Bacterial Corrinoid Metabolism Across Scales: From Molecular Specificity to Community Dynamics

PROPOSED ACTIVITIES RESEARCH STRATEGY Project Summary/Abstract Microbial communities inhabit nearly all environments on earth, including the human body, where they can influence health in myriad ways. These communities are often composed of hundreds or more species that form networks of metabolic interactions. Because metabolic interactions are complex and difficult to study at a

molecular level, my research program focuses on interactions involving one family of metabolites – corrinoid cofactors – as a model to understand metabolic interactions among bacteria. Corrinoids are the vitamin B12 family of cobalt-containing metabolites that are used as enzyme cofactors for a variety of reactions. Corrinoids,

like many amino acids, nucleobases, and other cofactors, are synthesized by only a fraction of bacteria that use them, and therefore are considered to be shared metabolites. Corrinoids are unique in their structural diversity, with over a dozen different forms discovered and up to eight of these forms found in microbial community

samples, including the human gut. This structural diversity is a significant factor in microbial interactions because most bacteria are selective in the corrinoids they can use. The hypothesis driving this work is that structurally distinct corrinoids can be used as handles to manipulate microbial communities. Our previous NIGMS-funded

research has laid the groundwork for the proposed research by establishing experimental methods; discovering and characterizing new genes; investigating corrinoid selectivity in enzymes, riboswitches, and bacteria; and creating a bioinformatic pipeline to predict corrinoid metabolism in bacteria. Our long-term vision is to build on

this foundation to generate a newly detailed understanding of microbial community interactions through the study of corrinoids across scales, from molecular mechanisms to whole community perturbations. We will achieve this goal by (1) identifying genome sequence signatures predictive of bacterial corrinoid preferences in corrinoid-

dependent enzymes and riboswitches, with an emphasis on evolutionary approaches and (2) investigating the molecular basis of corrinoid-dependent community dynamics by applying sequencing, culture-dependent, and genetic approaches to a model human gut-derived enrichment culture. As a test of our ability to understand and

predict corrinoid-based metabolism and community dynamics, we will design and build bacterial strains with corrinoid-dependent metabolic networks, as well as consortia of bacteria with predictable dynamics. This research will be accomplished by using a combination of genetics, biochemistry, microbiology, and

bioinformatics, building upon the past research of my group. Our work on corrinoids will not only serve as a model for microbial community interactions across systems, but may also lead to the development of new methods to alter microbial communities for beneficial outcomes. Specific Aims This proposal describes research projects to be conducted by two PhD students and one undergraduate.

This support will provide tailored mentorship to each student while expanding our research into new areas within the scope of the parent award, which aims to apply the corrinoid model to the study of microbial community interactions. Each specific aim describes a project to be conducted by one student.

Aim 1. Test the hypothesis that the Great Plate Count Anomaly can be influenced by corrinoids. PhD student Zoila Alvarez-Aponte will isolate bacteria from a human gut-derived bacterial enrichment culture in media containing different corrinoids to determine whether non-commercially available corrinoids can influence

culturability. Aim 2. Use comparative genomics to define and survey corrinoid metabolism in the domain Archaea. PhD student Eleanor Wang will identify archaeal genes for corrinoid biosynthesis and corrinoid-dependent functions and survey their abundances throughout the domain Archaea. This will enable us to include archaea

– understudied yet critical components of microbial communities – in future studies of microbial metabolic interactions. Aim 3. Construct and test riboswitch-based biosensors for rapid corrinoid detection. Undergraduate student Lesley Rodriguez will construct a panel of synthetic riboswitch-GFP reporters in Bacillus subtilis and test

each strain for the ability to sense corrinoids. She will then use these strains as biosensors to rapidly detect corrinoids from diverse biological samples with high sensitivity. These projects will contribute to the training of the next generation of scientists, while providing the Taga lab with opportunities to pursue exciting new research directions.