There are two characteristics that hold together the field of microbiology, one fundamental and the other less so. The fundamental characteristic of microorganisms are that they are small. In fact, most of the organisms studied by microbiologists – or, more broadly, introduced by general microbiology texts – are so small that studying individual organisms, other than via microscopy techniques, is technically demanding (as, too, is microscopy, though in this modern age we take for granted its sophistication relative to what was available before good, easy-to-use microscopes became widely available).

Other than microscopically, microbiological characterization typically involves the study of bulk properties, especially those of clonal populations rather than study of the properties of individual organisms. The consequence of this analysis of populations rather than of individual organisms is that a key step in microbiological characterization is to bring organisms into what is known as a pure culture, that is, clonal populations. This is equivalent, perhaps, to studying fish properties within an aquarium in which the fish are isolated from other fish. Microorganisms found in pure culture, however, are typically generated by microbial population growth rather than by the mixing together of individuals removed from communities containing other species. Notable additional differences between fish and microbes in this analogy are that fish more typically are sexual in their reproduction and fish also are less likely to be euthanized en masse for the sake of studying their common but nonetheless individual properties, whereas such mass killing of laboratory population is a standard technique within the microbiology laboratory.

The second key characteristic that unites much though not all of microbiology is medicine. Thus, there are organisms that are studied within the context of biomedicine that strictly are not microorganisms, but which nevertheless are small, pathogenic, and which can be analyzed via an approximation of typical microbiological techniques. These latter organisms include especially the helminthes, a.k.a., parasitic worms, though perhaps arguably also could include various additional multicellular eukaryotes such as molds or certain algae. Medical microbiology thus tends to encompass a greater as well as different diversity of organisms than does non-medical microbiology, focusing on organisms that are associated with infectious disease rather organisms that more strictly may be described as microorganisms.

Thus, though less germane to what exactly a microorganism is, a large fraction of microbiological research is medically oriented. This emphasis is a result of funding priorities. As a consequence, the microbiology literature tends to be dominated by studies that are initiated at least in part from a perspective of health issues. More generally, the types of organisms that microbiologists tend to study are ones that have health or economic relevance, or both. Microbial evolution studies are less bound by this need to be medically or economically relevant. Therefore what is studied and how can be more diverse than often is the case in more medically oriented microbiology laboratories. Nonetheless, the concentration of knowledge and funding on medical and otherwise economically relevant issues and organisms tends to ground microbial evolution-type studies closer to biomedicine than might otherwise have been the case. By way of example, it can be much simpler to receive funding to study, or otherwise publish in a prestigious location, the evolutionary diversification of a pathogen, e.g., such as of human immunodeficiency virus (HIV), than it can be to fund and publish the same research on viruses affecting a medically and economically irrelevant or otherwise non-charismatic species (e.g., such as hagfish pathogens). These emphases are not necessarily a bad thing, but are worth appreciating especially as a guide towards navigating the microbial population biology literature.