Great progress in microbiota research during last decades resulted in a growing corpus of publications mentioning the term 'microbiota'. Specifically, the human microbiota increasingly recognised nowadays as one of the most important health challenges is becoming an emerging research front. By examining over 28 000 microbiota-related papers from the Web of Science database, our study aims to characterise the evolution of publication patterns in this field between 1999 and 2017. The corpus is first analysed in terms of breakdown by journal subject categories, then an additional insight in the structuring of the microbiota research into different topics is provided by means of topic modelling. Our results demonstrate that over time (i) a substantial increase in the publications number is accompanied by a broad diversification of associated journal subject categories; (ii) the research focus moved outside from its primary research field showing successive shifts from dentistry and ecologically centred areas, through agri-food applied topics, towards the most recent clinical applications. The trends in thematic structure of the field presented from a historical perspective suggest that the current systemic approach to host-microbiota relationship inherited from the ecological background of the concept of microbiota has opened up a number of new research directions and perspectives.