically humans have eaten about 7,000 of them. We’re kind of like a walking repository for all this genetic material.”
What scientists learn from fecal DNA
Tracking the DNA in digested foods can provide researchers with useful data – information that might have a huge impact on dietary advice for individuals with obesity, digestive diseases and other gastrointestinal and dietary problems.
David and Petrones 2023 study Analysis of DNA in stool samples, published within the Proceedings of the National Academy of Sciences (PNAS)showed roughly what – and the way much – people ate.
They found that children with obesity had greater plant diversity than children without obesity. Sounds backwards – wouldn’t a baby who eats more plants have a healthier weight? “The more I looked into it, the more I realized that foods that are more processed often contain more ingredients. So a Big Mac, fries and a coffee contain 19 different types of plants,” said David.
In the longer term, he said, researchers may have to “think more concretely about how we think about dietary diversity. Not all plant species may contribute to health in the same way.”
“David's work provides an innovative way to conduct nutrition research,” said Jotham Suez, PhD, assistant professor within the Department of Molecular Microbiology and Immunology on the Johns Hopkins Bloomberg School of Public Health.
“We need ways to track 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 usual diet and track them yourself,” said Suez, who studies the intestinal microbiome.
“Recall bias” makes food questionnaires and apps unreliable. And Research suggests that some participants may under-report their dietary intake, perhaps because they are not looking for to be judged or because they misjudge how much they really consumed.
Stollman, an authority in fecal transplantation and diverticulitis and a trustee of the American College of Gastroenterology, sees many patients with diverticular disease who may gain advantage from such a research.
“One of the key questions in the diverticular world is what causes diverticular disease so that we can ideally prevent it? The theory has been around for decades that a low-fiber diet contributes to this, Stollman said, but DNA testing on patients' stools could help researchers examine the question in a new and potentially more nuanced and accurate way. The findings could allow scientists to find out: “Do people who eat X get polyps?” “Is this diet a risk factor for X, Y or Z diseases?” said Stollmann.
Future clinical applications
Brenda Davy, PhD, is a registered dietitian and professor within the Department of Human Nutrition, Food and Exercise at Virginia Tech. She conducts research examining the role of nutrition within the prevention and treatment of obesity and related diseases corresponding to type 2 diabetes. She also develops methods for dietary assessment. More than a decade ago, she developed considered one of the primary rapid assessment tools to quantify beverage consumption – the Beverage consumption questionnaire – an assessment that continues to be used today.
“Nutritional assessment is necessary in both research and clinical settings,” Davy said. “When a doctor diagnoses a patient with a particular condition, information about the patient'The patient's usual dietary habits can help prescribe dietary changes that may be helpful in treating this condition.
blook at Other methods, such as stool and urine samples, can be a safe and accurate way to collect this data, she said. Samples can be collected easily and non-invasively “in a variety of populations such as children or older adults” and in clinical settings.
Davy and her team use David's technology of their work – specifically a tool called FoodSeq that applies DNA metabarcoding to human stool to gather details about consumed food taxa. Their two labs are currently working together on a project that explores how one can do that highly processed foodss could impact the danger of type 2 diabetes and cardiovascular health.
David's lab desires to take its research in lots of directions, potentially collaborating with epidemiologists on global studies that may help them expand their DNA database and higher understand how climate change might affect dietary diversity, for instance, and learn more concerning the Nutrition in all areas to experience different populations.