Non-invasive single-cell morphometry and tracking in living bacterial biofilms

The National Institute of General Medical Sciences awarded the University of Virginia $425,145 on March 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to develop integrated microscopy and image processing technologies for long-term three-dimensional fluorescence imaging of bacterial biofilm communities on and within living human epithelial tissues. The project will create imaging and tracking systems capable of measuring single-cell three-dimensional bacterial morphometry and automatically tracking thousands of interacting bacterial cells over time within crowded biofilms, addressing current limitations in microscopy platforms that cannot resolve and track micrometer-sized cells in such environments. The resulting platform will visualize how bacterial populations colonize different niches on and within the human body to advance understanding of microbial life and its impact on human physiology, including how biofilms develop antibiotic tolerance and immune evasion mechanisms underlying hospital-acquired infections.

Work is performed in Charlottesville, Virginia, with a period of performance from March 1, 2026, through February 28, 2031. The University of Virginia, a public research institution, serves as the recipient. This is a Project Grant, the standard assistance type for investigator-initiated basic research under NIGMS's portfolio.

Abstract

Biofilms are cohesive, multicellular microbial communities that adhere to biotic or abiotic surfaces. Biofilms play crucial roles in the human microbiome, but also cause over half of the 1.7 million hospital-acquired infections in the US. Phenotypic diversity and coordination of cellular behaviors within biofilms provide bacterial populations with emergent capabilities beyond those of individual cells. Most notably, biofilms are orders of magnitude more tolerant to long-term antibiotic drug treatments and host immune responses. IT remains largely unknown how such remarkable capabilities emerge from the behaviors of individual cells and the interactions between them, mainly because currently available microscopy platforms cannot resolve and automatically track micrometer- sized bacterial cells within crowded biofilms. To address this challenge, the proposed research seeks to develop integrated microscopy and image processing technologies that enable long-term 3D fluorescence imaging of bacterial biofilm communities on and within living human epithelial tissues, and accurate single-cell 3D shape measurements and tracking of thousands of interacting bacterial cells over time. The resulting imaging platform will be applied to visualize, in 3D space and time, how bacterial populations colonize different niches on and within the human body, where they symbiotically support host tissue physiology or cause acute or chronic tissue pathology. Such information is critical to advance our understanding of microbial life and its impact on human physiology.