  Related groups of microbes are widely distributed across Earth's habitats,
implying numerous dispersal and adaptation events over evolutionary time.
However, to date, relatively little is known about the characteristics and
mechanisms of these habitat transitions, particularly for populations that
reside in animal microbiomes. Here, we review the existing literature
concerning habitat transitions among a variety of bacterial and archaeal
lineages, considering the frequency of migration events, potential
environmental barriers, and mechanisms of adaptation to new physicochemical
conditions, including the modification of protein inventories and other genomic
characteristics. Cells dependent on microbial hosts, particularly bacteria from
the Candidate Phyla Radiation (CPR), have undergone repeated habitat
transitions from environmental sources into animal microbiomes. We compare
their trajectories to those of both free-living cells - including the
Melainabacteria, Elusimicrobia, and methanogenic archaea - as well as cellular
endosymbionts and bacteriophages, which have made similar transitions. We
conclude by highlighting major related topics that may be worthy of future
study.
