A lightbulb moment hit as Lawrence David was chatting one day with an ecologist who studies the microbiomes and diets of large herbivores in the African savanna. David was envious. He’d been studying the human microbiome, and this ecologist had tons of animal statistics that were way more specific than what David had obtained from people.
“How on earth do you get all these dietary data?” David recalled asking. “Obviously, he didn’t ask the animals what they ate.”
All those specific statistics came from DNA sequencing of animal scat scooped up from the savanna.
Indeed.
Depending on when you read this, you may have the DNA of more than a dozen plant species, plus another three or four animal species, gurgling through your gut. That’s the straight poop taken straight from, well, poop.
Diet, DNA, and Feces
Everything we eat (except vitamins, minerals, and salt) came from something that was living, and all living things have genomes.
“A decent fraction of that DNA” goes undigested and is then excreted, said David, a PhD and associate professor of molecular genetics and microbiology at Duke University, Durham, North Carolina.
“We are using DNA sequencing to reconstruct what people eat,” David said. “We try to see if there are patterns in what people eat and how we can measure them by DNA, or kind of genetic forensics.” Then they connect that data to health outcomes like obesity.
A typical person’s excrement probably contains the DNA of 10-20 plant species and three or four types of animal DNA. “And that’s the average person. Some people may have more like 40 types at any given time,” David said.
Studying DNA in human feces has potential applications in research and in clinical settings. For instance, it could help design personalized nutrition strategies for patients, something that’s already being tested. He hopes that DNA information will help “connect patterns in what people eat to their microbiomes.”
One big advantage: Feces don’t lie. In reconstructing someone’s diet, people either forget what they ate, fudge the truth, or can’t be bothered to keep track.
“Patients report the fruit they ate yesterday but not the M&Ms,” said Neil Stollman, MD, chief of the division of gastroenterology at Alta Bates Summit Medical Center in Oakland, California.
Some people can’t write it all down because they’re too old or too young — the very people at highest risk of nutrition-associated disease, said David.
Fetching and Figuring Out Feces
It’s a lot of work to collect and analyze fecal matter, for ethical, legal, and logistical reasons. “And then there’s sort of an ick factor to this kind of work,” David said.
To get samples, people place a plastic collection cup under the toilet seat to catch the stool. The person then swabs or scoops some of that into a tube, seals the top, and either brings it in or mails it to the lab.
In the lab, David said, “if the DNA is still inside the plant cells, we crack the cells open using a variety of methods. We use what’s called ‘a stomacher,’ which is like two big paddles, and we load the poop [which is in a plastic bag] into it and then squash it — mash it up. We also sometimes load small particles of what is basically glass into it and then shake really hard — it is another way you can physically break open the plant cells. This can also be done with chemicals. It’s like a chemistry lab,” he said, noting that this process takes about half a day to do.
There is much more bacterial DNA in stool than there is food DNA, and even a little human DNA and sometimes fungi, said David. “The concentration of bacteria in stool is amongst the highest concentrations of bacteria on the planet,” he said, but his lab focuses on the plant DNA they find.
They use a molecular process called polymerase chain reaction (PCR) that amplifies and selectively copies DNA from plants. (The scientists who invented this “ingenious” process won a Nobel Prize, David noted.) Like a COVID PCR test, the process only matches up for certain kinds of DNA and can be designed to be more specific or less specific. In David’s lab, they shoot for a middle ground of specificity, where the PCR process is targeting chloroplasts in plants.
Once they’ve detected all the different sequences of food species, they need to find the DNA code, a time-consuming step. His colleague Briana Petrone compiled a reference database of specific sequences of DNA that correspond to different species of plants. This work took more than a year, said David, noting that only a handful of other labs around the country are sequencing DNA in feces, most of them looking at it in animals, not humans.
There are 200,000 to 300,000 species of edible plants estimated to be on the planet, he said. “I think historically, humans have eaten about 7000 of them. We’re kind of like a walking repository of all this genetic material.”