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Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut
Author(s) -
Ramazzotti Matteo,
Stefanini Irene,
Di Paola Monica,
De Filippo Carlotta,
Rizzetto Lisa,
Berná Luisa,
Dapporto Leonardo,
Rivero Damariz,
Tocci Noemi,
Weil Tobias,
Lenucci Marcello S.,
Lionetti Paolo,
Cavalieri Duccio
Publication year - 2019
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.14422
Subject(s) - biology , population genomics , genome , saccharomyces cerevisiae , genetics , population , phylogenetic tree , genomics , adaptation (eye) , evolutionary biology , yeast , human gastrointestinal tract , gene , bacteria , demography , neuroscience , sociology
Summary The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole‐genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain‐specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.