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.

Metrics

  • 838
    views
  • 149
    downloads
  • 0
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Share this article

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

Further reading

    1. Computational and Systems Biology
    2. Developmental Biology
    Arya Y Nakhe, Prasanna K Dadi ... David A Jacobson
    Research Article

    The gain-of-function mutation in the TALK-1 K+ channel (p.L114P) is associated with maturity-onset diabetes of the young (MODY). TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion. The KCNK16 gene encoding TALK-1 is the most abundant and β-cell-restricted K+ channel transcript. To investigate the impact of KCNK16 L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the Kcnk16 L114P mutation was generated. Heterozygous and homozygous Kcnk16 L114P mice exhibit increased neonatal lethality in the C57BL/6J and the CD-1 (ICR) genetic background, respectively. Lethality is likely a result of severe hyperglycemia observed in the homozygous Kcnk16 L114P neonates due to lack of glucose-stimulated insulin secretion and can be reduced with insulin treatment. Kcnk16 L114P increased whole-cell β-cell K+ currents resulting in blunted glucose-stimulated Ca2+ entry and loss of glucose-induced Ca2+ oscillations. Thus, adult Kcnk16 L114P mice have reduced glucose-stimulated insulin secretion and plasma insulin levels, which significantly impairs glucose homeostasis. Taken together, this study shows that the MODY-associated Kcnk16 L114P mutation disrupts glucose homeostasis in adult mice resembling a MODY phenotype and causes neonatal lethality by inhibiting islet insulin secretion during development. These data suggest that TALK-1 is an islet-restricted target for the treatment for diabetes.

    1. Computational and Systems Biology
    David Geller-McGrath, Kishori M Konwar ... Jason E McDermott
    Tools and Resources

    The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.