Microbial epigenetic regulation as a multilevel regulatory interface in host-microbe interactions

Animals coexist with complex microbial communities that influence their development, immunity, metabolism, and behavior. Evidence shows these effects arise not just from metabolic and immune signaling but also from epigenetic mechanisms that alter host gene expression. Microbial signals can modulate DNA methylation, histone modification, chromatin accessibility, and RNA pathways, reshaping transcription across tissues. This review synthesizes evidence from diverse animal systems to demonstrate how microbial communities influence epigenetic landscapes and contribute to immunity, development, metabolism, and neurobiology. We explore data suggesting that microbial epigenetic interactions extend into the tumor microenvironment, where intratumoral microbes may shape disease progression by remodeling epigenetic states. Comparative studies indicate that microbial regulation of host epigenetics is an evolutionarily conserved mechanism linking environmental signals to phenotype. Despite recent advances, questions remain about causality, cell-type specificity, persistence, and inheritability of these effects. We propose microbial epigenetic regulation as a key interface integrating microbial cues with host physiology and pathology, providing a framework for understanding host-microbe interactions across species.