A systems approach for elucidating the role of the microbiome in epigenetic cellular memory

The microbiome plays an essential role in the development of the immune system. Both the immune system and microbiome dynamically respond to internal and external cues, and dysregulation of either of these systems can lead to disease pathology. Separate from the adaptive immune system, the innate immune system retains a memory of inflammatory events that determine the quality of future immune responses. The phenomenon is characterized by epigenetic modifications that lead to immunosuppressive or hyperinflammatory cell phenotypes, collectively designated as epigenetic cellular memory. It remains unclear whether and how the microbiome influences epigenetic cellular memory phenotypes to promote immunopathology and chronic disease. Inflammatory signals from the microbiota regulate hematopoiesis and systemic immunity through the production of immunomodulatory ligands and activation of circulating immune cells; however, few studies have directly implicated these mechanisms in the development of epigenetic cellular memory. We posit that a multi-omic systems approach is well-suited to elucidating the complex factors mediating the microbiome's contribution to this phenomenon. By measuring responses to exogenous influences through multi-omic technologies, it will be possible to identify the regulatory axis that next-generation therapies should target to reverse immunopathology. As chronic inflammatory disorders are on the rise, it is imperative that future therapies leverage both dietary and pharmacological interventions to promote self-reinforcing homeostatic immunity by targeting the mechanisms of epigenetic cellular memory.