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Renzi et al. Microbiome Res Rep 2024;3:2 Microbiome Research
DOI: 10.20517/mrr.2023.27
Reports

Review Open Access

Yeast metagenomics: analytical challenges in the
analysis of the eukaryotic microbiome

Sonia Renzi # , Stefano Nenciarini # , Giovanni Bacci , Duccio Cavalieri

Department of Biology, University of Florence, Sesto Fiorentino 50019, Italy.
#
Authors contributed equally.
Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto
Fiorentino 50019, Italy. E-mail: duccio.cavalieri@unifi.it
How to cite this article: Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of
the eukaryotic microbiome. Microbiome Res Rep 2024;3:2. https://dx.doi.org/10.20517/mrr.2023.27

Received: 14 Apr 2023 First Decision: 12 Sep 2023 Revised: 9 Oct 2023 Accepted: 17 Oct 2023 Published: 23 Oct 2023
Academic Editor: Gabriele Andrea Lugli Copy Editor: Pei-Yun Wang Production Editor: Pei-Yun Wang

Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic
members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association
with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause
diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity
due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes
crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To
achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial
communities. To overcome the existing challenges in the study of fungal communities, the first step should be the
establishment of standardized techniques for the correct identification of species, even from complex matrices,
both in wet lab practices and in bioinformatic tools.

Keywords: Yeasts, fungi, microbiome, microbial eukaryotes, eukaryome, ngs, metagenomics, taxonomy

INTRODUCTION
In natural microbial systems, including host-associated microbiomes, microbial eukaryotes coexist with
[1]
bacteria, archaea, and viruses, acting as decomposers, predators, parasites, and producers . Theoretically,

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
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