The field of microbiota research is currently one of the ‘hottest’ areas in microbiology. A series of seminal discoveries made over the last decade have demonstrated the key role of the microbiota and individual bacterial constituents in health and disease. The explosion of the field has led to an increased awareness of the value of bacterial physiology, taxonomy and communication by many scientists for whom all bacteria used to be more or less alike and thus generated numerous opportunities for fruitful interdisciplinary collaborations. Enormous translational and economic potential of microbiota analysis and manipulation is anticipated, strikingly demonstrated by the fact that the human microbiome made it to the cover of a recent edition of ‘The Economist’.

There is certainly no dearth of review articles about microbiome research, but many recent synopses were focussed on few areas such as the gut microbiome or the microbiome and the immune system. In this Thematic Issue, ‘Host-associated microbiota: impact on health and disease’, we have assembled a collection of seven topical review articles covering very diverse host-associated microbiota, including the rhizosphere, milk, the insect gut, the mammalian stomach and the human vagina and gastrointestinal tract in the specific context of HIV infection. In addition to these reviews that summarize available knowledge of the composition and dynamics of the microbiota in these habitats and their functional roles, we also included reviews that focus on novel methodological and conceptual approaches to microbiota ecophysiology and the decoding of its metabolic interactions. We have conceived this Thematic Issue with the aim that it should provide the readers of FEMS Microbiology Reviews with insight into the breadth of microbiota/microbiome research as of 2013, an overview of the vast array of methods used to study it, and an appreciation of the rapid progress that has been made just as well as the staggering number of open questions and opportunities for future research. While we have kept this issue focussed on bacterial microbiota, we are aware of the importance of research on nonbacterial components of the microbiota, such as the ‘virome’ and the ‘fungome’.

On behalf of all editors of this issue, I would like to express our sincere thanks to all authors for their valuable contributions to this Thematic Issue. Committing to write comprehensive review articles in such a rapidly moving field is a very major investment and a largely altruistic service to the scientific community, which we highly appreciate.