Following further research, I have concluded that the correct term is "amphibiotic flora". That being said, the explanation provided by the person who suggested this translation was incorrect. In the context of pathogenic microorganisms, the term amphibiotic actually has a very different meaning from "semiaquatic". See the definition of the terms “amphibiont” and “amphibiosis” here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2094851/
It should be noted, however, that the adjective for "amphibiont" in English is "amphibiotic", not "amphibiontic". Helicobacter pylori is frequently cited as an example of an amphibiont. However, a search on pylori + amphibiontic only turns up scientific articles that were written by native speakers of Portuguese or Spanish. In contrast, a search on pylori + amphibiotic, turns up many articles that appear to have been written by native speakers of English and/or that were published in peer-reviewed English-language scientific journals. See, for example:
http://www.jci.org/articles/view/12672
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639765/
The translation workplace 
peer agreement (net): +4
