Biology subjects

Jiranek, V.

Publications and source records attributed to Jiranek, V..

11 recordsLinked to original sources

bioRxiv2026

LactoTypeDB: a regenerable, type-anchored 16S rRNA gene reference for species-level identification of the Lactobacillaceae in foods

Amplicon surveys of fermented and spoiled foods routinely resolve Lactobacillaceae, the lactic acid bacteria responsible for many food and beverage fermentations, only to genus, whereas registers such as the Inventory of Microbial Food Cultures require species-level identification. This shortfall arises from the 16S rRNA genes limited, region-dependent resolution and from incomplete, non-type-strain-anchored references that silently reassign missing species to their nearest relative. We built LactoTypeDB, a regenerable, type-anchored reference covering 434 of the familys 441 species and all 37 genera and substituted it into the Living Tree Project release LTP 08_2023 the fields default classifier uses. This eliminated species-level misassignment of type strains in all regions tested and cut misassignment of 10,329 other sequences from the same species from 1,374 errors down to 3 when the full-length 16S rRNA gene was used. Applied unmodified to 11,612 V3-V4 distinct sequences from a published survey of two meat production lines, the workflow returned a species for 213 and a genus for 5,926, and flagged 3,495 as undescribed candidates, more than a third of them nearest to Dellaglioa, a genus that includes a meat-spoilage organism tracked in that survey. The ambiguity that remains is the markers, since V3-V4 collapses 417 of the 434 species into 27 groups it cannot separate. For food microbiology laboratories, the practical change is that a species call from this family can now be trusted where the marker allows it, and a sequence matching nothing becomes a candidate worth isolating rather than a limitation to work around.

bioinformatics↗

bioRxiv2026

Stingless bees, turtle ants and tea plants are rich sources of undescribed Lactobacillaceae

Knowledge of the family Lactobacillaceae rests largely on isolates from foods and a few repeatedly sampled hosts. Reference databases give an unrecognised sequence the name of its nearest relative, so a lineage with no entry of its own is renamed rather than flagged. Here we classify the family across the public plant and invertebrate amplicon record to locate the hosts carrying undescribed lineages. Across 3,344 independent 16S rRNA gene amplicon studies, every sequence cluster was tested against a type-strain reference and placed at the deepest rank it supports. Of 204,813 classified clusters, 20,516 were named to species and 127,906 to genus, while 4,741 matched no described species. Six published datasets whose authors could name their Lactobacillaceae only as Lactobacillus, or not at all, are reclassified here. Genera described from one habitat occur far beyond it, three bee-associated genera occurring on Rosaceae and Brassicaceae at several times their rate on wind-pollinated grasses, and we found no published Bombilactobacillus record from a plant. Undescribed lineages concentrate in the least-cultured hosts, reaching 86.1% and 77.4% of studies in the stingless bees Melipona and Tetragonula, and are most divergent in the turtle ant Cephalotes and, among plants, in tea, Camellia. An independent genome-resolved survey of pot honey converges on the same two genera. The primary descriptions of forty-eight species from these hosts specify a supplemented medium, so the hosts carrying undescribed lineages also indicate how to culture them.

microbiology↗

bioRxiv2026

Understanding the impact of sodium sulfide on the invasive growth of wine yeast

Yeasts ability to invade surfaces has important implications for infections and food contamination. Invasive growth in yeast is influenced by genetic and environmental factors. In this exploratory study, we used a systematic experimental design to identify conditions under which sulfide-induced invasive growth can be reliably observed and quantified and investigated the effects of sulfide, gene deletions, and environmental conditions on the invasive behaviour of the wine yeast strain AWRI 796. Sulfide enhanced invasion in the (parent) AWRI 796 strain under nitrogen-limiting conditions, although its effect was obscured by experimental variability and pre-culture conditions. Genetic factors had a major effect on the overall invasive phenotype, with deletion of key genes suppressing invasion. Most gene-deletion mutants did not significantly affect how the colony responded to sulfide. In addition to sulfide and genotype, environmental conditions also influenced invasive behaviour. The pre-2xSLAD pre-culture condition was best for detecting sulfide-induced growth, and later plate washing time and decreased nutrient levels enhanced invasiveness. Our experimental design and findings provide a framework for understanding the determinants of yeast invasiveness, which may inform future studies on filamentous yeast behaviour.

microbiology↗

bioRxiv2025

Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional flow mathematical model

We use a combination of experiments, mathematical modelling, and parameter estimation to better understand how agar density affects colony biofilm growth of the yeast species Saccharomyces cerevisiae. We obtained 15 total experimental replicates on rectangular plates filled with 0.6%, 0.8%, 1.2%, and 2.0% agar. In the experiments, we measured the horizontal expansion over time, the number of living cells, and the colony-biofilm aspect ratio. These measurements quantify the colony-biofilm size, composition, and shape, respectively. We modelled colony-biofilm expansion using a thin-film extensional-flow mathematical model. By fitting five unknown model parameters to mean experimental data, we show that nutrient uptake decreases and biofilm-substratum adhesion strength increases with an increase in agar density. Sensitivity analysis, fitting to individual replicates, and synthetic-data analysis confirmed that increased biofilm-substratum adhesion is the most consistent effect of increased agar density. This finding aligns with similar results reported for bacteria, and suggests that substratum properties are important for yeast-colony-biofilm growth.

biophysics↗

bioRxiv2025

Agent-based modelling and time series inference of filamentous yeast colonies

The bakers yeast Saccharomyces cerevisiae can form invasive filamentous colonies with non-uniform spatiotemporal patterns. We aimed to better understand how individual cellular actions give rise to colony-scale patterns. We used an off-lattice agent-based model to simulate colony growth, and used a neural likelihood estimator (NLE) to infer parameters for experimental photographs. Li et al. [1] used approximate Bayesian computation (ABC) to infer parameters using coarse summary statistics obtained from a single time point averaged across experimental replicates. The NLE overcomes the computational expense of ABC, allowing us to infer the parameters of individual colonies from a full time series of experimental photographs. To demonstrate the capabilities of our model and inference technique, we tested extensively on synthetic data and then predicted yeast growth under three different experimental conditions. As before, the proportion of total colony growth above which pseudohyphal growth is permitted was a key parameter that contributed to colony morphology. Since our NLE-based approach incorporates time series data, it yielded better parameter estimates and more accurate predictions compared to our ABC-based method. This updated approach improved understanding of how the probability that a stated cell produces a pseudohyphal cell influences colony morphology. In this way, the model also has the potential to generate hypotheses, which can be tested through biological experiments to increase the understanding of the basis for different growth patterns in yeast.

cell biology↗

bioRxiv2025

Modelling the emergence of spiral colony morphology in the yeast Magnusiomyces magnusii

Yeast species have several adaptations that enable them to survive in harsh environments. These adaptations include biofilm formation, where the secretion of extracellular polymeric substances can protect the cells from a hostile environment, or, under nutrient-limited conditions, pseudohyphal or hyphal growth, where the colony can send out long tendrils to explore the environment and seek nutrients. Recently, we observed a spiral colony morphology emerge in an isolate of the hyphae-forming yeast Magnusiomyces magnusii grown under laboratory conditions. We use an off-lattice agent-based model (ABM) that simulates colony development to investigate the hypothesis that bias in the angle between successive hyphal segments causes the spiral morphology. The model involves biologically-motivated rules of hyphal extension, with key model parameters including the colony size at the onset of hyphal filaments, and the angle between the penultimate and the apical segments. Using one example of an experimentally-grown colony, we use a sequential neural likelihood method to perform likelihood-free Bayesian inference to infer the model parameters. Our results indicate a mean angle between hyphal segments of 2.3{whitebullet} [1.1{whitebullet}, 3.6{whitebullet}] (95% credible interval). To confirm the models applicability to colony growth, we use biologically-feasible parameter values to yield morphologies observed in M. magnusii experiments.

microbiology↗

bioRxiv2025

Accidental and Regulated Cell Death in Yeast Colony Biofilms

The yeast species Saccharomyces cerevisiae is one of the most intensively studied organisms on the planet due to being an excellent eukaryotic model organism in molecular and cell biology. In this work, we investigate the growth and morphology of yeast colony biofilms, where proliferating yeast cells reside within a self-produced extracellular matrix. This research area has garnered significant scientific interest due to its applicability in the biological and biomedical sectors. A central feature of yeast colony biofilm expansion is cellular demise, which is onset by one of two independent mechanisms: either accidental cell death (ACD) or regulated cell death (RCD). In this article, we generalise a recently developed continuum model for the nutrient-limited growth of a yeast colony biofilm to include the effects of ACD and RCD. This new model involves a system of four coupled nonlinear reaction-diffusion equations for the yeast-cell density, the nutrient concentration, and two species of dead cells. Numerical solutions of the spatially one and two-dimensional governing equations reveal the impact that ACD and RCD have on expansion speed, morphology and cell distribution within the colony biofilm. Our results show good qualitative agreement with our own experiments.

microbiology↗

bioRxiv2024

An off-lattice discrete model to characterise filamentous yeast colony morphology

We combine an off-lattice agent-based mathematical model and experimentation to explore filamentous growth of a yeast colony. Under environmental stress, Saccharomyces cerevisiae yeast cells can transition from a bipolar (sated) to unipolar (pseudohyphal) budding mechanism, where cells elongate and bud end-to-end. This budding asymmetry yields spatially non-uniform growth, where filaments extend away from the colony centre, foraging for food. We use approximate Bayesian computation to quantify how individual cell budding mechanisms give rise to spatial patterns observed in experiments. We apply this method of parameter inference to experimental images of colonies of two strains of S. cerevisiae, in low and high nutrient environments. The initial nutrient concentration and a forking mechanism for pseudohyphal cell proliferation are the key features driving colony morphology. Simulations run with the most likely inferred parameters produce colony morphologies that closely resemble experimental results.

cell biology↗

bioRxiv2021

QTL mapping: an innovative method for investigating the genetic determinism of yeast-bacteria interactions in wine

The two most commonly used wine microorganisms, Saccharomyces cerevisiae yeast and Oenococcus oeni bacteria, are responsible for completion of alcoholic and malolactic fermentation (MLF), respectively. For successful co-inoculation, S. cerevisiae and O. oeni must be able to complete fermentation, however, this relies on compatibility between yeast and bacterial strains. For the first time, Quantitative Trait Loci (QTL) analysis was used to elucidate whether S. cerevisiae genetic makeup can play a role in the ability of O. oeni to complete MLF. Assessment of 67 progeny of an S. cerevisiae SBxGN cross, co-inoculated with a single O. oeni strain, SB3, revealed a major QTL linked to MLF completion by O. oeni. This QTL encompassed a well-known translocation, XV-t-XVI, that results in increased SSU1 expression and is functionally linked with numerous phenotypes including lag phase duration and sulfite export and production. A reciprocal hemizygosity assay was performed to elucidate the effect of the gene SSU1 in the SBxGN background. Our results instead revealed a strong effect of SSU1 haploinsufficiency on O. oenis ability to complete malolactic fermentation during co-inoculation, and paves the way for the implementation of QTL mapping projects for deciphering the genetic bases of microbial interactions. Key pointsFor the first time QTL analysis has been used to study yeast-bacteria interactions. A QTL encompassing a translocation, XV-t-XVI, was linked to MLF outcomes. S. cerevisiae SSU1 haploinsufficiency positively impacted MLF by O. oeni.

microbiology↗

bioRxiv2020

The effect of grape juice dilution on oenological fermentation

The impact of water addition to grape juice in winemaking, on both alcoholic and malolactic fermentation duration and outcome has been examined using commercial wine yeasts, Lalvin EC1118 and Lalvin R2 and malolactic bacteria Lalvin VP41. As expected, dilution with water did not impede fermentation, instead resulted in shortened duration, or in the case of malolactic fermentation enabled completion in these conditions. Addition of complex organic nutrient further shortened alcoholic fermentation by Lalvin R2 and in some conditions also reduced the duration of malolactic fermentation. In general, volatile compounds and some major yeast metabolites were present at lower concentrations at the end of fermentation where juices were diluted and the addition of organic complex nutrient also influenced the concentration of some compounds in wine. These findings are significant to commercial winemaking, highlighting that winemakers should consider potential impacts of juice dilution on processing efficiencies along with wine flavour and aroma. Highlights: Gardner et al. The effect of grape juice dilution on fermentationO_LIGrape juice dilution shortened both alcoholic and malolactic fermentation C_LIO_LIIn some conditions addition of commercial nutrient decreased fermentation duration C_LIO_LIIn general wine volatiles decrease with grape juice dilution C_LIO_LIIsoamyl acetate can be decreased in wine by grape juice dilution C_LI

microbiology↗

bioRxiv2018

A study of phenotypic plasticity of Saccharomyces cerevisiae in natural grape juices shed light on allelic variation under balanced selection.

The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasted response is due to allelic variations and is caused by gene-by-environment interactions (GxE). Finding the genes and the cellular functions that interact with the environment is a current challenge for better understanding the genetic bases of phenotypic plasticity. In order to study the impact of natural allelic variations having a contrasted but relevant effect in a changing environment, we investigated the phenotypic response of the wine yeast Saccharomyces cerevisiae fermented in various grape juices. In this study we implemented a QTL mapping program using two independent offspring (~100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to high throughput sequencing approaches, both populations were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the nature of the fermented juice or fermentation conditions. Molecular dissection of a major QTL showed that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits. Both alleles have positive effect according to external condition in phenotypes related to yeast fitness suggesting an example of balanced selection. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity.

genetics↗