Metabolic-network-driven analysis of bacterial ecological strategies

Abstract

Background: The growth-rate of an organism is an important phenotypic trait, directly affecting its ability to survive in a given environment. Here we present the first large scale computational study of the association between ecological strategies and growth rate across 113 bacterial species, occupying a variety of metabolic habitats. Genomic data are used to reconstruct the species' metabolic networks and habitable metabolic environments. These reconstructions are then used to investigate the typical ecological strategies taken by organisms in terms of two basic species-specific measures: metabolic variability--the ability of a species to survive in a variety of different environments; and co-habitation score vector--the distribution of other species that co-inhabit each environment.

Results: We find that growth rate is significantly correlated with metabolic variability and the level of co-habitation (that is, competition) encountered by an organism. Most bacterial organisms adopt one of two main ecological strategies: a specialized niche with little co-habitation, associated with a typically slow rate of growth; or ecological diversity with intense co-habitation, associated with a typically fast rate of growth.

Conclusions: The pattern observed suggests a universal principle where metabolic flexibility is associated with a need to grow fast, possibly in the face of competition. This new ability to produce a quantitative description of the growth rate-metabolism-community relationship lays a computational foundation for the study of a variety of aspects of the communal metabolic life.

Figure 1

Mean co-habitation (population) levels of environments occupied by bacteria of a given lifestyle. Annotations of lifestyle are according to [19] (specialized, obligatory symbionts, aquatic, multiple, faculatative symbionts, and terrestrial) and according to identification of species in environmental samples (human gut; see Materials and methods). The number of environments in each lifestyle (in the same order as in the figure) are 11, 81, 5, 144, 157, 38, and 117 (environments can include species of more than a single lifestyle). Error bars show the standard error.

Figure 2

Environmental scope index versus maximal co-habitation score. The size of dots corresponds to duplication time - larger size corresponds to longer duplication time and slower growth rate. The color of dots corresponds to their ecological habitat (Additional data file 1): red, obligatory host-associated; green, specialized; blue, aquatic; black, host-associated (non-obligatory); orange, multiple; brown, terrestrial. DT, duplication time; BL, bottom left (47 species); BR, bottom right (10 species); TL, top left (16 species); TR, top right (40 species). The plot is divided according to median values of the axes.