Publications by authors named "Polonca Stefanic"

Cooperative behaviours in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behaviour remain poorly understood.

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The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification.

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Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination.

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Bacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species.

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Kin discrimination in nature is an effective way for bacteria to stabilize population cooperation and maintain progeny benefits. However, so far, the research on kin discrimination for still has concentrated on "attack and defense" between cells and diffusion-dependent molecular signals of quorum sensing, kin recognition in , however, has not been reported. To determine whether flagellar is involve in the kin recognition of , we constructed Bacillus velezensis SQR9 assembled with flagellin of its kin and non-kin strains, and performed a swarm boundary assay with SQR9, then analyzed sequence variation of flagellin and other flagellar structural proteins in B.

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is the leading cause of bacterial gastroenteritis, or campylobacteriosis, in humans worldwide, and poultry serves as a major source of infection. To reduce the risk associated with transmission via poultry meat, effective interventions during poultry production are needed, and the use of probiotics is a promising approach. In this study, 15 strains were initially screened for their anti- activities.

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In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle.

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sp. strains that are beneficial to plants are widely used in commercial biofertilizers and biocontrol agents for sustainable agriculture. Generally, functional strains are applied as single-strain communities since the principles of synthetic microbial consortia constructed with strains remain largely unclear.

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As the incidence of and campylobacteriosis grows, so does the need for a better understanding and control of this pathogen. We studied the interactions of NCTC 11168 and a potential probiotic, PS-216, in cocultures at different starting ratios and temperatures (20 °C, 37 °C, 42 °C), under different atmospheres (aerobic, microaerobic), and in different growth media (Mueller-Hinton, chicken litter medium, chicken intestinal-content medium). Under microaerobic conditions, effectively inhibited the growth of at 42 °C (log reduction, 4.

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Swarming is the collective movement of bacteria across a surface. It requires the production of surfactants (public goods) to overcome surface tension and provides an excellent model to investigate bacterial cooperation. Previously, we correlated swarm interaction phenotypes with kin discrimination between B.

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Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains.

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Genetic competence for the uptake and integration of extracellular DNA is a key process in horizontal gene transfer (HGT), one of the most powerful forces driving the evolution of bacteria. In several species, development of genetic competence is coupled with cell lysis. Using as a model bacterium, we studied the role of surfactin, a powerful biosurfactant and antimicrobial lipopeptide, in genetic transformation.

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Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells.

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Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region.

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Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism.

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Kin discrimination, broadly defined as differential treatment of conspecifics according to their relatedness, could help biological systems direct cooperative behavior toward their relatives. Here we investigated the ability of the soil bacterium Bacillus subtilis to discriminate kin from nonkin in the context of swarming, a cooperative multicellular behavior. We tested a collection of sympatric conspecifics from soil in pairwise combinations and found that despite their history of coexistence, the vast majority formed distinct boundaries when the swarms met.

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Article Synopsis
  • Members of the Bacillaceae family are highly resilient bacteria largely due to their ability to create resistant endospores, which significantly shapes their ecological roles.
  • They contribute importantly to soil health by cycling organic matter and supporting plant growth through pathogen suppression and nutrient solubilization.
  • The review highlights the diverse functions and behaviors of Bacillaceae, emphasizing the importance of understanding their cell-to-cell interactions for enhancing their application in agriculture and plant health management.
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Rationale: Distinguishing between individual bacterial strains below the species level is a challenge to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial profiling. We propose a quick method for improving strain differentiation of two Staphylococcus and one Bacillus species.

Methods: An alternative procedure to the extraction protocol recommended by Bruker Daltonics was developed.

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Bacteria coordinate their behavior using quorum sensing (QS), whereby cells secrete diffusible signals that generate phenotypic responses associated with group living. The canonical model of QS is one of extracellular signaling, where signal molecules bind to cognate receptors and cause a coordinated response across many cells. Here we study the link between QS input (signaling) and QS output (response) in the ComQXPA QS system of Bacillus subtilis by characterizing the phenotype and fitness of comQ null mutants.

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Article Synopsis
  • Ecological sociobiology connects social evolution to ecological adaptation, particularly in the study of quorum sensing diversity in bacteria.
  • Researchers sampled Bacillus subtilis from soil to identify distinct ecotypes and associated pherotypes, finding that pherotypes typically align with specific ecotypes.
  • The study proposes two models explaining pherotype diversity: one where minority pherotypes cheat social interactions for survival, and another suggesting potential benefits of cross-communication between ecotypes at low population densities.
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Article Synopsis
  • Bacteria called Bacillus subtilis use a communication system called comQXPA for regulating gene expression in stationary phase.
  • There’s a high level of genetic variation in the comQXP' region among closely related strains found in desert soil, creating distinct communication groups or "pherotypes" that can only effectively exchange information within their own group.
  • Microscale analysis of B. subtilis from tiny soil samples showed the same number of pherotypes as larger samples, supporting ongoing evolution of their communication system, potentially leading to new communication "languages" among these bacteria.
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Article Synopsis
  • EMA (ethidium monoazide) is used in real-time PCR to reduce signals from free DNA and dead bacterial cells by entering damaged cells and blocking DNA amplification.
  • The study focused on its effects on the foodborne pathogens Campylobacter jejuni and Listeria monocytogenes, using various methods to evaluate cell viability.
  • Results showed that EMA underestimated viable cells and affected both viable and dead cells, indicating that EMA in real-time PCR is not a reliable measure of cell viability.
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