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Author: Sotaro Takano, Jean C.C. Vila, Alvaro Sanchez, Djordje Bajić
Microorganisms typically display a wide, and often overlapping, range of metabolic capabilities. In theory, this should favor competitive exclusion, and thus seems at odds with the pervasive coexistence and the diversity observed in natural microbiomes. One form of resource specialization that could partly explain the observed coexistence is the preference hierarchy for different substrates exhibited by most microbes, reflected in well-known diauxic growth patterns. Resource preferences have been shown to impact ecology by allowing microbes with different hierarchies to temporally partition the available resources and coexist. Yet, the extent to which substrate preference hierarchies can evolve and diversify remains largely unexplored. Here, we use a genome-scale metabolic model of a large-scale empirical genotype-phenotype map to show that alterations in the structure of metabolic networks often result in altered substrate preferences. By exploring a universal microbial metabolic genotype space in silico, we show that preference ranks tend to be more evolvable for specific substrates, and for pairs of substrates that are processed by different sets of reactions. We show that the diversification of metabolic preferences strongly depends on the specific topology of metabolism, with key reactions acting as capacitors and potentiators and influencing the evolvability of rank hierarchy. Our analysis sheds light on the evolvability and genetic determinants of microbial resource preference ranks.
