A new, rapid multiplex PCR method identifies frequent probiotic origin among clinical Saccharomyces isolates

Imre, Alexandra; Rácz, Hanna Viktória; Antunovics, Zsuzsa; Rádai, Zoltán; Kovács, Renátó; Lopandić, Ksenija; Pócsi, István; Pfliegler, Walter P.

doi:10.1016/j.micres.2019.126298

Cited by 14 publications

(20 citation statements)

References 30 publications

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“…The species is not merely utilized for industrial ermentations but may be part of the human microbiome or be used as a probiotic (under the taxonomically obsolete name Saccharomyces boulardii ), whereas in some cases, it also has been reported as an opportunistic human pathogen (Pérez‐Torrado & Querol, 2015; Peter et al, 2018; Zhu et al, 2016). Importantly, colonizing and infectious isolates are often derived from commercial probiotic or baking strains or are known to be members of the wine yeast clade (Imre et al, 2019; Pérez‐Torrado & Querol, 2015; Peter et al, 2018; Pfliegler et al, 2017; Zhu et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Rácz

Mukhtar

Imre

et al. 2021

Yeast

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Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single‐cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single‐cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single‐cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single‐cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.

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Section: Introductionmentioning

confidence: 99%

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Rácz

Mukhtar

Imre

et al. 2021

Yeast

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“…Franzot et al 1998;Abbey et al 2014) or in the context of heteroresistance to antimycotics (Stone et al 2019). As clinical Saccharomyces isolates are regularly derived from commercial (baking and probiotic) yeasts (Pfliegler et al 2017;Imre et al 2019), the clonal heterogeneity inside yeast products should be taken more often into account, when the goal is to understand how stress resistance of industrial yeasts translates into colonizing and pathogenic potential. For example, in a recent study, we compared commercial and clinical yeasts, but did not test multiple subclone lineages of a given strain (Pfliegler et al 2017), a fact that may have influenced our observations due to founder effects.…”

Section: Discussionmentioning

confidence: 99%

“…We performed our recently developed interdelta and microsatellite fingeprinting multiplex PCR method to rule out that the subclones obtained from products are contaminations that do not correspond to the actual strain. Briefly, we combined interdelta, microsatellite (YLR177w, YOR267c), and as a control, ITS 1-4 primer pairs in a single PCR reaction (Imre et al 2019).…”

Section: Methodsmentioning

confidence: 99%

“…The species is not merely utilized for industrial fermentations, but may be part of the human microbiome or be used as a probiotic (under the taxonomically obsolete name S. boulardii), while in some cases, it also has been reported as an opportunistic human pathogen (Peter et al 2018). Importantly, colonizing and infectious isolates are often derived from commercial probiotic or baking strains, or are known to be members of the wine yeast clade (Zhu, Sherlock and Petrov 2016;Pfliegler et al 2017;Peter et al 2018;Imre et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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How to characterize a strain? The neglected influence of clonal heterogeneity on the phenotypes of industrialSaccharomyces

Rácz

Mukhtar

Imre

et al. 2020

Preprint

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Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is non-trivial to assess methodologically. The practice of isolating single cell colonies for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain. We used six industrial yeasts to assess the level of heterogeneity in clonal populations, especially in terms of stress tolerance. First, we uncovered the existence of genome structure variants in available sequenced genomes of clonal lineages of thes strains. Subsequent phenotyping of strains and their newly isolated subclones showed that single-cell bottlenecks during isolation can considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single cell colonies. We used the obtained data on colony area for statistical modeling of the heterogeneity in phenotypes. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype, but also in the level of heterogeneity. Thereby we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on geno- and phenotype, and also on heterogeneity.

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“…W 2019 roku zaproponowano nową metodę typowania, łączącą zalety typowania metodami MLST (multilocus sequence typing, analiza porównawcza sekwencji genów metabolizmu podstawowego), MSP (methylation-specific PCR) oraz analizy regionów mikrosatelitarnych i polimorficznych regionów delta w obrębie retrotranspozonów Ty. Bazując na technice multiplex PCR, w której amplifikowane są mikrosatelity genów YLR177w, YOR267c i region ITS, możliwe jest odróżnienie szczepów probiotycznych od pozostałych szczepów S. cerevisiae [65].…”

Section: Izolacja I Taksonomia Probiotycznego Szczepu S Cerevisiae Var Boulardiiunclassified

Saccharomyces Cerevisiae Var. Boulardii Probiotic Yeasts As Etiological Agents Of Oportunistic Infections In Humans

Roeske

Zasuń

Cieślik

et al. 2020

Postępy Mikrobiologii - Advancements of Microbiology

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Streszczenie: Drożdże S. cerevisiae var. boulardii, historycznie stanowiące odrębny gatunek, uznawane są obecnie za podgatunek drożdży S. cerevisiae. Szczepy Saccharomyces cerevisiae var. boulardii są powszechnie wykorzystywane w profilaktyce i leczeniu zaburzeń układu pokarmowego. Stosowanie preparatów na bazie S. cerevisiae var. boulardii wpływa na funkcjonowanie bariery jelitowej, co prowadzi do zmiany składu mikrobioty przewodu pokarmowego i łagodzi nieprawidłowości warstwy nabłonkowej jelita. Mimo klinicznie potwierdzonych, probiotycznych właściwości tych jednokomórkowych drobnoustrojów, wzrasta liczba doniesień na temat wywoływanych przez nie zakażeń u ludzi. Badania populacyjne sugerują, że drożdże S. cerevisiae są odpowiedzialne za 0,1-3,6% wszystkich przypadków grzybic, stwierdzanych u pacjentów stosujących terapię środkami probiotycznymi zawierającymi S. cerevisiae var. boulardii. Za czynniki predysponujące do rozwoju zakażeń uznaje się obecność centralnego cewnika żylnego, żywienie pozajelitowe, immunosupresję oraz choroby współistniejące. W niniejszej pracy zebrano najważniejsze informacje dotyczące biologii S. cerevisiae var. boulardii, a także przedstawiono najnowsze dane epidemiologiczne dotyczące fungemii wywoływanych przez te grzyby.

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A new, rapid multiplex PCR method identifies frequent probiotic origin among clinical Saccharomyces isolates

Cited by 14 publications

References 30 publications

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

How to characterize a strain? The neglected influence of clonal heterogeneity on the phenotypes of industrialSaccharomyces

Saccharomyces Cerevisiae Var. Boulardii Probiotic Yeasts As Etiological Agents Of Oportunistic Infections In Humans

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