Microbiota Metallophores: Probing Interactions and Nutrient Dynamics of the Human Gut

Project Summary/Abstract A healthy human microbiome is intrinsically linked to vital physiological aspects such as development, immune function, and nutrition. The composition and function of the human microbiota is significantly influenced by access to key metal micronutrients including iron, copper, zinc, and cobalt. Although mechanisms of competition for metals have been studied in metal-limited environmental systems, how the human microbiota acquires metals and responds to changes in host metal homeostasis remains under investigated, even as microorganisms must compete with one another for limited resources at metal-limited body sites. Production of metallophores, small- molecule natural products that bind metals with high affinity and selectivity, can enable colonization of metal- limited environments; for example, we recently showed that Escherichia coli Nissle 1917 persists in the zinc- limited inflamed gut by producing zinc-binding yersiniabactin. Metallophore-production can also benefit other, non-producer organisms in microbial systems, as metallophores can be shared goods in complex microbial communities. Recent examples have revealed that Bacteroides thetaiotaomicron, a human commensal bacterium, uses siderophores produced by other bacteria for iron acquisition during iron-limitation. However, despite significant numbers of metallophore biosynthetic gene clusters (BGCs) present in metagenomics sequencing data from human-derived microbiota samples, elucidation of the chemical structures and properties of these microbial molecules remain limited by various analytical, chemical, and biological challenges. This lack of reliable methods precludes our understanding of functional roles of these molecules. Therefore, the goal of this proposal is to elucidate the structure and functions of microbially-derived metallophores as modulating microbe-microbe and community interactions within human microbiomes. To accomplish this, our laboratory will investigate several critical questions, broadly these are: 1) what metallophores are produced by the human microbiota and how are they biosynthesized? 2) what are their metal preferences and specificities? 3) how do these molecules modulate microbial interactions? 4) what are the effects of altered microbial interactions? With these questions in mind, we develop discovery-based approaches to find uncharacterized microbial metallophores, pursue chemical structure elucidation and characterization of biosynthesis, and investigate growth and metal acquisition of wild-type and genetic deletion mutants (lacking metallophore-production ability) to understand functional roles of these molecules in monoculture, co-culture, and in complex microbial model systems. Elucidating the metal-uptake molecules and mechanisms used by the microbiota to withstand altered metal homeostasis may allow for the development of microbiome-based therapeutics, identification of microbiome-derived biomarkers, and an improved understanding of metal imbalances. This research will provide fundamental insight how members of the microbiota interact through metal competition, a key mechanism by which both opportunistic infections and probiotic organisms are established and persist within the microbiome.