An interaction between two microbes is illustrated on the left of the figure, with the green microbe producing a signal (purple hexagons) that causes the orange microbe to respond in one of the manners illustrated on the right. The signals discussed here fall primarily into two classes: known metabolites (such as peptidoglycan, antibiotics, and intraspecies signals) that cause unexpected responses affecting other microbial speces, and novel secondary metabolites; in some cases the signals are still unknown. Upon detecting the signal, the responding organism may experience changes in metabolism (growth inhibition or stimulation, or production of new small molecules) or morphological and developmental changes (alterations in cell shape or morphology; production of biofilms or fruiting bodies; or specialized processes such as sporulation and germination). More than one response is possible to a single signal.

Some fatty acids and alcohols produced by fungi and bacteria have roles as interspecies signals. The wavy arrows indicate the production of small molecules by particular microbes; if known, the effects of these compounds on the behavior of other organisms is indicated by smooth arrow- or bar-headed lines. See text in section IIC for more details.