Variation in gut microbiota composition impacts host gene expression

Variation in gut microbiome is associated with wellness and disease in humans, yet the molecular mechanisms by which this variation affects the host are not well understood. A likely mechanism is through changing gene regulation in interfacing host epithelial cells. Here, we treated human colonic epithelial cells with live microbiota from five healthy individuals and demonstrate that both natural and controlled microbiome composition lead to distinct, and predictable, gene expression profiles in the host. We also identified chromatin accessibility changes induced by the microbiota that explain a fraction of the gene expression response.