Trillions of commensal microbes reside on and inside the human body, including

the intestinal and respiratory tracts, which encompass various microbial taxa, such

as bacteria, fungi, archea and viruses. The close proximity of microbes with the

host provides an opportunity to continually interact with each other. Advances in

research approaches, including high-throughput sequencing, have allowed us to

study host and commensal microbes at the genetic and functional levels. Recent

studies suggest that commensal microbes play a crucial role in the development of

the host’s immune system and induce innate and adaptive immune responses against

pathogens. It is also becoming apparent that the gut commensals are endowed with

a capacity to alter immune responses in organs beyond the intestine, such as the

lungs, highlighting the significance of the gut commensals in controlling systemic

immunity. On the other hand, the host’s immune system possesses the ability to

shape the repertoire of commensal microbes and contribute to the establishment

of beneficial relationships with them. A better understanding of host-commensal

interactions will be important for designing effective vaccines and therapeutics

against pathogens.

This Research Topic sheds light on our current understanding of the interplay between

the host’s immune system and commensal microbes and how this interplay can be

exploited for prophylactic and/or therapeutic strategies against pathogens.