A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Abstract

Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and used over the past 20 years. Recently, with the number of genome sequences exponentially increasing, multi-strain GEMs have proved valuable to define the properties of a species. Here, through four major stages, we extend the original Protocol used to generate a GEM for a single strain to enable multi-strain GEMs: (i) obtain or generate a high-quality model of a reference strain; (ii) compare the genome sequence between a reference strain and target strains to generate a homology matrix; (iii) generate draft strain-specific models from the homology matrix; and (iv) manually curate draft models. These multi-strain GEMs can be used to study pan-metabolic capabilities and strain-specific differences across a species, thus providing insights into its range of lifestyles. Unlike the original Protocol, this procedure is scalable and can be partly automated with the Supplementary Jupyter notebook Tutorial. This Protocol Extension joins the ranks of other comparable methods for generating models such as CarveMe and KBase. This extension of the original Protocol takes on the order of weeks to multiple months to complete depending on the availability of a suitable reference model.

Figure 1:. Applications of multi-strain GEMs:

The workflow of genome comparison to generate a homology matrix of percentage identity values (PIDs), which is in turn used to generate strain-specific models of the target strains. The number of strains considered in this fashion enables various types of analyses including: 1) comparison of strain nutrient utilization and identification of strain-specific auxotrophies; 2) interrogation of genome architecture and classification of strains by niche or by pathotype; 3) investigation of allele frequencies among strains and mapping to protein structural information; and, 4) linking to epidemiology and tracking of strains/infections.

Figure 2:

Overall workflow for multi-strain GEMs generation.

Figure 3:. Workflow to generate base model from reference genome sequence.

This workflow presents the four major steps involved in reconstructing a reference model as outlined originally by Thiele et al..