Microbiota and Extracellular Matrix Interactions that Drive Host Tissue Remodeling

PROJECT SUMMARY Knowledge about the human microbiome has increased exponentially in the last twenty years, leading to its association with a wide variety of conditions and diseases. However, many of the mechanisms underlying the relationships between microbes and their human hosts have not been elucidated, particularly at the tissue level.

The human extracellular matrix (ECM) provides important structural and biochemical cues for the development and homeostasis of all human tissues. Extensive ECM remodeling is a prominent feature of several diseases linked to human microbiome dysfunction including pulmonary cystic fibrosis, inflammatory bowel disease, and

cervical cancer. Yet, regardless of tissue or body part, host cells (e.g. fibroblasts, macrophages, and neutrophils) are considered the primary drivers of ECM degradation, even though human-associated microorganisms are known to secrete active proteases. Thus, crucial ECM-microbiome interactions should be included in existing

paradigms of host ECM remodeling. To address this important knowledge gap, our lab develops in vitro and ex vivo models using biomaterials and tissue engineering strategies to explore the fundamental mechanisms behind ECM-microbe interactions. We hypothesize that commensal microbiota can degrade human ECM and that

ECM remodeling, in turn, alters host cell behavior. The proposed research program will initially answer three key questions: 1) What environmental conditions enable bacterial degradation of host ECM? Our preliminary data demonstrates that commensal bacteria grown in complete growth medium can degrade

individual ECM components in vitro. Because environmental factors influence bacterial metabolism, we will explore how factors such as pH, and nutrient source impact ECM degradation by gut and vaginal bacterial species. 2) How do human-associated bacteria remodel host ECM? In parallel to question 1, we will use

metaproteomics and inhibition studies to identify the specific proteases and carbohydrate degrading enzymes involved in ECM degradation. Additionally, we will develop an ex vivo tissue culture model to characterize the extent of bacterial ECM remodeling. 3) What are the consequences of microbiota-driven ECM remodeling

for host immune cells? Because the ECM regulates cell behavior, we will test the hypothesis that ECM modified by the microbiome impacts host cell function. We will generate in vitro biomaterial platforms that capture the properties of native ECM and incubate them with microbiota culture supernatant. We will then expose innate

immune cells to the remodeled matrices and evaluate their phenotype. This ESI-MIRA award will enable my group to discover interactions between bacterial microbiota and host ECM, shedding light on the microbiome’s underexplored contributions to tissue maintenance and dysfunction. Ultimately, the vision for my research

program is to determine the impact of the human microbiome on ECM remodeling and leverage this new knowledge to develop novel diagnostics and therapeutic strategies.