This colloquium examines how animals across evolutionary lineages maintain microbial homeostasis at mucosal surfaces through active selection of beneficial microbes and exclusion of pathogens. Using a comparative approach, it traces microbial selection strategies from marine invertebrates to terrestrial mammals, highlighting both conserved mechanisms and lineage-specific innovations used by different species to create symbiotic bonds with specific microbes. Interactions ranging from those between the hawaiian bobtail squid (Euprymna scolopes), which creates a chemically selective microenvironment that recruits luminescent V. fischeri to the squid light organs while excluding competitors, to zebrafish and suppression of MyD88 to mediate selection of host microbiome will be discussed and compared with regards to the environmental pressures and immune system differences. Together, these findings illustrate a complexity trajectory from binary, innate-based symbioses to complex, multi-layered host-microbe interactions, positioning the immune system as both gatekeeper and gardener of the microbiota.
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