IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1006960.html
   My bibliography  Save this article

Modeling the temporal dynamics of the gut microbial community in adults and infants

Author

Listed:
  • Liat Shenhav
  • Ori Furman
  • Leah Briscoe
  • Mike Thompson
  • Justin D Silverman
  • Itzhak Mizrahi
  • Eran Halperin

Abstract

Given the highly dynamic and complex nature of the human gut microbial community, the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and functions of this ecosystem. One factor that could affect such time-dependent patterns is microbial interactions, wherein community composition at a given time point affects the microbial composition at a later time point. However, the field has not yet settled on the degree of this effect. Specifically, it has been recently suggested that only a minority of taxa depend on the microbial composition in earlier times. To address the issue of identifying and predicting temporal microbial patterns we developed a new model, MTV-LMM (Microbial Temporal Variability Linear Mixed Model), a linear mixed model for the prediction of microbial community temporal dynamics. MTV-LMM can identify time-dependent microbes (i.e., microbes whose abundance can be predicted based on the previous microbial composition) in longitudinal studies, which can then be used to analyze the trajectory of the microbiome over time. We evaluated the performance of MTV-LMM on real and synthetic time series datasets, and found that MTV-LMM outperforms commonly used methods for microbiome time series modeling. Particularly, we demonstrate that the effect of the microbial composition in previous time points on the abundance of taxa at later time points is underestimated by a factor of at least 10 when applying previous approaches. Using MTV-LMM, we demonstrate that a considerable portion of the human gut microbiome, both in infants and adults, has a significant time-dependent component that can be predicted based on microbiome composition in earlier time points. This suggests that microbiome composition at a given time point is a major factor in defining future microbiome composition and that this phenomenon is considerably more common than previously reported for the human gut microbiome.Author summary: The ability to characterize and predict temporal trajectories of the microbial community in the human gut is crucial to our understanding of the structure and functions of this ecosystem. In this study we develop MTV-LMM, a method for modeling time-series microbial community data. Using MTV-LMM we find that in contrast to previous reports, a considerable portion of microbial taxa in both infants and adults display temporal structure that is predictable using the previous composition of the microbial community. In reaching this conclusion we have adopted a number of concepts common in statistical genetics for use with longitudinal microbiome studies. We introduce concepts such as time-explainability and the temporal kinship matrix, which we believe will be of use to other researchers studying microbial dynamics, through the framework of linear mixed models. In particular we find that the association matrix estimated by MTV-LMM reveals known phylogenetic relationships and that the temporal kinship matrix uncovers known temporal structure in infant microbiome and inter-individual differences in adult microbiome. Finally, we demonstrate that MTV-LMM significantly outperforms commonly used methods for temporal modeling of the microbiome, both in terms of its prediction accuracy as well as in its ability to identify time-dependent taxa.

Suggested Citation

  • Liat Shenhav & Ori Furman & Leah Briscoe & Mike Thompson & Justin D Silverman & Itzhak Mizrahi & Eran Halperin, 2019. "Modeling the temporal dynamics of the gut microbial community in adults and infants," PLOS Computational Biology, Public Library of Science, vol. 15(6), pages 1-21, June.
  • Handle: RePEc:plo:pcbi00:1006960
    DOI: 10.1371/journal.pcbi.1006960
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006960
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006960&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1006960?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. Charlie G. Buffie & Vanni Bucci & Richard R. Stein & Peter T. McKenney & Lilan Ling & Asia Gobourne & Daniel No & Hui Liu & Melissa Kinnebrew & Agnes Viale & Eric Littmann & Marcel R. M. van den Brink, 2015. "Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile," Nature, Nature, vol. 517(7533), pages 205-208, January.
    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. Peter M Visscher & Gibran Hemani & Anna A E Vinkhuyzen & Guo-Bo Chen & Sang Hong Lee & Naomi R Wray & Michael E Goddard & Jian Yang, 2014. "Statistical Power to Detect Genetic (Co)Variance of Complex Traits Using SNP Data in Unrelated Samples," PLOS Genetics, Public Library of Science, vol. 10(4), pages 1-10, April.
    4. Alessandro Marino & Paolo Aversa & Luiz Mesquita & Jaideep Anand, 2015. "Driving Performance via Exploration in Changing Environments: Evidence from Formula One Racing," Organization Science, INFORMS, vol. 26(4), pages 1079-1100, August.
    5. Peter J. Turnbaugh & Ruth E. Ley & Michael A. Mahowald & Vincent Magrini & Elaine R. Mardis & Jeffrey I. Gordon, 2006. "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, Nature, vol. 444(7122), pages 1027-1031, December.
    6. Peter J. Turnbaugh & Micah Hamady & Tanya Yatsunenko & Brandi L. Cantarel & Alexis Duncan & Ruth E. Ley & Mitchell L. Sogin & William J. Jones & Bruce A. Roe & Jason P. Affourtit & Michael Egholm & Be, 2009. "A core gut microbiome in obese and lean twins," Nature, Nature, vol. 457(7228), pages 480-484, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).
    2. Tyler A Joseph & Liat Shenhav & Joao B Xavier & Eran Halperin & Itsik Pe’er, 2020. "Compositional Lotka-Volterra describes microbial dynamics in the simplex," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-22, May.

    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. Shinji Fukuda & Yumiko Nakanishi & Eisuke Chikayama & Hiroshi Ohno & Tsuneo Hino & Jun Kikuchi, 2009. "Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping," PLOS ONE, Public Library of Science, vol. 4(3), pages 1-10, March.
    2. Hannah Lees & Jonathan Swann & Simon M Poucher & Jeremy K Nicholson & Elaine Holmes & Ian D Wilson & Julian R Marchesi, 2014. "Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
    3. Chihiro Morita & Hirokazu Tsuji & Tomokazu Hata & Motoharu Gondo & Shu Takakura & Keisuke Kawai & Kazufumi Yoshihara & Kiyohito Ogata & Koji Nomoto & Kouji Miyazaki & Nobuyuki Sudo, 2015. "Gut Dysbiosis in Patients with Anorexia Nervosa," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-13, December.
    4. Koji Hosomi & Mayu Saito & Jonguk Park & Haruka Murakami & Naoko Shibata & Masahiro Ando & Takahiro Nagatake & Kana Konishi & Harumi Ohno & Kumpei Tanisawa & Attayeb Mohsen & Yi-An Chen & Hitoshi Kawa, 2022. "Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Dongyang Yang & Wei Xu, 2023. "Estimation of Mediation Effect on Zero-Inflated Microbiome Mediators," Mathematics, MDPI, vol. 11(13), pages 1-16, June.
    6. Gertrude Ecklu-Mensah & Candice Choo-Kang & Maria Gjerstad Maseng & Sonya Donato & Pascal Bovet & Bharathi Viswanathan & Kweku Bedu-Addo & Jacob Plange-Rhule & Prince Oti Boateng & Terrence E. Forrest, 2023. "Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Li, Jie & Shen, Xuzhu & Li, YaoTang, 2021. "Modeling the temporal dynamics of gut microbiota from a local community perspective," Ecological Modelling, Elsevier, vol. 460(C).
    8. Małgorzata Moszak & Monika Szulińska & Marta Walczak-Gałęzewska & Paweł Bogdański, 2021. "Nutritional Approach Targeting Gut Microbiota in NAFLD—To Date," IJERPH, MDPI, vol. 18(4), pages 1-32, February.
    9. Marina Sanchez & Shirin Panahi & Angelo Tremblay, 2014. "Childhood Obesity: A Role for Gut Microbiota?," IJERPH, MDPI, vol. 12(1), pages 1-14, December.
    10. Tyler A Joseph & Liat Shenhav & Joao B Xavier & Eran Halperin & Itsik Pe’er, 2020. "Compositional Lotka-Volterra describes microbial dynamics in the simplex," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-22, May.
    11. Alessandra N. Bazzano & Kaitlin S. Potts & Lydia A. Bazzano & John B. Mason, 2017. "The Life Course Implications of Ready to Use Therapeutic Food for Children in Low-Income Countries," IJERPH, MDPI, vol. 14(4), pages 1-19, April.
    12. Jeffrey D Galley & Michael Bailey & Claire Kamp Dush & Sarah Schoppe-Sullivan & Lisa M Christian, 2014. "Maternal Obesity Is Associated with Alterations in the Gut Microbiome in Toddlers," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-13, November.
    13. Carolina Rojas-Córdova & Amanda J. Williamson & Julio A. Pertuze & Gustavo Calvo, 2023. "Why one strategy does not fit all: a systematic review on exploration–exploitation in different organizational archetypes," Review of Managerial Science, Springer, vol. 17(7), pages 2251-2295, October.
    14. Doratha A Byrd & Jun Chen & Emily Vogtmann & Autumn Hullings & Se Jin Song & Amnon Amir & Muhammad G Kibriya & Habibul Ahsan & Yu Chen & Heidi Nelson & Rob Knight & Jianxin Shi & Nicholas Chia & Rashm, 2019. "Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations," PLOS ONE, Public Library of Science, vol. 14(11), pages 1-19, November.
    15. Patrick D Schloss, 2009. "A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-9, December.
    16. John Molloy & Katrina Allen & Fiona Collier & Mimi L. K. Tang & Alister C. Ward & Peter Vuillermin, 2013. "The Potential Link between Gut Microbiota and IgE-Mediated Food Allergy in Early Life," IJERPH, MDPI, vol. 10(12), pages 1-22, December.
    17. Bharati Patel & Kadamb Patel & Shabbir Moochhala, 2020. "Diet-Derived Post-Biotic Metabolites to Promote Microbiota Function and Human Health," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 28(2), pages 21520-21524, June.
    18. Ahmed A Metwally & Philip S Yu & Derek Reiman & Yang Dai & Patricia W Finn & David L Perkins, 2019. "Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks," PLOS Computational Biology, Public Library of Science, vol. 15(2), pages 1-16, February.
    19. 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.
    20. 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.

    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:pcbi00:1006960. 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: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    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.