On 1970s Carl Woese and George Fox opened a new research frontier by producing sequence-

based measures of phylogenic relationships and this led to one new understanding that reflects strong
interdependencies that exist between these complex multicellular organisms and their associated
microbes. We chose to focus on animal–bacterial interactions and begin by describing what we know
about the evolution of animals and their interactions with bacteria.

The major underpinnings of animal–bacterial interactions- nutrition, recognition, cell adhesion,

and signaling—guide two types of choanoflagellate behavior that may have been key to the origin of
animals: predation (8) and colony formation. As early animals diversified, animal–bacterial interactions
continued to shape evolution in new ways. Bacteria took on a new role in animal nutrition, serving not
only as prey but also as producers of digestible molecules in the animal gut. The evolution of form and
function in other organ systems may have also been influenced by interactions with bacterial partners.
Evolution with animals, whether in symbiosis or via shared habitats, has also influenced the distribution
and diversification of bacteria. The evolution of animals provided novel physical environments for
bacterial colonization.

Bioinformatic analyses have revealed that interactions with animals also influence the size and
content of the genomes of their bacterial partners. As early animals diversified, animal–bacterial
interactions continued to shape evolution in new ways. Bacteria took on a new role in animal nutrition,
serving not only as prey but also as producers of digestible molecules in the animal gut. The genomic
basis for other microbial adaptations among gut microbes is less clear. One possible selection pressure is
host temperature.

Although animals and bacteria have different forms and lifestyles, they recognize one another
and communicate in part because, as described above, their genomic “dictionaries” share a common
and deep evolutionary ancestry. As much as a third of an animal’s metabolome—i.e., the diversity of
molecules carried in its blood—has a microbial origin; thus, the circulatory system extends the chemical
impact of the microbiota throughout the human body

Viewing animals as host–microbe ecosystems has given us new insights into the maintenance of
human health. The application of ecological approaches, including successional assembly and diversity
analysis, has proven valuable in understanding how animal–microbial alliances function

The current focus on studies of humans and their microbiota has provided compelling evidence that the
composition and activity of resident microbes play crucial roles in shaping the metabolic and regulatory
networks that define good health, as well as a spectrum of disease states. The goal must be to apply an
understanding of the relationships between microbes and other organisms to predict and manipulate
microbial community structure and activity so as to promote ecosystem health. Successful development
of research on our microbial world will result only with the breakdown of existing intellectual barriers,
we foresee a day when microbiology will be a centerpiece not only of biological research, but also of
high school, undergraduate, and graduate biology education.