A new study has shown that DNA metabarcoding serves as a powerful new tool for monitoring humans’ intake of plants, which could help researchers understand more about what we eat and how it affects the gut microbiome.
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The study also suggested that a similar approach could be used to determine animal and fungal components of our diets.
DNA barcoding and metabarcoding
DNA barcoding is a technique that uses short DNA sequences to rapidly identify an organism’s species. Across the globe, scientists have been collaborating to get all living things DNA barcoded.
DNA metabarcoding is a special type of barcoding that can be applied to samples containing more than one organism. It uses the same reference databases as barcoding does, but allows taxa from mixed samples to be identified using high-throughput sequencing methods. The potential of the technique is expansive, with it enabling species composition to be determined in virtually any sample.
Advantages over other techniques
The current study, which was recently published in the journal mSystems, showed that dietary plant DNA in human stool samples can be amplified and sequenced using techniques commonly applied in wildlife studies.
"DNA sequencing has given us a large amount of new data on things like microbiology in the gut and personal genetics. This study suggests that the same powerful technology could also start telling us about what we eat, which is often a hard thing to measure.
Senior author Lawrence David, from the Duke Center for Genomic and Computational Biology
Many techniques are already used to assess dietary intake but most of them depend on people’s self-reporting of what they have eaten. This data-gathering method is subject to errors in memory and bias in reporting as well as being dependent on a person’s cognitive ability to answer surveys.
Using DNA metabarcoding, scientists can amplify DNA present in a stool sample and use a reference database to map the sequences to food items.
“A particular DNA sequence as a unique identifier for a particular food species”
"I think of DNA metabarcoding very much like a barcode at a supermarket. We can think of a particular DNA sequence as a unique identifier for a particular food species," says co-author Brianna Petrone, also from Duke University.
David and co-first author Aspen Reese from Harvard University, were prompted to start the study after they met ecologists Rob Pringle from Princeton University and Tyler Kartzinel from Brown University. Those researchers used DNA metabarcoding to analyse complex food webs among herbivores in the African savanna.
David and Reese wondered whether the method could also be used to study people.
There is a growing body of work in the microbiome field indicating that specific foods are likely to be altering or shaping levels of specific bacteria in the gut, but we often don't have accompanying diet data for the microbiome studies."
For the study, the researchers took DNA out of cold storage that had been extracted from stools used in one of their previous studies.
"We happened to do a study a couple years ago where we were preparing foods for participants in a microbiome diet intervention, and we knew exactly what they were eating in a given week when their stool was being collected," says David.
They sequenced a barcode region from chloroplast DNA in samples taken from 11 people who had followed both freely selected and controlled diets.
They successfully amplified plant DNA for approximately half of the samples, which increased to 70% when samples from people consuming a controlled, plant-rich diet were used.
Most of the DNA matched commonly eaten foods
Most of the DNA that was sequenced matched human food plants widely consumed by people, including grains, vegetables and fruits.
"Overall, there was good broad agreement between the foods that were listed in the diaries kept by the study participants and the ones that we sequenced from stool," says David. "If a food was written in the diet record, about 80% of the time, we also found it by this metabarcoding approach."
Room for improvement
The relatively high rate of PCR failure and the inability to distinguish certain plants at the sequence level leaves room for improvement in the future.
For example, cabbage, broccoli, kohlrabi and Brussel sprouts are all plant varieties within the same species and the researchers were unable to differentiate between them using the chloroplast DNA sequences.
The only food recorded in the diet that was not detectable was coffee, possibly due to its DNA having deteriorated or become diluted through roasting and brewing.
The technique could be used for both new and old studies
David expects that DNA metabarcoding will be used in future studies, as well as for diet analysis in previous studies.
Similar to this study, I could imagine this getting used on archived DNA to see whether or not there are underlying dietary differences that might explain some of the microbiome patterns that may have been observed in a study. Going forward, we can also imagine this being used in new microbiome studies to identify relationships between specific foods and gut bacteria, as well as in broader studies of nutrition as a complement to traditional diet assessment techniques."