Constructing and Analyzing Metabolic Flux Models of Microbial Communities

Abstract

Here we provide a broad overview of current research in modeling the growth and behavior of microbial communities, while focusing primarily on metabolic flux modeling techniques, including the reconstruction of individual species models, reconstruction of mixed-bag models, and reconstruction of multi-species models. We describe how flux balance analysis may be applied with these various model types to explore the interactions of a microbial community with its environment, as well as the interactions of individual species with each other. We demonstrate all discussed model reconstruction and analysis approaches using the Department of Energy's Systems Biology Knowledgebase (KBase), constructing and importing genomescale metabolic models of Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii, and subsequently combining them into a community model of the gut microbiome. We also use KBase to explore how these species interact with each other and with the gut environment, exploring the trade-offs in information provided by applying each metabolic flux modeling approach. Overall, we conclude that no single approach is better than the others, and often there is much to be gained by applying multiple approaches synergistically when exploring the ecology of a microbial community.

Microbial Community Metabolic Modeling: A Community Data‐Driven Network Reconstruction

“…Community networks can be constructed from individual species’ genomes in many different forms. At the simplest level, we can take a mixed‐bag (or gene‐soup) approach by treating a microbial community as a single supra‐organism (Abubucker et al, ; Faria et al, ). The metabolic pathways and transmembrane transport reactions, resulting from all members, are combined by ignoring species boundaries.…”

Problèmes d’optimisation combinatoire pour l’étude du métabolisme

“…Comme nous allons le voir dans les deux sous-sections suivantes, le niveau de modélisation (compartimentalisé ou non) est lié à la quantité de données disponibles, et à la qualité de ces données (Faria et al, 2016 ;Henry et al, 2016), mais aussi au nombre d'organismes à considérer, allant d'une petite communauté d'une dizaine d'espèces (García-Jiménez et al, 2018) à un ensemble composé de centaines ou quelques milliers d'organismes (Eng & Borenstein, 2016).…”

Mechanistic models of microbial community metabolism

“… 20 The bag-of-genes approach combines all the genetic makeup for the integrated models into one “super” bacterium. 28 This approach has been used to construct metabolic models of microbial communities belonging to the human microbiome from metagenomic shotgun sequencing data. 29 The authors explored community metabolic capabilities without the challenge of sorting reads into single-organism genomes.…”