IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0229204.html
   My bibliography  Save this article

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample

Author

Listed:
  • Sarah L Hagerty
  • Kent E Hutchison
  • Christopher A Lowry
  • Angela D Bryan

Abstract

The human gut microbiome has emerged as a potential key factor involved in the manifestation of physical and mental health. Despite an explosion of cross-disciplinary interest in researching the gut microbiome, there remains to be a gold-standard method for operationalizing gut microbiome alpha diversity. Given researchers’ interest in examining the relationships among gut microbiome alpha diversity and health-related outcomes of interest, a way of operationalizing the microbiome that yields a numeric value, which could be used in common statistical approaches, is needed. Thus, the current study aims to provide methodological guidance for how to operationalize microbiome alpha diversity. Findings suggest that alpha diversity of the human gut microbiome is comprised of two sub-constructs (richness and evenness), and we propose a step-by-step method of creating alpha diversity composite measures based on this key insight. Finally, we demonstrate that our empirically derived richness and evenness composite measures are significantly associated with health-related variables of interest (alcohol use, symptoms of depression) among a human clinical sample.

Suggested Citation

  • Sarah L Hagerty & Kent E Hutchison & Christopher A Lowry & Angela D Bryan, 2020. "An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample," PLOS ONE, Public Library of Science, vol. 15(3), pages 1-21, March.
    • Handle: RePEc:plo:pone00:0229204
    DOI: 10.1371/journal.pone.0229204
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229204
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0229204&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0229204?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Lawrence A. David & Corinne F. Maurice & Rachel N. Carmody & David B. Gootenberg & Julie E. Button & Benjamin E. Wolfe & Alisha V. Ling & A. Sloan Devlin & Yug Varma & Michael A. Fischbach & Sudha B. , 2014. "Diet rapidly and reproducibly alters the human gut microbiome," Nature, Nature, vol. 505(7484), pages 559-563, January.
    2. Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
    3. Ruth E. Ley & Peter J. Turnbaugh & Samuel Klein & Jeffrey I. Gordon, 2006. "Human gut microbes associated with obesity," Nature, Nature, vol. 444(7122), pages 1022-1023, December.
    4. Paul T E Cusack, 2020. "The Human Brain," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 31(3), pages 24261-24266, October.
    5. Catherine A. Lozupone & Jesse I. Stombaugh & Jeffrey I. Gordon & Janet K. Jansson & Rob Knight, 2012. "Diversity, stability and resilience of the human gut microbiota," Nature, Nature, vol. 489(7415), pages 220-230, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lena Takayasu & Wataru Suda & Eiichiro Watanabe & Shinji Fukuda & Kageyasu Takanashi & Hiroshi Ohno & Misako Takayasu & Hideki Takayasu & Masahira Hattori, 2017. "A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-20, August.
    2. Sean M Gibbons & Sean M Kearney & Chris S Smillie & Eric J Alm, 2017. "Two dynamic regimes in the human gut microbiome," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-20, February.
    3. Kiran Konain & Sadia & Turfa Nadeem & Adeed Khan & Warda Iqbal & Arsalan & Amir Javed & Ruby Khan & Kainat Jamil & Kainat Jamil, 2018. "Importance of Probiotics in Gastrointestinal Tract," Journal of Asian Scientific Research, Asian Economic and Social Society, vol. 8(3), pages 128-143, March.
    4. Pirjo Wacklin & Harri Mäkivuokko & Noora Alakulppi & Janne Nikkilä & Heli Tenkanen & Jarkko Räbinä & Jukka Partanen & Kari Aranko & Jaana Mättö, 2011. "Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-10, May.
    5. Elio L Herzog & Melania Wäfler & Irene Keller & Sebastian Wolf & Martin S Zinkernagel & Denise C Zysset-Burri, 2021. "The importance of age in compositional and functional profiling of the human intestinal microbiome," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-13, October.
    6. Lucía Guadamuro & M. Andrea Azcárate-Peril & Rafael Tojo & Baltasar Mayo & Susana Delgado, 2021. "Impact of Dietary Isoflavone Supplementation on the Fecal Microbiota and Its Metabolites in Postmenopausal Women," IJERPH, MDPI, vol. 18(15), pages 1-11, July.
    7. Gregory E Miller & Phillip A Engen & Patrick M Gillevet & Maliha Shaikh & Masoumeh Sikaroodi & Christopher B Forsyth & Ece Mutlu & Ali Keshavarzian, 2016. "Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults," PLOS ONE, Public Library of Science, vol. 11(2), pages 1-17, February.
    8. Zahraa Al Bander & Marloes Dekker Nitert & Aya Mousa & Negar Naderpoor, 2020. "The Gut Microbiota and Inflammation: An Overview," IJERPH, MDPI, vol. 17(20), pages 1-21, October.
    9. Yongli Han & Courtney Baker & Emily Vogtmann & Xing Hua & Jianxin Shi & Danping Liu, 2021. "Modeling Longitudinal Microbiome Compositional Data: A Two-Part Linear Mixed Model with Shared Random Effects," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 243-266, July.
    10. Qian Zhang & Lijuan Zhang & Yang Lyu & Yutao Shi & Liangyun Zhu & Min Zhang & Yuyan Zhao & Di Zhao & Lei Wang & Dan Yi & Yongqing Hou & Tao Wu, 2022. "Dietary supplementation of Lactobacillus zeae regulated the gut microbiome in piglets infected with enterotoxigenic Escherichia coli," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 67(1), pages 27-38.
    11. Dominic Holland & Oleksandr Frei & Rahul Desikan & Chun-Chieh Fan & Alexey A Shadrin & Olav B Smeland & V S Sundar & Paul Thompson & Ole A Andreassen & Anders M Dale, 2020. "Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model," PLOS Genetics, Public Library of Science, vol. 16(5), pages 1-30, May.
    12. Shilan Li & Jianxin Shi & Paul Albert & Hong-Bin Fang, 2022. "Dependence Structure Analysis and Its Application in Human Microbiome," Mathematics, MDPI, vol. 11(1), pages 1-14, December.
    13. Jos A. Bosch & Max Nieuwdorp & Aeilko H. Zwinderman & Mélanie Deschasaux & Djawad Radjabzadeh & Robert Kraaij & Mark Davids & Susanne R. Rooij & Anja Lok, 2022. "The gut microbiota and depressive symptoms across ethnic groups," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    14. Daphna Rothschild & Erez Dekel & Jean Hausser & Anat Bren & Guy Aidelberg & Pablo Szekely & Uri Alon, 2014. "Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-9, May.
    15. Julia Berezutskaya & Zachary V Freudenburg & Umut Güçlü & Marcel A J van Gerven & Nick F Ramsey, 2020. "Brain-optimized extraction of complex sound features that drive continuous auditory perception," PLOS Computational Biology, Public Library of Science, vol. 16(7), pages 1-34, July.
    16. Jae-Chang Cho, 2021. "Human microbiome privacy risks associated with summary statistics," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-11, April.
    17. Joe J. Lim & Christian Diener & James Wilson & Jacob J. Valenzuela & Nitin S. Baliga & Sean M. Gibbons, 2023. "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    18. Abigail B. Schneider & Bridget Leonard, 2022. "From anxiety to control: Mask‐wearing, perceived marketplace influence, and emotional well‐being during the COVID‐19 pandemic," Journal of Consumer Affairs, Wiley Blackwell, vol. 56(1), pages 97-119, March.
    19. Geonhui Lee & Woong Choi & Hanjin Jo & Wookhyun Park & Jaehyo Kim, 2020. "Analysis of motor control strategy for frontal and sagittal planes of circular tracking movements using visual feedback noise from velocity change and depth information," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-22, November.
    20. Kenneth A. Wilson & Sudipta Bar & Eric B. Dammer & Enrique M. Carrera & Brian A. Hodge & Tyler A. U. Hilsabeck & Joanna Bons & George W. Brownridge & Jennifer N. Beck & Jacob Rose & Melia Granath-Pane, 2024. "OXR1 maintains the retromer to delay brain aging under dietary restriction," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0229204. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.