Metabolic model-based ecological modeling for probiotic design

  1. James D Brunner  Is a corresponding author
  2. Nicholas Chia  Is a corresponding author
  1. Los Alamos National Laboratory, United States
  2. Argonne National Laboratory, United States

Abstract

The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter 'probiotic' treatments intended to alter the composition of the microbiome. Despite so much promise and commercial interest, the factors that contribute to the success or failure of microbiome-targeted treatments remain unclear. We investigate the biotic interactions that lead to successful engraftment of a novel bacterial strain introduced to the microbiome as in probiotic treatments. We use pairwise genome-scale metabolic modeling with a generalized resource allocation constraint to build a network of interactions between taxa that appear in an experimental engraftment study. We create induced sub-graphs using the taxa present in individual samples and assess the likelihood of invader engraftment based on network structure. To do so, we use a generalized Lotka-Volterra model, which we show has strong ability to predict if a particular invader or probiotic will successfully engraft into an individual's microbiome. Furthermore, we show that the mechanistic nature of the model is useful for revealing which microbe-microbe interactions potentially drive engraftment.

Data availability

Data from the study that we used to evaluate our method can be found at the following source:https://www.ncbi.nlm.nih.gov/bioproject/PRJNA324129/Our method is implemented as the \emph{friendlyNets} package, available for download at \url{https://github.com/lanl/friendlyNets} along with re-formatted data and python scripts for the analysis found in this paper.

The following previously published data sets were used

Article and author information

Author details

  1. James D Brunner

    Biosciences Division, Los Alamos National Laboratory, Los Alamos, United States
    For correspondence
    jdbrunner@lanl.gov
    Competing interests
    James D Brunner, is an employee of Triad National Security, LLC.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8147-2522
  2. Nicholas Chia

    Data Science and Learning, Argonne National Laboratory, Lemont, United States
    For correspondence
    chia@anl.gov
    Competing interests
    Nicholas Chia, is an employee of UChicago Argonne, LLC.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9652-691X

Funding

U.S. Department of Energy (255LANL2018)

  • James D Brunner

Mayo Clinic

  • Nicholas Chia

Los Alamos National Laboratory (Center For Nonlinear Studies)

  • James D Brunner

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Babak Momeni, Boston College, United States

Version history

  1. Received: September 24, 2022
  2. Preprint posted: October 6, 2022 (view preprint)
  3. Accepted: February 19, 2024
  4. Accepted Manuscript published: February 21, 2024 (version 1)
  5. Version of Record published: March 15, 2024 (version 2)

Copyright

© 2024, Brunner & Chia

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. James D Brunner
  2. Nicholas Chia
(2024)
Metabolic model-based ecological modeling for probiotic design
eLife 13:e83690.
https://doi.org/10.7554/eLife.83690

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https://doi.org/10.7554/eLife.83690

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