I think it is a case of mistranslation or misinterpretation that got to stick.
What has always struck me personally was "gut flora". I know that "flora" is plants (flower) and fauna is animals. Biome seems a more adequate term to use, as bacteria is neither plant nor animal, that is "a community of biological life inhabiting a specific environment". In fact, the terminology for microorganisms that dwell on or in the human is known as human microbiota.
In short, as I mentioned, one of the many cases of fallacies that got to stick. Like calling Native Americans "Indians", or "begging the question", there are many others too, especially in layman modern day language.
The wikipedia article linked above confirms my initial suspicion was correct:
Though widely known as flora or microflora, this is a misnomer in
technical terms, since the word root flora pertains to plants, and
biota refers to the total collection of organisms in a particular
ecosystem. Recently, the more appropriate term microbiota is applied,
though its use has not eclipsed the entrenched use and recognition of
flora with regard to bacteria and other microorganisms. Both terms are
being used in different literature.