Learn English – General term for both clients and customers

No single term would cover both viruses and bacteria because there are other biological entities that are similar enough to each, such as prions or protozoa, that would need to be covered by a word that included viruses and bacteria.

The context in which you want to use this term would be useful. For non-technical audiences, you already said that microbe would work because you believed it included viruses. (And I think most non-technical readers would believe the same thing.) Germ might be a better word than you give it credit, for non-technical audiences at least.

Germ is a deceptively simple word that came to us from Latin germen, meaning a sprout, bud, or offshoot. In all of its meanings, the term germ retains the idea of developing into something more mature.

From MedicineNet. Germ as used in the phrase, germ theory of disease, means a small thing that develops into a mature disease.

For technical audiences, I think you accidentally made the best phrase in your question and comments. Something such as sub-multicellular biological entities with basic reproductive capabilities is precise, clear, and unambiguous. A technical reader will understand that this at least includes viruses and bacteria and will likely recognize the other potential members. This phrase could include loose genetic material, too.

You might try moving away from the word biological and towards the word organic. A prion, a virus, and a bacteria are all organic and all have the ability to replicate in the right conditions. Therefore, a phrase such as organic entity with reproductive capacity might work, but it is arguable that a virus does not have the capacity.