Mapping the bacterial ways of life

TL;DR

This paper uses manifold learning to map the metabolic niche space of bacteria, revealing major strategies and enabling ecological descriptions of microbiomes based on metabolic roles.

Contribution

It introduces a novel approach to visualize and analyze bacterial metabolic niches across thousands of genera using manifold learning.

Findings

Metabolic niche space has a complex branching geometry.

Major bacterial strategies span different habitats and hosts.

Microbiome communities map to characteristic regions in the niche space.

Abstract

The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results reveal a metabolic niche space with a complex branching geometry, whose branches constitute major strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this new functional coordinate system, permitting ecological descriptions of microbiomes in terms of large scale metabolic roles that may be filled.