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The gut microbiome contributes to the overall metabolism of numerous compounds that circulate in and out of the gastrointestinal tract, including endogenous, dietary, and pharmaceutical molecules. Herein, three projects are presented aimed at uncovering bacterial species and genes responsible for the chemistry carried out by the gut microbiome. In the first, a previously unreported route for the production of dopamine by gut bacteria is posed. Dopamine, which is abundant in the gut, is converted to 3-methoxytyramine (3MT) by the human enzyme catechol O-methyltransferase (COMT). Communities of fecal bacteria are demonstrated to O-demethylate 3MT to produce dopamine. Two prominent acetogens found in the GI tract, Eubacterium limosum and Blautia producta, are shown to carry out this metabolism. This metabolism is shown to likely be carried out by cobalamin-dependent methyltransferases, as metabolism is reversibly inhibited by propyl iodide. In the second, I identify additional guaiacol metabolites that E. limosum and B. producta can O-demethylate to their respective guaiacols: vanillylmandelic acid, 3-O-methyldopa, and 2-methoxyestradiol. In the third, I determined that the gut bacterial protein called enterodiol lactonizing enzyme (Edl) is sufficient for converting enterodiol (END)—produced by gut bacterial metabolism of diet-derived molecules—into the phytoestrogen enterolactone (ENL). ENL has been reported to have anti-breast cancer effects in rodent models and humans. Thus, an absence of the bacterial genes required to produce ENL in an individual’s gut microbiome may serve as a biomarker for an increased risk for breast cancer.

The development of sustainable synthesis methods for societally important chemical products which serve as fuels, industrial feedstocks and materials is a pressing global challenge. Many of these target molecules are currently produced from fossil fuel-derived starting materials, which is problematic due both to the impending exhaustion of these resources and the dire environmental consequences of unrestrained carbon dioxide release into the atmosphere. An attractive alternative is using carbon dioxide along with sustainable energy sources for the production of these chemical targets. This thesis explores the development of multiple sustainable synthesis platforms based on interfacing inorganic materials, which function well for solar energy capture and charge transfer, with autotrophic microorganisms, which serve as biocatalysts, able to fix carbon dioxide into value-added products using the energy provided by the inorganic components. An initial approach focused on the development of a hybrid bioinorganic device in which sustainable electrical and/or solar input drove production of hydrogen gas from water splitting using biocompatible inorganic catalysts. The hydrogen was then used by autotrphic microorganisms as a source of reducing equivalents for conversion of CO2 to the value-added chemical product methane. Employing platinum or a newly synthesized earth-abundant substitute, α-NiS, as biocompatible hydrogen evolution reaction (HER) electrocatalysts and Methanosarcina barkeri as a biocatalyst for CO2 fixation, robust and efficient electrochemical CO2 to CH4 conversion was demonstrated at up to 86% overall Faradaic efficiency for ≥7 d. Introduction of indium phosphide photocathodes and titanium dioxide photoanodes afforded a fully solar-driven system for methane generation from water and CO2, establishing that compatible inorganic and biological components can synergistically couple light-harvesting and catalytic functions for solar-to-chemical conversion.A second device attempted to mimic the biosynthetic process of natural photosynthesis, where solar energy powers the reduction of CO2 to common biochemical building blocks, which are subsequently used for the synthesis of the complex mixture of molecular products that form biomass. The artificial photosynthesis system described here functions via a similar two-step process: A biocompatible high-surface-area silicon nanowire array harvests light energy to provide reducing equivalents to the obligately anaerobic acetogen, Sporomusa ovata, for the photoelectrochemical production of acetic acid with low overpotential (η < 200 mV), high Faradaic efficiency (up to 90%), and long-term stability (up to 200 h). The resulting acetate (∼6 g/L) can be activated to acetyl coenzyme A (acetyl-CoA) by strains of genetically engineered Escherichia coli and used as a building block for a variety of value-added chemicals, such as n-butanol, polyhydroxybutyrate (PHB) polymer, and three different isoprenoid natural products. Due to the local chemical environment within the nanowire array, the systems was also shown to perform well under aerobic conditions (21% O2), allowing the cultivation of an obligate anaerobe using oxygen-containing gas feedstocks for growth. This system demonstrated the power of interfacing biocompatible solid-state nanodevices with living systems in order to create programmable platforms for chemical synthesis entirely powered by sunlight. Informed by the successes of the previous systems, a next generation device was envisioned in which the autotrophic microorganism, which was interfaced with the biocompatible inorganic components, is directly engineered to produce value-added products, offering the simplicity of a single organism system with the product scope of co-culture platforms. Towards this goal methods for metabolic engineering of Methanococcus maripaludis, a methanogenic archaea, have been developed. These efforts have chiefly focused on achieving robust expression of multienzyme heterologous pathways, a goal complicated by the incompletely understood translational machinery in this organism. For optimization the 3-hydroxybutyrate pathway was used, which results in production of a monomer unit, which can be polymerized into the bioplastic PHB. Robust expression of the full 3-hydroxybutyrate biosynthetic pathway was achieved using a strong Methanosarcina barkeri promoter. Activity of all pathway enzymes was demonstrated in cell lysates; however, no product formation was observed. It is currently hypothesized that this is due to a lack of appropriate redox cofactors, specifically NADH. The NADH pool observed in M. maripaludis was found only to be 3% of that observed in E. coli. Current efforts are underway to enlarge this cofactor pool and incorporate it into the redox metabolism of the organism. This work has demonstrated the power of hybrid biological-inorganic devices for the sustainable synthesis of value-added products. Systems have been developed that are fueled using sustainable sources of electric current or directly by illumination. A variety of product has been produced, both native products as well as more complex products, using a co-culture system. Efforts are ongoing to develop metabolic engineering tools for the unique class of organisms amenable to integration with inorganic materials. These engineering efforts will pave the way for future simplified devices with expanded product scopes.

The interplay of chemistry and biology holds many opportunities to address the woes of the modern world. As synthetic chemistry and cell biology have married together to make great strides in health and medicine, an amalgamation of inorganic materials chemistry and microbiology holds similar promise to revolutionize our approach to transducing solar energy into chemical bonds. By combining the superior light harvesting of inorganic semiconductors with enzymatic biocatalysts, high efficiency solar-to-chemical production of complex molecules and materials may outcompete natural photosynthesis. In this work, I describe a series of investigations into the physical and chemical interactions of inorganic-biological hybrid organisms. In the Sporomusa ovata-silicon nanowire system, changes in salt concentrations predictably controlled cell-nanowire alignment, producing a predictive model of inorganic-biological colloidal interaction. The hybrid organism Moorella thermoacetica-cadmium sulfide self-photosensitized the synthesis of acetic acid from CO2 via bioprecipitated CdS nanoparticles. A titanium dioxide-manganese(II) phthalocyanine photocatalyst system extended oxygenic photosynthesis in M. thermoacetica-CdS through a photoregenerative cysteine-cystine redox couple. Finally, transient absorption spectroscopy, time-resolved infrared spectroscopy and biochemical assays suggested a two-pathway mechanism of charge and energy transport between M. thermoacetica and CdS. These initial works at the nexus of materials chemistry and biology lay the foundation for deeper understanding of this complex interface as well as for the development of advanced solar-to-chemical production systems.