We can speak of "microbes" or "micro-organisms," and I used to think that these terms clearly included viruses. And they are used this way by at least some other people; here's a website that refers to viruses as a category of microbe.
However, I recently discovered that these terms are usually defined as referring to microscopic "life," and the definition of "life" with regards to viruses is a contentious topic.
When dealing with disease-causing agents, we can use the word "pathogen." However, not all bacteria and viruses are pathogenic.
All viruses must infect living cells to reproduce, so it is appropriate to refer to all viruses as "infectious agents" (this is what the Wikipedia article on viruses uses in its introduction). However, not all bacteria are necessarily infectious.
The informal terms "bug" and "germ" do exist. While these don't seem strictly limited to pathogens, that seems to be their most typical use. But for a technical audience, does any term exist for which there is a consensus that it refers to both all bacteria and all viruses?
If no single word exists, a short two-word phrase along the lines of "biological entity" would also be OK. (This phrase also comes from the "virus" Wikipedia article, and seems to be the best fit I've found so far. I can also think of a few others along these lines, like "microbial entity" which could be seen as a shorter equivalent to "microscopic biological entity.")
Here are the most important criteria I'll consider when deciding whether to accept an answer:
- technical correctness: The term must be acceptable regardless of whether one considers viruses to be living or non-living, organisms or not organisms. "Micro-organism" does not meet this criterion because some people do not consider viruses to be organisms.
- positive scope: It must include all viruses and all bacteria. "Pathogen" does not meet this criterion because not all viruses or bacteria are pathogenic.
- negative scope: It should not include inorganic objects, whether microscopic or macroscopic. E.g. rock particles. It's OK if it includes protists or multi-cellular organisms, or prions and other "pro-life," or some combination of any of these.
Other important criteria for me:
- established terminology: I'd prefer a term that is already in use to a neologism. If a neologism seems to be necessary, I'd like it to be linguistically well-formed and etymologically transparent.
- length: all else equal, I'd prefer a shorter term.
- grammatical number: I'd prefer a term that can be used in the singular to refer to a single species of viruses or bacteria, as opposed to an always-plural word or a singular mass noun.