Cell Systems
Volume 7, Issue 3, 26 September 2018, Pages 245-257.e7
Journal home page for Cell Systems

Article
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

https://doi.org/10.1016/j.cels.2018.08.003Get rights and content
Under a Creative Commons license
open access

Highlights

  • In vitro monoculture and co-culture of six members of a defined murine microbiota

  • Growth and metabolome profiling to identify ecological and metabolic interactions

  • Development and application of a constant yield expectation (ConYE) model

  • Testing of inferred cross-feeding that contributed to commensal interaction

Summary

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.

Keywords

metabolism
microbial community
interspecies interactions
metabolic cross-feeding
microbial ecology
emergent behavior
systems biology
mathematical modeling
microbiome
microbiota

Cited by (0)

7

Lead Contact