This paper aims to outline the phenomena emerged from a terminographical analysis in Italian and German within the frame of the TERMit project. The topic examined is the microbiota, an innovative and interdisciplinary research field in medicine and consequently of paramount importance in translation as well as terminology. After a brief diachronic and scientific introduction along with a section regarding the research methodology and the corpus analyzed, the terminological aspects identified will be discussed. Firstly, the paper will examine terms and their improper usage, surveying extensively the dichotomy between “microbiota” and “microbiome” – one of the focal points of the analysis. Secondly, it will deal with some peculiarities concerning definitions of the concepts in this discipline. Thirdly, it will focus on terminological variation, namely synonyms and variants occurring in the special language of medicine – more specifically, within the multifaceted subfield of the microbiota – and will attempt to categorize them.