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Renzi et al. Microbiome Res Rep 2024;3:2 https://dx.doi.org/10.20517/mrr.2023.27 Page 3 of 16

indicate the fungal component of every microbial ecosystem. Within the fungal kingdom, the term “yeast” is
used to describe any fungus that reproduces asexually by budding or fission, produces single-cell stages, and
[28]
has sexual structures that are not enclosed in a fruiting body . This broad description is frequently used to
encompass dimorphic lineages that produce mycelial growth in their sexual phases, as well as biotrophic
diseases and black yeasts. As a result, they do not constitute a taxonomic unit but rather a lifestyle shared by
multiple distinct lineages, even though there are several exceptions and comments to the labile border
between yeasts and dimorphic filamentous fungi that produce yeast-like stages, along with yeast lineages
[29]
that grow solely as filamentous, are outlined .
Yeasts occur in the division Ascomycota, mainly in the subdivisions Saccharomycotina (so-called budding
yeasts) and Taphrinomycotina (that also includes so-called fission yeasts), as well as in three subdivisions of
[30]
Basidiomycota, namely Ustilaginomycotina, Pucciniomycotina, and Agaricomycotina .
These unicellular organisms have become popular in a various applications, including baking, brewing,
winemaking, distilling, and an assortment of other conventional and non-conventional fermentations. They
also serve as a versatile tool in biotechnology , encompassing some of the most widely used model species
[31]
(e.g., Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans). The rapid expansion of
scientific understanding of yeast diversity is attributed to the uncovering of new species in nature and the
use of specific identification tools like nutritional tests, biochemical and molecular characterizations, and
DNA barcode technology. As a result of this technological advancement, previously identified fungal species
are continuously reevaluated, and the concept of yeast species itself is evolving .
[32]

According to existing estimates, only a small fraction (about 5%-10%, depending on the environment) of the
entire variety of fungi has been identified [33,34] . It is estimated that Earth hosts between 2.2 and 3.8 million
[36]
[35]
fungal species , yet only about 4% of these are cataloged . This situation likely holds true for yeast as well.
Out of the approximately 150,000 fungal species described so far , only around 2,000 are yeasts. The
[37]
mycobiome is often neglected, both due to its lower abundance compared to bacteria and the
methodological challenges associated with its detection .
[38]
The high incidence of cryptic and hybrid species hampers efforts to accurately quantify species diversity.
These issues have long been acknowledged, but the advent of whole-genome sequencing has brought them
[39]
to the forefront . In fact, when speaking about genomes, fungi exhibit more complex genetic features
compared to bacteria, including multiple chromosomes, expanded repeated regions, and larger genome
sizes, all of which introduce inaccuracies during sequence classification. Therefore, there is a need for
comprehensive benchmarking of both classification algorithms and databases to optimize identification
pipelines for the fungal kingdom.

CHARACTERISING THE MYCOBIOME: IDENTIFICATION AND TECHNOLOGICAL ISSUES
As mentioned above, many questions regarding mycobiota remain to be addressed. Several methodologies
commonly applied for the investigation of the bacteriome are not consistent when used for studying the
fungal community. Consequently, non-standardized techniques, technical challenges, restricted availability
[40]
of reference data, and other issues have emerged . Therefore, it is crucial to enhance our knowledge and
expand the spectrum of available technologies in order to address the challenges posed by the fungal
communities inhabiting the environmental ecosystem and our bodies.