The coevolution of mammalian hosts and their commensal microbiota has led
to the development of complex symbiotic relationships between resident microbes
and mammalian cells. Epigenomic modifications enable host cells to alter gene
expression without modifying the genetic code, and therefore represent potent
mechanisms by which mammalian cells can transcriptionally respond, transiently
or stably, to environmental cues. Advances in genome-wide approaches are
accelerating our appreciation of microbial influences on host physiology, and
increasing evidence highlights that epigenomics represent a level of regulation
by which the host integrates and responds to microbial signals. In particular,
bacterial-derived short chain fatty acids have emerged as one clear link between
how the microbiota intersects with host epigenomic pathways. Here we review
recent findings describing crosstalk between the microbiota and epigenomic
pathways in multiple mammalian cell populations. Further, we discuss interesting
links that suggest that the scope of our understanding of epigenomic regulation
in the host-microbiota relationship is still in its infancy.