[2S00e] 01. ASBA - Part 6

5:05 PM - 5:20 PM JST(8:05 AM - 8:20 AM UTC)

[2ASBA-14-2] Engineering Microbial Biocatalysis: Decoding Genetic Modules for the Bioactivation of Dietary Botanicals into Precision Anti-Infectives

○Gavin Kuziel (National University of Singapore (Singapore))

Keywords:

Microbial Biocatalysis,Functional Genomics,Colonization Resistance,Botanical Bioactivation,Synthetic Synbiotics

Diet is a primary driver of human health, yet the "black box" of host-associated microbial metabolism often obscures our ability to predict therapeutic outcomes from dietary interventions. Beyond traditional fiber, the gut microbiome performs complex biotransformations of plant-derived small molecules (botanicals), transforming inactive precursors into potent bioactive metabolites. Understanding the genetic logic and biochemical constraints of these pathways is essential for the rational design of synthetic microbial therapies and precision functional foods. Using a systems biology framework integrating chemical biology, functional genomics, and in vivo disease models, we mapped botanical metabolism across taxonomically diverse members of the gut microbiota. We identified the Bacteroidales as a dominant metabolic chassis for phytochemical catabolism. Through comparative genomic analysis and genetic dissection of two key species, Bacteroides ovatus (Bo) and Bacteroides uniformis (Bu), we identified two fundamentally divergent metabolic architectures. While Bo utilized a promiscuous, non-specific enzymatic module for broad-spectrum phytochemical and disaccharide catabolism, Bu harbored a highly orthogonal, multi-locus system with high selectivity for specific phytochemical substrates. These findings defined the design principles of microbial specialization: "generalist" vs. "specialist" modules that can be leveraged as programmable parts for the generation of engineered probiotics. We further demonstrated that this microbial metabolism functions as a distributed biosynthetic system that expands dietary chemical diversity by generating metabolites with bioactivities distinct from their parent molecules. Against a panel of multidrug-resistant enteric pathogens, several Bacteroides-liberated phytochemical aglycones, phloretin and resveratrol, exhibited potent and selective antimicrobial activity against Clostridioides difficile. In contrast, their parent glycosides were inactive, identifying microbial bioactivation as an essential step for therapeutic efficacy. This antimicrobial effect was conserved across 20 unique clinical isolates of C. difficile, regardless of toxin profile or virulence. In a mouse model of C. difficile infection, the administration of Bacteroides-liberated aglycones significantly reduced pathogen burden while maintaining community diversity. Furthermore, functional assessment of related, natural stilbene derivatives identified analogs with enhanced potency, defining the structural basis for microbe-mediated colonization resistance. Altogether, these findings established microbial bioactivation as a previously unrecognized mechanism for colonization resistance in the gut. By defining the specific microbiome-diet axes and the underlying genetic machinery, this work provides a framework for the development of synthetic probiotics and precision botanical-based therapeutics to combat enteric infection.