DNA metabarcoding captures dietary plant diversity in individuals and cohorts

Eating a varied diet is a central tenet of good nutrition. Here, we develop the first molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL -P6 marker to 1,001 fecal samples from 310 participants across four cohorts. The number of plant taxa per sample (plant metabarcoding richness, or pMR) correlated with recorded intakes in interventional diets (ρ=0.31) and with indices calculated from a food-frequency questionnaire in freely-chosen diets (ρ=0.40-0.63). In adolescents unable to collect validated dietary survey data, trnL metabarcoding detected 111 plant taxa, with 86 consumed by more than one individual and four (wheat, chocolate, corn, and potato family) consumed by >70% of individuals. Adolescent pMR was associated with age and income, replicating prior epidemiologic findings. Overall, trnL metabarcoding promises an objective and accurate measure of the number and types of plants consumed that is applicable to diverse human populations. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded by the NIH (5R24DK110492-05 to JFR and PCS; 5R01DK116187-05 to LAD), the Burroughs Wellcome Fund Pathogenesis of Infectious Disease Award (LAD), a Duke Microbiome Center Development Grant (LAD), a Springer Nature Limited Global Grant for Gut Health (LAD), a fellowship from Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) program (BLP), the Triangle Center for Evolutionary Medicine (BLP), and the Duke Medical Scientist Training program (BLP), and used a high-performance computing facility partially supported by grants 2016-IDG-1013 (HARDAC+: Reproducible HPC for Next-generation Genomics) and 2020-IIG-2109 (HARDAC-M: Enabling memory-intensive computation for genomics) from the North Carolina Biotechnology Center. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of Duke University waived ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes trnL metabarcoding data for all samples will be deposited to the European Nucleotide Archive prior to publication. De-identified clinical metadata associated with this study are available upon request and will be shared when consistent with applicable study agreements, regulations, and ethical standards.