Microbes are microscopic organisms that cannot be seen by the human eye. They can be unicellular or multicellular and include at least some organisms in all the major kingdoms including bacteria, fungi, protists, plants, and animals. Viruses are also included under microbes.
Microbes exist in all different ecosystems on the planet, even including the deepest ocean trenches, inside active volcanoes, and under arctic ice. They are the most numerous of all life forms on the planet. Ecosystems for microbes also include living organisms. All complex animals including carnivores and herbivores have microbes in their bodies that often aid in digestion. Nectar feeders like insects also contain specific strains of microbes as well. So the answer to your question is yes.