Nutrition science breakthrough: DNA barcoding can identify exactly what a person ate

Scientists at the Duke School of Medicine have developed a cutting-edge method that uses DNA barcoding to identify the plant-based foods an individual has consumed, based on analysis of DNA markers in fecal samples. 

This innovative technique promises to bridge the gap between what people say they’ve eaten and what they’ve actually consumed. These two things often diverge significantly. The breakthrough could improve the accuracy of clinical trials, nutrition studies, and much more.

DNA barcoding tech uses genetic markers

This technology builds upon previous research that sought to compare the DNA found in feces to reported diets.

Under the direction of Professor Lawrence David, who specializes in molecular genetics and microbiology, researchers have developed a genetic marker for plant-based foods. 

“We can go back after the fact and detect what foods were eaten,” explained study lead author Brianna Petrone.

The marker identified is a specific region of DNA that plants utilize to power chloroplasts, the organelles responsible for converting sunlight into sugars. Known as trnL-P6, this genomic region is present in all plants, but varies subtly from species to species.

The team put their marker to the test. They analyzed more than 1,000 fecal samples from 324 study participants across five different studies. Approximately 20 of these participants maintained high-quality dietary records.

As reported in the journal Proceedings of the National Academy of Sciences, the team found that these DNA markers can indicate not only what foods were consumed. They can also identify the relative quantities of specific food species.

The researchers observed that a person’s diet, age, and household income influenced the diversity of plant DNA found in their feces.

Distinguishing between major crops

For the investigation, Professor David’s lab made use of a reference database that contains markers for 468 species of plants typically consumed by Americans in plant-based foods.

By associating detected versions of trnL-P6 with specific plant sources, their DNA barcoding method was able to distinguish 83 percent of all major crop families.

Petrone noted that people in other parts of the world tend to consume the subset of crop families that are currently undetectable. The lab is now working on adding crops such as pearl millet and pili nuts to their database. 

The team has yet to track meat intake, but Professor David assures that the technology has that capability as well. “That relative ratio of plant to animal intake is probably one of the most important nutritional factors we might look at,” he said.

The researchers applied their DNA barcoding technique to fecal samples from participants of a weight loss intervention program. By examining the DNA markers, the team knew exactly what the participants had been fed a day or two prior.

For instance, the scientists searched for markers of a dish called mushroom wild rice pilaf’s components in fecal samples after serving it.

DNA markers reveal dietary patterns 

The team found that the DNA barcoding technique not only identified the plants but also the relative amounts consumed of certain plants.

“When big portions of grains or berries were recorded in the meal, we also saw more trnL from those plants in stool,” Petrone said.

The team then analyzed samples from 60 adults who participated in two fiber supplementation studies. The number of plants detected by trnL aligned well with dietary diversity and quality as estimated from participants’ survey responses.

Researchers later applied DNA barcoding to a study involving 246 adolescents from diverse racial, ethnic, and socioeconomic backgrounds.

The study revealed 111 different markers from 46 plant families and 72 species in the adolescents’ diet. Notably, over two-thirds of the subjects consumed wheat, chocolate, corn, and the potato family.

The technique is not without its limitations. For example, it can’t distinguish between individual members of closely related plant families, such as the brassica family, which includes broccoli, Brussels sprouts, kale, and cauliflower. 

However, the research revealed a pattern of greater dietary variety among higher-income study participants and a decline in fruit, vegetable, and whole grain food intake as the adolescents aged. This may be a result of older children eating less often with their families.

Professor David is optimistic about the potential of the barcoding technique. He asserts that it can effectively identify the diversity of plants found in a sample as a surrogate for dietary diversity. Dietary diversity is a well-known indicator of nutrient adequacy and superior heart health.

Future research opportunities 

Interestingly, the researchers conducted these genomic analyses on samples they had collected years prior. This suggests that researchers could potentially use the DNA barcoding method to reconstruct dietary data for already concluded studies.

The research team believes that this novel methodology will significantly benefit various studies of human nutrition. 

“We are limited in how we can track our diets, or participate in nutrition research or improve our own health, because of the current techniques by which diet is tracked,” said Professor David.

“Now we can use genomics to help gather data on what people eat around the world, regardless of differences in age, literacy, culture, or health status.”

Looking to the future, the team plans to apply this technique to global studies of disease. They also plan to monitor food biodiversity in settings facing climate instability or ecological distress.

More about DNA barcoding

DNA barcoding is a method of identifying species. It uses a short DNA sequence from a specific part of the genome.

In animals, the commonly used barcode region is a portion of the mitochondrial cytochrome c oxidase 1 gene (CO1). Researchers use this gene because it varies highly among species and is relatively stable within species. For plants, the standard barcode regions are two chloroplast genes, matK and rbcL.

The process begins by extracting DNA from a small tissue sample of an organism. Next, the DNA is amplified using a technique called Polymerase Chain Reaction (PCR).

This step makes numerous copies of the barcode region. Scientists then sequence the amplified DNA to determine the order of nucleotides, forming a unique pattern for different species.

Researchers compare the obtained sequence to a reference database. If researchers find a match, they identify the species. If they find no match, the sequence could represent a new species.

DNA barcoding has several applications. Researchers use it in species identification, biodiversity studies, and food safety. It helps in identifying mislabeled products, detecting invasive species, and understanding ecosystem dynamics.

Despite its strengths, DNA barcoding has limitations. These include difficulty in distinguishing closely related species and potential errors due to contamination or sequencing errors.

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