Biology subjects

Pocsi, I.

Publications and source records attributed to Pocsi, I..

5 recordsLinked to original sources

bioRxiv2026

A comparison of commercially available Saccharomyces mead yeasts.

We present a comparative analysis of 13 yeasts available for mead (honey wine) fermentation, a source of Saccharomyces cerevisiae diversity that has not yet been analyzed in detail. Using genomic, phenotyping, and analytic methods, we show that currently available mead yeasts belong to various clades of the species, most commonly to the Commercial Wine clade (5 of 13 samples). Mead yeasts in this group displayed genome structure variations and occasional loss of killer activity, despite being closely related. Historic European and traditional African mead isolates with sequenced genomes were found not to be closely related to any contemporary mead yeast product. The 13 yeasts tested here displayed high variability in oenological characteristics and in aroma production. Maximum ethanol tolerance ranged from 15 to 22% v/v, however, the most tolerant strain produced lower ethanol levels and retained high fructose content in experimental meads. The most abundant aroma components produced in meads were ethyl acetate, ethyl caprylate, isoamyl alcohol, and ethyl caprate, with similar aroma profiles in members of the Commercial Wine clade, and pronounced differences among other yeasts. Our results contribute to the knowledge of Saccharomyces yeasts in various fermentation environments, adding mead to the list of alcoholic beverages with a known diversity of starter cultures. Our results may aid strain selection for honey wine fermentations and inspire strain improvement.

microbiology↗

bioRxiv2025

Commercial Saccharomyces cerevisiae baker's yeasts: strain redundancy, genome plasticity, and colonization of the sourdough environment and the human body

Leavening dough is one of the most widespread applications of fermentative yeast and the most common practice for the general public to come into contact with microbial cultures. Saccharomyces cerevisiae is the typical species used for dough making, but the evolutionary origin of strains isolated from dough is mixed. Here, using 49 newly sequenced and 183 previously described isolates from the bakery environment, we show that the traditional strains used in Europe for sourdough making are more closely related to Chinese Mantou sourdough lineages than to commercially used baker yeast strains. Surprisingly, the expansion of these traditional European strains into other human-associated niches, including the human body, has been very limited. This is in stark contrast to the Mixed-origin clade commercial baking yeasts, which consists of only a few globally distributed clonal lineages that dominate the yeast market and recurrently colonize sourdoughs and human hosts. These clonal lineages consistently maintain their ploidy, unique heterozygous chromosomal rearrangements, and stable aneuploidies in addition to several diverse structural variants. In addition to the previously known diploid and tetraploid groups of commercial isolates, we describe a widely distributed stable triploid aneuploid clonal lineage. We show that company practices and global trade help the distribution of these clonal clusters and that these yeasts are characterized by their exclusively mitotic reproduction.

microbiology↗

bioRxiv2022

Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans

Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production enhanced following 2 hours of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, fermentation, fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy. ImportanceAlthough gut colonization by Candida albicans can be considered normal, it may be associated with intestinal diseases. Furthermore, Candida dominance in the gut may pose a potent risk for systemic candidiasis, especially for immunocompromised individuals. In recent years, interest has been growing for the use of Bacillus subtilis as a safe and effective probiotic for human healthcare. Surfactin is a B. subtilis-derived lipopeptide with potential antifungal activity; however, the mechanism underlying this remains unknown. In this study, surfactin negatively affected the adherence, morphogenesis and metabolism of C. albicans and increased ethanol production. These were associated with a reduction in intracellular iron, manganese and zinc while the copper content was not affected. Alongside these physiological modulations, surfactin also had a potent synergistic effect on fluconazole. Our results provide a definitive explanation for the surfactin-related antifungal effect of B. subtilis; furthermore, these data provide a good basis for future probiotic development.

microbiology↗

bioRxiv2021

Transcriptional profiling of the Candida auris response to exogenous farnesol exposure

The antifungal resistance threat posed by Candida auris necessitates bold and innovative therapeutic options. Farnesol, a quorum-sensing molecule with a potential antifungal and/or adjuvant effect; it may be a promising candidate in alternative treatment regimens. To gain further insights into the farnesol-related effect on C. auris, genome-wide gene expression analysis was performed using RNA-Seq. Farnesol exposure resulted in 1,766 differentially expressed genes. Of these, 447 and 304 genes with at least 1.5-fold increase or decrease in expression, respectively, were selected for further investigation. Genes involved in morphogenesis, biofilm events (maturation and dispersion), gluconeogenesis, iron metabolism, and regulation of RNA biosynthesis showed down-regulation, whereas those related to antioxidative defense, transmembrane transport, glyoxylate cycle, fatty acid {beta}-oxidation, and peroxisome processes were up-regulated. In addition, farnesol treatment increased the expression of certain efflux pump genes, including MDR1, CDR1, and CDR2. Growth, measured by change in CFU number, was significantly inhibited within 2 hours of the addition of farnesol (5.8x107{+/-}1.1x107 and 1.1x107{+/-}0.3x107 CFU/ml for untreated control and farnesol-exposed cells, respectively) (p<0.001). In addition, farnesol treatment caused a significant reduction in intracellular iron (152.2{+/-}21.1 vs. 116.0{+/-}10.0 mg/kg), manganese (67.9{+/-}5.1 vs. 18.6{+/-}1.8 mg/kg), and zinc (787.8{+/-}22.2 vs. 245.8{+/-}34.4 mg/kg) (p<0.05-0.001) compared to untreated control cells, whereas the level of cooper was significantly increased (274.6{+/-}15.7 vs. 828.8{+/-}106.4 mg/kg) (p<0.001). Our data demonstrate that farnesol significantly influences the growth, intracellular metal ion contents, and gene expression related to fatty acid metabolism, which could open new directions in developing alternative therapies against C. auris. ImportanceCandida auris is a dangerous fungal pathogen that causes outbreaks in health care facilities, with infections associated with high mortality rate. As conventional antifungal drugs have limited effects against the majority of clinical isolates, new and innovative therapies are urgently needed. Farnesol is a key regulator molecule of fungal morphogenesis, inducing phenotypic adaptations and influencing biofilm formation as well as virulence. Alongside these physiological modulations, it has a potent antifungal effect alone or in combination with traditional antifungals, especially at supraphysiological concentrations. However, our knowledge about the mechanisms underlying this antifungal effect against C. auris is limited. This study has demonstrated that farnesol enhances the oxidative stress and reduces the fungal survival strategies. Furthermore, it inhibits manganese, zinc transport, and iron metabolism as well as increases fungal intracellular copper content. In addition, metabolism was modulated towards {beta}-oxidation. These results provide definitive explanations for the observed antifungal effects.

microbiology↗

bioRxiv2020

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

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.

microbiology↗