Abstract
The human gastrointestinal tract is a unique mucosal barrier with a tremendous surface area that is subject to continuous exposure to the environment. The immune system must remain poised to protect this organ system from potential pathogens while restraining chronic inflammatory responses that negatively impact physiological functions or facilitate malignancy. Innate lymphocytes emerged as major regulators of gut health through numerous key functions. Recent evidence indicates that these cells are adaptively influenced by specialized microniches, or distinct aggregates of cells that engage in dynamic crosstalk at a microscopic level and integrate signals from the environment to perform specialized functions with regional precision. Here, we explore our current understanding of how microniches in the gut shape the biology of innate lymphocytes, with a focus on an interplay of diet and microbial exposure, selective cell-cell communication networks, and spatiotemporal properties. We also discuss how these microniches may be altered in human diseases or could be harnessed to better protect the gut. Finally, we identify current gaps in knowledge in this rapidly emerging field.