Biology subjects

Vulin, C.

Publications and source records attributed to Vulin, C..

12 recordsLinked to original sources

bioRxiv2026

A reproductive hierarchy controls mating fates among sibling yeast gametes

Mating strategies shape inbreeding, gene flow and genetic diversity, yet their outcomes remain challenging to quantify. In Saccharomyces, population-genomic models predict mating predominantly between sibling meiotic products, with rare selfing and outcrossing. Here we developed an integrated framework combining multicolor flow cytometry, time-resolved imaging and mathematical modelling to directly quantify mating across scales. Bulk measurements revealed coexisting strategies whose frequencies vary with density, genotype and environment. A minimal stochastic model uses these population-level patterns to infer probabilistic hierarchies among mating modes, which single-tetrad analyses independently support. These reveal divergent and interdependent reproductive trajectories among sibling gametes, with one pair typically mating first and reshaping opportunities for the others. Temporal heterogeneity in germination and mating further diversifies reproductive outcomes and shapes compatibility, as experimental synchronization overcomes temporal reproductive barriers, enabling hybridization. Together, reproductive strategy emerges from heterogeneous gamete fates, raising the possibility that sibling diversification constitutes reproductive bet-hedging.

genetics↗

bioRxiv2025

Feeding your enemy's enemy: Acidifying bacteria inhibit pathogenic bacteria more strongly with increasing glucose

Classical microbiology has focused on directly suppressing pathogens using drugs, ignoring other harmless microbial species living alongside the pathogens. We now have a much better understanding of how species interact and affect one anothers growth within microbial communities, for example through chemical production. Here we capitalize on this understanding to demonstrate how one can manipulate and control the strength of interactions between bacterial species, and combine this with antibiotics to fully suppress and eliminate pathogens. Using experiments and a mathematical model, we first show how Citrobacter freundii can reduce the environmental pH to enhance the effect of ampicillin on the pathogen Pseudomonas aeruginosa. This negative interaction from C. freundii to P. aeruginosa can be strengthened by increasing glucose concentrations. Our proof-of-concept approach also worked against other pathogens: Klebsiella pneumoniae and Agrobacterium tumefaciens, and a different commensal: Lactobacillus plantarum, a common probiotic species. Overall, we show that taking advantage of the community and chemical context in which microbes live can help to develop efficient strategies to control them. In the medical context, this approach can help to eliminate pathogens thereby reducing our reliance on antibiotics.

microbiology↗

bioRxiv2024

Screening clinical Candida albicans isolates for invasiveness by mimicking the human environment

ObjectivesCandida albicans colonizes a wide range of human body niches, but also causes severe invasive infections, such as candidemia. No screening method exists to predict which colonizer may lead to invasive infections. Invasiveness and virulence are associated with yeast filamentation, triggered by environmental factors encountered in the host. Here, we monitored the filamentation profile and colony appearance time of a C.albicans strain isolated from a patients abscess. Using eight additional C.albicans clinical isolates, we established an in vitro screening-framework of filamentation to assess the invasiveness potential of individual isolates. MethodsWe monitored the filamentation pattern of nine C.albicans clinical isolates over 14 days in 48 environmental conditions, including combinations of glucose/nitrogen concentrations, pH and temperature, to mimic host environment variations. Additionally, we tested invasiveness by growing isolates on modified filtration membranes, mimicking physical human body barriers usually colonized by Candida. An automated image analysis pipeline was developed to quantify filamentation. ResultsTwo types of colony filamentation morphology were differentiated, star and hazy. The total filamentation area depended on environmental factors. Based on their filamentation response to environmental changes, the isolates clustered in three distinct groups reflecting their site of isolation in the host. We moreover found that filamentation morphologies on modified filtration membranes could be predictors of invasiveness. ConclusionThis work lays the ground for screening assays, which could help assessing the potential of a colonizing Candida isolate to cause invasive disease, paving the way for tailored preventive therapy regimens in the future.

microbiology↗

bioRxiv2023

Substrate complexity buffers negative interactions in a synthetic microbial community of leaf litter degraders.

Microbes associated with leaf litter, the top layer of soil, collectively decompose organic matter such as plant polysaccharides, and respire carbon dioxide, regulating the land-atmosphere fluxes of carbon. Therefore, it is crucial to understand the processes limiting biopolymer degradation and their influences on soil community properties. For example, it is still unclear how substrate complexity - defined as the structure of the saccharide and the amount of external processing by extracellular enzymes - influences species interactions and species coexistence. Here, we tested the hypothesis that growth on monosaccharides (i.e., xylose) promotes negative interactions through resource competition, and growth on polysaccharides (i.e., xylan) promotes neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in co-culture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose. A mathematical model parameterized from single-species growth behaviors showed that in xylose these dynamics could be explained by resource competition. Instead, the resource competition model could not predict the coexistence patterns in xylan. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders that can serve as a model for studying carbon cycling and climate change. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/573222v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@abf5aeorg.highwire.dtl.DTLVardef@18e99d5org.highwire.dtl.DTLVardef@1158650org.highwire.dtl.DTLVardef@252623_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

C-di-AMP levels modulate Staphylococcus aureus cell wall thickness as well as virulence and contribute to antibiotic resistance and tolerance

Beta-lactam antibiotics are widely used to treat infections caused by the important human pathogen Staphylococcus aureus. Resistance to beta-lactams, as found in methicillin-resistant S. aureus (MRSA), renders effective treatment difficult. The second messenger cyclic di-3',5'- adenosine monophosphate (c-di-AMP) promotes beta-lactam resistance in clinical S. aureus isolates. C-di-AMP plays a crucial role in the regulation of cellular processes such as virulence, cell wall homeostasis and resistance to beta-lactams in many bacterial species. In S. aureus, c-di-AMP synthesis is mediated by the diadenylate cyclase DacA, while its degradation is carried out by the phosphodiesterases GdpP and Pde2. In this work, we assessed the effect of altered c-di-AMP levels due to mutations in cacA, gdpP or gdpP/pde2 on virulence determinants. We report that a previously described growth defect in bacteria producing high c-di-AMP levels is mainly attributable to smaller cell size. High c-di-AMP levels also led to decreased survival upon oxidative stress, reduced production of the antioxidant staphyloxanthin, increased oxacillin and fosfomycin resistance and increased cell wall thickness. While resistance to ceftaroline was not affected, high c-di-AMP levels promoted tolerance to this antibiotic. In response to cell wall stress induced by antibiotics, the three-component regulatory system VraTSR mediates an increase in cell wall synthesis via the cell wall stress stimulon (CWSS). Increased c-di-AMP levels led to an activation of the CWSS. Upon deletion of vraR, resistance to oxacillin and fosfomycin as well as cell wall thickness diminished in the {Delta}gdpP mutant, indicating a contribution of the VraTSR system to the cell wall related phenotypes. ImportanceAntibiotic resistance and tolerance are substantial health-care related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat MRSA infections, were observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.

microbiology↗

bioRxiv2021

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

BackgroundDifficult-to-treat infections caused by antibiotic susceptible strains have been linked with the occurrence of persisters. Persisters are a subpopulation of dormant bacteria that tolerate antibiotic exposure despite lacking genetic resistance. They can be identified phenotypically upon plating on nutrient agar because of their altered growth dynamics, resulting in colony size heterogeneity. The occurrence of within-patient bacterial phenotypic heterogeneity in various infections and clinical determinants of persister formation remain unknown. MethodsWe plated bacteria derived from 132 patient-samples of difficult-to-treat infections directly on nutrient-rich agar and monitored colony growth by time-lapse imaging. Of these, we retained 36 Staphylococcus aureus mono-cultures for further analysis. We investigated clinical factors potentially associated with increased colony growth-delay with regression analyses. Additionally, we corroborated the clinical findings using in vitro grown static biofilms, exposed to distinct antibiotics. ResultsThe extent of phenotypic heterogeneity of patient-derived S. aureus varied substantially between patients. Increased heterogeneity coincided with increased median growth-delay. Multivariable regression showed that rifampicin treatment was significantly associated with increased median growth-delay. S. aureus grown in biofilms and exposed to high concentrations of rifampicin or a combination of rifampicin with either clindamycin or levofloxacin exhibited prolonged growth-delay, correlating with a strain-dependent increase in antibiotic tolerance. ConclusionsUpon direct cultivation on nutrient-rich agar, S. aureus from difficult-to-treat infections commonly exhibited colony size heterogeneity. This was due to heterogeneous delays in growth resumption, with delays larger than two days in the most extreme cases. Since bacteria in a dormant state are tolerant to antibiotics, the observation of large growth-delays might have direct clinical implications. Future studies are needed to assess the potential of bacterial phenotypic heterogeneity quantification for staphylococcal infections prognosis.

microbiology↗

bioRxiv2021

Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence in Staphylococcus aureus

Staphylococcus aureus colonizes 30 to 50% of healthy adults and can cause a variety of diseases, ranging from superficial to life-threatening invasive infections such as bacteraemia and endocarditis. Often, these infections are chronic and difficult-to-treat despite adequate antibiotic therapy. Most antibiotics act on metabolically active bacteria in order to eradicate them. Thus, bacteria with minimized energy consumption resulting in metabolic quiescence, have increased tolerance to antibiotics. The most energy intensive process in cells - protein synthesis - is attenuated in bacteria entering into quiescence. Eukaryote-like serine/threonine kinases (STKs) and phosphatases (STPs) can fine-tune essential cellular processes, thereby enabling bacteria to quickly respond to environmental changes and to modulate quiescence. Here, we show that deletion of the only annotated functional STP, named Stp, in S. aureus leads to increased bacterial lag-phase and phenotypic heterogeneity under different stress challenges, including acidic pH, intracellular milieu and in vivo abscess environment. This growth delay was associated with reduced intracellular ATP levels and increased antibiotic persistence. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified possible targets of Ser/Thr phosphorylation that regulate cellular processes and bacterial growth, such as ribosomal proteins including the essential translation elongation factor EF-G. Finally, we show that acid stress leads to a reduced translational activity in the stp deletion mutant indicating metabolic quiescence correlating with increased antibiotic persistence. One-sentence summaryPhospho-regulation mediates quiescence and antibiotic persistence in Staphylococcus aureus.

microbiology↗

bioRxiv2021

Blunted Fas signaling favors RIPK1-driven neutrophil necroptosis in critically ill COVID-19 patients

Critically ill COVID-19 patients are characterized by a severely dysregulated cytokine profile and elevated neutrophil counts, which are thought to contribute to disease severity. However, to date it remains unclear how neutrophils contribute to pathophysiology during COVID-19. Here, we assessed the impact of the dysregulated cytokine profile on the tightly regulated cell death program of neutrophils. We show that in a subpopulation of neutrophils, canonical apoptosis was skewed towards rapidly occurring necroptosis. This phenotype was characterized by abrogated caspase-8 activity and increased RIPK1 levels, favoring execution of necroptosis via the RIPK1-RIPK3-MLKL axis, as further confirmed in COVID-19 biopsies. Moreover, reduction of sFas-L levels in COVID-19 patients and hence decreased signaling to Fas directly increased RIPK1 levels and correlated with disease severity. Our results suggest an important role for Fas signaling in the regulation of cell death program ambiguity via the ripoptosome in neutrophils during COVID-19 and a potential therapeutic target to curb inflammation and thus influence disease severity and outcome.

immunology↗

bioRxiv2020

Neutrophil and monocyte dysfunctional effector response towards bacterial challenge in critically-ill COVID-19 patients

COVID-19 displays diverse disease severities and symptoms. Elevated inflammation mediated by hypercytokinemia induces a detrimental dysregulation of immune cells. However, there is limited understanding of how SARS-CoV-2 pathogenesis impedes innate immune signaling and function against secondary bacterial infections. We assessed the influence of COVID-19 hypercytokinemia on the functional responses of neutrophils and monocytes upon bacterial challenges from acute and corresponding recovery COVID-19 ICU patients. We show that severe hypercytokinemia in COVID-19 patients correlated with bacterial superinfections. Neutrophils and monocytes from acute COVID-19 patients showed severely impaired microbicidal capacity, reflected by abrogated ROS and MPO production as well as reduced NETs upon bacterial challenges. We observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes leading to a suppressive autocrine and paracrine signaling during bacterial challenges. Our data provide insights into the innate immune status of COVID-19 patients mediated by their hypercytokinemia and its transient effect on immune dysregulation upon subsequent bacterial infections

immunology↗

bioRxiv2020

ColTapp, an automated image analysis application for efficient microbial colony growth dynamics quantification

Phenotypic heterogeneity occurs in a population of genetically identical bacteria due to stochastic molecular fluctuations and environmental variations. In extreme cases of phenotypic heterogeneity, a fraction of the bacterial population enters dormancy, and these metabolically inactive or non-dividing bacteria persist through most antibiotic challenges. These subpopulations of persister cells are difficult to study in patient samples. However, the proportion of persisters in a sample can be accessed by physically separating bacteria on a plate measuring the time until colonies become visible as dormant bacteria resume growth later than their active counterparts and form smaller colonies. Here, we present ColTapp (Colony Time-lapse app), an application dedicated to bacterial colony growth quantification, freely available for download together with its MATLAB source code or as a MacOS/Windows executable. ColTapps intuitive graphical user interface allows users without prior coding knowledge to analyze endpoint or time-lapse images of colonies on agar plates. Colonies are detected automatically, and their radius can be tracked over time. Downstream analyses to derive colony lag time and growth rate are implemented. We demonstrate here the applicability of ColTapp on a dataset of Staphyloccocus aureus colony time-lapse images. Colonies on dense plates reached saturation early, biasing lag time estimation from endpoint images. This bias can be reduced by considering the area available to each colony on a plate. By facilitating the analysis of colony growth dynamics in clinical settings, this application will enable a new type of diagnostics, oriented towards personalized antibiotic therapies.

bioinformatics↗

bioRxiv2019

Emergence of metabolic landscapes in yeast monolayer colonies

Microbial colonies are fascinating structures in which growth and internal organization reflect complex morphogenetic processes. Here, we generated a microfluidics device with arrays of long monolayer yeast colonies to further global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined boundary conditions. We observed the emergence of stable glucose gradients using fluorescently labelled hexose transporters and quantified the spatial correlations with intracolony growth rates and expression of other genes regulated by glucose availability. These landscapes depended on the external glucose concentration as well as secondary gradients, e.g., amino acid availability. This work demonstrates the regulatory genetic networks governing cellular physiological adaptation are the key to internal structuration of cellular assemblies. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development and morphogenesis in more complex systems.

biophysics↗

bioRxiv2018

Prolonged lag time results in small colony variants and reflects a sub-population of persisters in vivo

Treatment failure and recurrent infections can occur even when patients are treated with antibiotics to which bacteria are susceptible. These treatment failures could be due to a sub-population of bacteria persisting through the treatment. In this study, we tested the hypothesis that such bacterial persisters manifest in clinical samples as small colony variants (SCVs). We worked with the bacterial pathogen Staphylococcus aureus, where SCVs are frequently observed in clinics. The small size of SCV-colonies is often considered to be the result of mutations that reduce the bacterial growth rate. Alternatively, it is possible that the small colony size could result from a long lag time of bacteria in plated samples. We used automated plate imaging and single-cell microscopy to precisely quantify growth kinetics of bacteria sampled from patient and mice abscesses, and from low-pH in vitro cultures mimicking the host. Under these conditions, the small colony size was the consequence of a long lag time and was associated with tolerance towards antibiotics. We found that bacteria with a long lag time emerged de novo during the growth phase in the murine abscess as well as in the low-pH in vitro cultures, and that their proportion increased during stationary phase. Antibiotic exposure further increased the proportion of bacteria with a long lag time. Thus, the persisters found in low-pH host compartments could be a cause of treatment failure, and antibiotic treatment potentially aggravates the problem. These insights call for antibiotic treatment strategies that explicitly address the problem of persister formation.\n\nSignificance StatementBacterial pathogens often contain subpopulations that are multidrug tolerant and metabolically inactive. These subpopulations are known as persisters and are hypothesised to be linked to treatment failure and recurrent infections even in bacteria that are not genetically resistant to antibiotics. Identifying persisters in clinical samples remains a challenge due to their metabolicaly active state. Here, we used time-lapse plate imaging and single cell microscopy to link the presence of persisters to the nonstable small colony variant (SCV) phenotype that is observed in some Staphylococcus aureus infections. These findings may help to identify treatment regimens that prevent or address the emergence of persistence and thus to reduce relapses.

microbiology↗