For a long time, the main purpose of host-associated microbiology was to study pathogenic bacteria and infectious disease; the potential benefit of good bacteria remained unrecognized. In the last 10 years, biology has made revolutionary advances from century-old debates about the relative importance of non-pathogenic bacteria. Today we know that individuals are not solitary, homogenous entities but consist of complex communities of many species that likely evolved during a billion years of coexistence. Many questions arise when considering an organism a multispecies metaorganism.

For example:

• How has the immune system been shaped by the need to accommodate symbionts?
• How does it coevolve with a symbiotic microbiota to both shape and accommodate community assembly?
• How do the resident symbionts influence fitness and thus ecologically important traits of their hosts?
• Is there a mutual intertwining between the stem cell regulatory machinery of the host and the resident symbiotic microbe composition, such that disturbances in either trigger a restructuring and resetting of the other?