Lisa Rizzetto, Carlotta De Filippo and Duccio Cavalieri
The advent of metagenomics has profoundly revolutionized our way to describe microbial communities and discover sequence based biomarkers of health and disease. Similarly to bacteria commensal fungi are an essential part of human ecosystems being involved in the normal development of the immune system and for the maintenance of healthy tissues and physiological processes. More and more frequently patterns of fungal species are associated to immune disorders and increasing evidences are accumulating of the importance to study the co-occurrence of fungal flora and its microbial counterpart to understand the cross-talk between opportunistic fungi and the mammalian host. Here we critically analyze the studies investigating thefungal communities inhabiting ourbody, addressing at what extent the selection of the approaches and the molecular markers used determine the results obtained.