Microbiomes, consisting of bacteria, archaea, viruses, or unicellular eukaryotes, and their metabolites, interact with the human body in many ways. While many metabolic capacities of human-associated microbes are already known through multiomics studies, the molecular and biochemical mechanisms of host-microbe interactions are often not well understood. Here we invite authors to submit their latest studies, perspectives or reviews on mechanistic insights how microbes interact with the human host via molecules, pathways or cellular connections.