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Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.

Kiumars Badr¹, Q Peter He¹, Jin Wang¹

¹Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA.

Microbiome Research Reports

|October 18, 2024

Summary

A new dynamic genome-scale metabolic modeling (GEM) approach, DynamiCom, accurately predicts metabolic interactions and their evolution in a synthetic methanotroph-photoautotroph coculture, enhancing our understanding of microbial communities.

Keywords:

Synthetic microbiome dynamic modeling genome-scale metabolic modeling interspecies metabolic interactions methanotroph-photoautotroph coculture steady state modeling

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Area of Science:

Microbial Ecology
Systems Biology
Metabolic Engineering

Background:

Microbial communities are crucial for ecosystem function, but interspecies metabolic interactions remain poorly understood.
Natural microbiomes are complex, limiting detailed study of metabolic exchanges.
Synthetic cocultures offer tractable models to investigate these interactions.

Purpose of the Study:

To evaluate genome-scale metabolic modeling (GEM) approaches for analyzing metabolic interactions in a synthetic methanotroph-photoautotroph (M-P) coculture.
To understand how these interactions contribute to enhanced growth and evolve over time.
To develop an improved dynamic GEM approach for coculture analysis.

Main Methods:

Compared SteadyCom (steady-state GEM) and DFBA Lab (dynamic GEM) with a newly proposed dynamic GEM approach, DynamiCom.
Utilized batch growth data from a model M-P coculture.
Validated DynamiCom's predictions against literature and kinetic models.

Main Results:

SteadyCom predicted interactions but not dynamics; DFBA Lab predicted dynamics but not interactions.
DynamiCom successfully identified cross-fed metabolites and predicted the evolution of interspecies interactions.
DynamiCom accurately predicted key exchanged metabolites and nitrogen exchange between the methanotroph and cyanobacteria.

Conclusions:

DynamiCom is a novel dynamic GEM approach suitable for modeling M-P cocultures.
The developed approach elucidates the dynamic metabolic exchanges and mutualistic relationships within microbial cocultures.
Findings provide insights into microbial community structure, function, and evolution.