Your gut bacteria don't just digest food — they produce metabolites that chemically modify the proteins wrapped around your DNA, called histones. These modifications, known as post-translational modifications or PTMs, act like molecular switches that turn genes on or off. A new perspective article in Nature Metabolism highlights how the microbiome shapes a range of newly discovered histone marks beyond the classic well-studied ones. These emerging modifications influence how genes are expressed in the intestine and connected tissues. The authors explain the molecular pathways by which microbial metabolites reach chromatin and alter gene regulation, and they explore how these changes connect to normal physiology and disease. Understanding this microbiome-to-epigenome axis opens fresh possibilities for targeting the microbiome to influence gene expression patterns relevant to aging and metabolic health.