Mapping the bacterial metabolic niche space

Abstract

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