Defining microbial metabolic interactions in polymicrobial environments

The University of Tennessee received a $1.92 million Project Grant from the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training program (CFDA 93.859) awarded August 1, 2025, with completion targeted for July 31, 2029. This grant funds fundamental biomedical research investigating microbial metabolic interactions in polymicrobial environments, with a specific focus on chronic wounds as a model system. The research employs interdisciplinary approaches combining top-down and bottom-up methodologies to map the nutritional landscape of microbial communities and determine how nutritional factors impact community assembly, spatial organization, and microbe-to-microbe interactions at multiple scales—from macro to micron to chemical scales.

The project delivers research outputs utilizing advanced analytical technologies including high-resolution confocal imaging, imaging mass spectrometry, and spatial metatranscriptomics, coupled with an innovative computational pipeline to quantify the three-dimensional metabolic landscape of polymicrobial communities at micron-scale resolution. These research activities aim to generate an unprecedented visualization of microbes in their natural environment and establish fundamental biological principles governing how microbes interact, the spatial constraints to these interactions, and the molecular mechanisms driving sustained cooperative and competitive dynamics within host-associated microbial communities. The research is conducted at the University of Tennessee's Knoxville, Tennessee facility.

Abstract

Polymicrobial communities are ubiquitous and the interactions between microbes are critical drivers of overall community function. The commensal, pathogenic, and mutualistic organisms in host-associated microbial communities display synergies as a direct result of the interplay between their metabolic activities and spatial arrangement relative to each other, leading to sustained cooperative and competitive interactions. However, the fundamental biological principles of how microbes interact and the spatial constraints to these interactions, from the macro to micron to chemical scale, remain largely unknown. To fill this knowledge GAP, we propose interdisciplinary approaches to map the nutritional landscape and determine how the nutritional landscape impacts microbial community assembly, spatial organization, and interactions within host-associated microbial communities. Here, we use chronic wounds as a model system, as they have features conducive to addressing our goal: 1) sustained interactions in their native environment; 2) access to in situ sampling and visualization; and 3) measurable outcomes of interactions. Our objective is to combine top-down and bottom-up approaches to define the processes by which structured microbial communities form, the molecular mechanisms governing interactions between microbes, and the spatial parameters that dictate microbe-microbe interactions. First, we will use high-resolution confocal imaging, imaging mass spectrometry, and spatial metatranscriptomics to quantify the metabolic landscape of polymicrobial communities, in three-dimensions at the micron scale with an innovative computational pipeline we developed. This will yield an unprecedented view of microbes in their natural environment and provide a platform for visualizing polymicrobial communities. Further, we will evaluate how this landscape shifts in response to changes in community composition and host environment. Next, we will use -omic and genetic approaches to define how shifts in nutrient availability due to changes in community composition and host nutritional status impacts cellular metabolism, cooperation, and competition within microbial communities. Collectively, this proposal will provide a framework for understanding the ecological factors that contribute to community composition, stability, and interactions in host-associated polymicrobial environments. While this project is centered on chronic wounds, the long-term goal is to apply this platform broadly across microbial communities. This work will advance our fundamental knowledge of microbe-microbe interactions and identify new strategies that leverage these interactions to improve human health.