Diversity of plant DNA in stool is linked to dietary quality, age, and household income

Brianna L. Petrone; Ammara Aqeel; Sharon Jiang; Heather K. Durand; Eric P. Dallow; Jessica R. McCann; Holly K. Dressman; Zhengzheng Hu; Christine B. Tenekjian; William S. Yancy; Pao Hwa Lin; Julia J. Scialla; Patrick C. Seed; John F. Rawlsa; Sarah C. Armstrong; June Stevens; Lawrence A. Davida

doi:10.1073/pnas.2304441120

Diversity of plant DNA in stool is linked to dietary quality, age, and household income

Brianna L. Petrone, Ammara Aqeel, Sharon Jiang, Heather K. Durand, Eric P. Dallow, Jessica R. McCann, Holly K. Dressman, Zhengzheng Hu, Christine B. Tenekjian, William S. Yancy, Pao Hwa Lin, Julia J. Scialla, Patrick C. Seed, John F. Rawlsa, Sarah C. Armstrong, June Stevens, Lawrence A. Davida^*

^*Corresponding author for this work

Pediatrics

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (δ = 0.40 to 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 household 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.

Original language	English (US)
Article number	e2304441120
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	120
Issue number	27
DOIs	https://doi.org/10.1073/pnas.2304441120
State	Published - 2023

Funding

ACKNOWLEDGMENTS. We thank our study volunteers for their participation; Verónica Palacios for human study support; Michelle Kirtley for manuscript edits; Tyler Kartzinel for experimental and conceptual insights; and Tonya Snipes, Lisa Alston-Latta, and Margaret Huggins for keeping our lab spaces and glassware clean. Funding for this work came from the National Institute of Diabetes and Digestive and Kidney Diseases (grants R24-DK110492, R01-DK116187, and R01-DK128611), the Burroughs Wellcome Fund Pathogenesis of Infectious Disease Award, the Duke Microbiome Center, the Springer Nature Limited Global Grant for Gut Health, the Chan Zuckerberg Initiative, the Triangle Center for Evolutionary Medicine, the Integrative Bioinformatics for Investigating and Engineering Microbiomes Graduate Student Fellowship, and the Ruth L.Kirschstein National Research Service Award to the Duke Medical ScientistTraining Program.This work 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.

Keywords

diet quality
dietary assessment
food biodiversity
high-Throughput sequencing
nutrition

ASJC Scopus subject areas

General

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10.1073/pnas.2304441120

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Petrone, B. L., Aqeel, A., Jiang, S., Durand, H. K., Dallow, E. P., McCann, J. R., Dressman, H. K., Hu, Z., Tenekjian, C. B., Yancy, W. S., Lin, P. H., Scialla, J. J., Seed, P. C., Rawlsa, J. F., Armstrong, S. C., Stevens, J., & Davida, L. A. (2023). Diversity of plant DNA in stool is linked to dietary quality, age, and household income. Proceedings of the National Academy of Sciences of the United States of America, 120(27), Article e2304441120. https://doi.org/10.1073/pnas.2304441120

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title = "Diversity of plant DNA in stool is linked to dietary quality, age, and household income",

abstract = "Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (δ = 0.40 to 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 household 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.",

keywords = "diet quality, dietary assessment, food biodiversity, high-Throughput sequencing, nutrition",

author = "Petrone, {Brianna L.} and Ammara Aqeel and Sharon Jiang and Durand, {Heather K.} and Dallow, {Eric P.} and McCann, {Jessica R.} and Dressman, {Holly K.} and Zhengzheng Hu and Tenekjian, {Christine B.} and Yancy, {William S.} and Lin, {Pao Hwa} and Scialla, {Julia J.} and Seed, {Patrick C.} and Rawlsa, {John F.} and Armstrong, {Sarah C.} and June Stevens and Davida, {Lawrence A.}",

note = "Publisher Copyright: Copyright {\textcopyright} 2023 the Author(s). Published by PNAS.",

year = "2023",

doi = "10.1073/pnas.2304441120",

language = "English (US)",

volume = "120",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

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Petrone, BL, Aqeel, A, Jiang, S, Durand, HK, Dallow, EP, McCann, JR, Dressman, HK, Hu, Z, Tenekjian, CB, Yancy, WS, Lin, PH, Scialla, JJ, Seed, PC, Rawlsa, JF, Armstrong, SC, Stevens, J & Davida, LA 2023, 'Diversity of plant DNA in stool is linked to dietary quality, age, and household income', Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 27, e2304441120. https://doi.org/10.1073/pnas.2304441120

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T1 - Diversity of plant DNA in stool is linked to dietary quality, age, and household income

AU - Petrone, Brianna L.

AU - Aqeel, Ammara

AU - Jiang, Sharon

AU - Durand, Heather K.

AU - Dallow, Eric P.

AU - McCann, Jessica R.

AU - Dressman, Holly K.

AU - Hu, Zhengzheng

AU - Tenekjian, Christine B.

AU - Yancy, William S.

AU - Lin, Pao Hwa

AU - Scialla, Julia J.

AU - Seed, Patrick C.

AU - Rawlsa, John F.

AU - Armstrong, Sarah C.

AU - Stevens, June

AU - Davida, Lawrence A.

PY - 2023

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N2 - Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (δ = 0.40 to 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 household 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.

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KW - food biodiversity

KW - high-Throughput sequencing

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Diversity of plant DNA in stool is linked to dietary quality, age, and household income

Abstract

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Keywords

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