The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases

The gut microbiota is a dense and diverse ecosystem that is involved in many physiological functions as well as in disease pathogenesis. It is dominated by bacteria, which have been extensively studied in the past 15 years; however, other microorganisms, such as fungi, phages, archaea and protists, are also present in the gut microbiota. Exploration of the fungal component, namely, the mycobiota, is at an early stage, and several specific technical challenges are associated with mycobiota analysis. The number of fungi in the lower gastrointestinal tract is far lower than that of bacteria, but fungal cells are much larger and much more complex than bacterial cells. In addition, a role of the mycobiota in disease, notably in IBD, is indicated by both descriptive data in humans and mechanistic data in mice. Interactions between bacteria and fungi within the gut, their functional roles and their interplay with the host and its immune system are fascinating areas that researchers are just beginning to investigate. In this Review, we discuss the newest data on the gut mycobiota and explore both the technical aspects of its study and its role in health and gastrointestinal diseases. The authors review the newest data on the gut fungal microbiota. They explore technical aspects of its analysis, how the mycobiome is influenced by immune and environmental factors, including fungi–bacteria interactions, and links between the mycobiota and gut diseases. Key points Interest in the study of the fungal microbiota has been rising over the past decade, resulting in the accumulation of various data sets that describe the mycobiota in health and disease. This young research area requires standardization of techniques and bioinformatic analysis, as well as complete, curated databases, to reach a level of insight similar to that of the bacterial microbiota. Similar to the bacterial microbiota, environmental conditions, in particular diet, considerably influence the fungal microbiota. Deciphering the multitude of interactions between bacteria and fungi in the gut and in other niches is one of the most promising areas of investigation for gut microbiota manipulation. Many findings now demonstrate that the gut mycobiota can strongly influence the host immune system, but considerable research is still needed to better characterize these interactions. Current observations of the direct or indirect effects of the fungal microbiota on gastrointestinal diseases advocate further invest