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Modeling the temporal dynamics of gut microbiota from a local community perspective

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  • Li, Jie
  • Shen, Xuzhu
  • Li, YaoTang

Abstract

Given gut microbiota's important role in human health, a clear understanding of the microbial ecosystem dynamics is vital. Mathematical models for analyzing time-series data of gut microbiotas would, therefore, be highly beneficial. Although a generalized Lotka–Volterra (gLV) model for identifying the interactions between gut microbiota members and quantifying the effects of external factors already exists, it is limited in its practical applications. Therefore, we established a stochastic gLV model for analyzing temporal data about the gut microbiota from a local community perspective and provided a reliable parameter estimation method for our model. Our model has abilities similar to those of the existing gLV model but can also capture emigration/immigration effects and avoid the existing model's inadequacies. To test our model's applicability, we fitted our model on a previously published data set. We found the interactions between the gut microbiota of different individuals and between different periods for the same individual were different in the data sets. Analysis of the random dynamic characteristics of the gut microbiota revealed that the number of microorganisms in the local community tended to decrease as a result of random factors, but the numbers were restored by the immigration of external microbes .

Suggested Citation

  • 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).
    • Handle: RePEc:eee:ecomod:v:460:y:2021:i:c:s0304380021002854
    DOI: 10.1016/j.ecolmodel.2021.109733
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    References listed on IDEAS

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    1. 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.
    2. Peter Langfelder & Rui Luo & Michael C Oldham & Steve Horvath, 2011. "Is My Network Module Preserved and Reproducible?," PLOS Computational Biology, Public Library of Science, vol. 7(1), pages 1-29, January.
    3. Jacopo Grilli & György Barabás & Matthew J. Michalska-Smith & Stefano Allesina, 2017. "Higher-order interactions stabilize dynamics in competitive network models," Nature, Nature, vol. 548(7666), pages 210-213, August.
    4. 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.
    5. Charles K Fisher & Pankaj Mehta, 2014. "Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression," PLOS ONE, Public Library of Science, vol. 9(7), pages 1-10, July.
    6. 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.
    7. 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.
    8. Jonathan M. Levine & Jordi Bascompte & Peter B. Adler & Stefano Allesina, 2017. "Beyond pairwise mechanisms of species coexistence in complex communities," Nature, Nature, vol. 546(7656), pages 56-64, June.
    9. 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.
    10. Yu Shang & Johannes Sikorski & Michael Bonkowski & Anna-Maria Fiore-Donno & Ellen Kandeler & Sven Marhan & Runa S Boeddinghaus & Emily F Solly & Marion Schrumpf & Ingo Schöning & Tesfaye Wubet & Franc, 2017. "Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-24, March.
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