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Thinking of the diversity of the microbial world most readers will focus their attention to the bacteria and archea. However, among most of the ecosystems present on Earth, such as soil or intestine of animals, another microbial group has established: the yeasts. Their biodiversity has been hardly investigated although they possess probably as much adaptation potential as bacteria, considering the enormous differences between the habitats and the challenges the different ecosystems must face. In the chapter the authors would like to provide to the reader the state of the art in the field of intestinal yeast research, with focus on the diversity of the yeasts in the gastrointestinal tract of animals – insects and mammals. Up to date there are about 1,500 yeast species known, belonging to two phyla Ascomycota (Suh et al., 2006a) and Basidiomycota (Fell et al., 2000; Scorzetti et al., 2002) of the Dikarya subkingdom (Kurtzman & Fell, 2006). These unicellular fungi are considered as ubiquitous microorganisms, which can be found in a vast variety of different ecological systems associated with terrestrial and underwater flora and fauna (Rosa & Peter, 2006). Nevertheless, based on the currently researches it could be suggested that only 1% of the diversity of yeast species has been described yet (Kurtzman & Fell, 2006). The gastrointestinal tract (GIT) of animals remains a largely unexplored habitat. Most of the yeasts were isolated from the GIT of beetles and other insects. The current knowledge about yeasts’ diversity in the digestive tract of vertebrates, especially of farm animals, is still based generally on the findings from 50’s and 70’s of the XXth Century. Furthermore, the taxonomy of yeasts undergoes continuous revision, e.g., variety of yeasts has double names or even many synonyms. This came off due to the fact that sometimes the same yeasts have been described by different scientists (Kurtzman & Fell, 1998) or several yeasts were invalidly classified, e.g., species assigned to genus Torulopsis were reclassified to the genus Candida (Yarrow & Meyer, 1978). Moreover, it transpires frequently when yeast species previously described based on its phenotypic characteristics has been later phylogenetically analysed and on that basis reclassified into another genus, consequently obtained a new name (Kurtzman & Fell, 2006). Therefore, few yeast species will be mentioned in the further sections with a double name. Furthermore, in this review we will provide some consideration to the importance of the yeasts for the host. Advantages and disadvantages of the contemporary methods used for diversity studies will also be pointed.

Biodiversity of Yeasts in the Gastrointestinal Ecosystem with Emphasis on Its Importance for the Host