Biology subjects

Czyz, D. M.

Publications and source records attributed to Czyz, D. M..

7 recordsLinked to original sources

bioRxiv2026

Soil-derived Bacillus pumilus strains demonstrate antagonistic activity against Magnaporthe oryzae and multiple plant growth-promoting traits

Biological control strategies are increasingly being explored as sustainable alternatives for managing rice blast disease caused by Magnaporthe oryzae. In this study, we characterized three Bacillus pumilus isolates (DC01, DC09, and DC13) and evaluated their antifungal and plant-beneficial properties against M. oryzae. Whole genome sequencing revealed multiple biosynthetic gene clusters associated with the production of antimicrobial metabolites. All three isolates inhibited fungal growth in dual-culture assays, whereas heat-stable diffusible antifungal activity was primarily associated with the cell-free supernatants of DC09 and DC13. Exposure to bacterial supernatants disrupted fungal development, inducing abnormal hyphal morphology characterized by bulbous swelling, altered polarity, and increased branching in M. oryzae. Volatile organic compound assays further revealed that the DC isolates suppress fungal growth in the absence of physical contact. The isolates additionally inhibited the growth of other phytopathogenic fungi and selected human bacterial pathogens. All strains exhibited plant growth-promoting traits, including indole-3-acetic acid production and osmotic stress tolerance, whereas DC09 also displayed phosphate-solubilizing activity. Importantly, root inoculation with the DC isolates significantly reduced rice blast disease severity and induced expression of defense-associated genes involved in jasmonic acid/ethylene signaling and immune priming. Collectively, these findings identify the DC isolates, particularly DC09 and DC13, as promising multi-mechanistic biological control agents for sustainable rice blast management.

microbiology↗

bioRxiv2025

High-content assessment of Pseudomonas aeruginosa bacteriophage efficacy reveals host genetic factors involved in phage specificity

Pseudomonas aeruginosa infects immunocompromised and hospitalized individuals, resulting in over 500,000 annual deaths. With emerging multidrug resistance and stagnating antibiotic development, alternative antimicrobials are desperately needed. Bacteriophages (phages) offer a promising, effective, and safe alternative. We developed and optimized a high-content liquid assay screen and a stringent assessment of efficacy to isolate and characterize seven novel P. aeruginosa phages. Phages were screened individually and in cocktail, inhibiting the growth of over 90% (50/55) of multidrug-resistant clinical strains and [~]75% (102/137) of animal, environmental, and human isolates. When tested in a mouse bacteremia model, the phage cocktail successfully eradicated P. aeruginosa. A proteome-wide bi-directional BLAST identified eight proteins that influenced phage infection. The functional analysis of the corresponding genes reveals their putative roles involving genome modification and transcriptional regulation, metabolic processes, and structural components essential for phage docking. Collectively, we have developed a rigorous high-content approach to identify effective phages, which, coupled with functional genomics, revealed genes that affect phage-bacteria interaction. Author SummaryIn this study, we explored the potential of bacteriophages (phages) isolated from municipal and hospital wastewater sources for combating multidrug-resistant Pseudomonas aeruginosa, an opportunistic pathogen known for posing significant clinical challenges. A rigorous stepwise screen aimed at enhancing specificity against a broad set of 55 clinical P. aeruginosa strains allowed us to isolate diverse class phages that can target over 90% of the clinical isolates. Our phage efficacy assessments employed a colorimetric MTT assay to measure the metabolic activity of P. aeruginosa strains in response to phage exposure. Notably, the phages demonstrated broad coverage against the P. aeruginosa library, with individual phages showing varying degrees of efficacy and a cocktail exhibiting superior inhibitory properties. Further validation using a mouse bacteremia model confirmed the exceptional efficacy of the cocktail, supported by a complete attenuation of clinical signs of infection and a significant reduction of bacterial loads across all organs, supporting their utility as potential phage therapy. Finally, a comprehensive comparative genomic analysis of target bacteria combined with phage efficacy revealed novel genes that are potentially involved in phage infection. These findings provide a foundation for understanding phage-host interactions and pave the way for the development of targeted phage therapies against antibiotic-resistant bacterial infections.

microbiology↗

bioRxiv2025

Targeting deubiquitinating enzymes (DUBs) and ubiquitin pathway modulators to enhance host defense against bacterial infections

The rise of antibiotic-resistant bacterial pathogens poses a critical global health challenge, necessitating innovative therapeutic approaches. This study explores host-targeted therapies (HTTs) by focusing on deubiquitinating enzymes (DUBs), essential modulators of the ubiquitin-proteasome system (UPS) that regulate host-pathogen interactions during many bacterial infections. Using Salmonella-infected macrophages as a model, we identified UPS modulators that enhance bacterial clearance and observed significant changes in DUB expression, particularly USP25, USP46, and Otud7b. The small-molecule DUB inhibitor AZ-1 significantly reduced intracellular bacterial loads in vitro and mitigated early disease severity in a murine model by decreasing fecal bacterial loads and preserving host weight. However, AZ-1 alone did not achieve complete clearance of Salmonella and required combination with extracellular-targeting antibiotics for optimal efficacy. Notably, AZ-1 demonstrated broad-spectrum activity against multidrug-resistant pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Transcriptomic analyses revealed infection-induced DUB regulation and highlighted pathways modulating immune responses, including TNF- secretion. These findings highlight the potential of targeting the UPS as a host-directed antimicrobial strategy and provide a foundation for developing innovative therapies to combat antimicrobial resistance.

microbiology↗

bioRxiv2024

SARITA: A Large Language Model for Generating the S1 Subunit of the SARS-CoV-2 Spike Protein

The COVID-19 pandemic has profoundly impacted global health, economics, and daily life, with over 776 million cases and 7 million deaths from December 2019 to November 2024. Since the original SARS-CoV-2 Wuhan strain emerged, the virus has evolved into variants such as Alpha, Beta, Gamma, Delta, and Omicron, all characterized by mutations in the Spike glycoprotein, critical for viral entry into human cells via its S1 and S2 subunits. The S1 subunit, binding to the ACE2 receptor and mutating frequently, affects infectivity and immune evasion; the more conserved S2, on the other hand, facilitates membrane fusion. Predicting future mutations is crucial for developing vaccines and treatments adaptable to emerging strains, enhancing preparedness and intervention design. Generative Large Language Models (LLMs) are becoming increasingly common in the field of genomics, given their ability to generate realistic synthetic biological sequences, including applications in protein design and engineering. Here we present SARITA, an LLM with up to 1.2 billion parameters, based on GPT-3 architecture, designed to generate high-quality synthetic SARS-CoV-2 Spike S1 sequences. SARITA is trained via continuous learning on the pre-existing protein model RITA. When trained on Alpha, Beta, and Gamma variants (data up to February 2021 included), SARITA correctly predicts the evolution of future S1 mutations, including characterized mutations of Delta, Omicron and Iota variants. Furthermore, we show how SARITA outperforms alternative approaches, including other LLMs, in terms of sequence quality, realism, and similarity with real-world S1 sequences. These results indicate the potential of SARITA to predict future SARS-CoV-2 S1 evolution, potentially aiding in the development of adaptable vaccines and treatments.

bioinformatics↗

bioRxiv2024

Sub-therapeutic Concentrations of Antibiotics Induce Prophage-driven Superinfection Exclusion and Fitness Cost in Pseudomonas aeruginosa

Bacteria and other microbes can naturally produce antibiotics within their native soil environment, but often at sub-inhibitory concentrations; consequently, the exact role of antibiotics within bacterial native communities remains unknown. We have shown that subtherapeutic quantities of naturally occurring antibiotics can induce the Pseudomonas prophage Pf4, and superinfection of Pseudomonas aeruginosa cells by this phage leads to their reduced virulence, as demonstrated by impaired twitching motility, compromised macrophage evasion, and increased killing by macrophages in vitro. Thus, the production of subtherapeutic concentrations of antibiotics by environmental microbes may provide the producers an evolutionary advantage associated with reduced fitness induced by prophages in the competing bacteria. Collectively, these results reveal the role of naturally occurring antibiotics in altering fitness by phage-mediated superinfection exclusion and provide potential clinical implications in the application of phage therapy. Significance StatementThis study provides insights into the mechanisms by which sub-inhibitory concentrations of environmentally-produced antibiotics induce Pseudomonas aeruginosa prophages, revealing a potential evolutionary strategy for competitive advantage among bacteria. By activating prophages, antibiotics can induce fitness defects in neighboring bacteria, impacting their motility, phagocytosis, and survival within macrophages. Such previously unrecognized role for environmental antibiotics in bacterial ecosystems may offer insights into enhancing phage therapy by exploiting phage-antibiotic synergies. Understanding phage-host interactions can enhance therapeutic strategies to mitigate bacterial infections and antimicrobial resistance.

microbiology↗

bioRxiv2023

Identification of proteotoxic and proteoprotective bacteria that non-specifically affect proteins associated with neurodegenerative diseases

Neurodegenerative protein conformational diseases (PCDs), such as Alzheimers, Parkinsons, and Huntingtons, are a leading cause of death and disability worldwide and have no known cures or effective treatments. Emerging evidence suggests a role for the gut microbiota in the pathogenesis of neurodegenerative PCDs; however, the influence of specific bacteria on the culprit proteins associated with each of these diseases remains elusive, primarily due to the complexity of the microbiota. In the present study, we employed a single-strain screening approach to identify human bacterial isolates that enhance or suppress the aggregation of culprit proteins and the associated toxicity in Caenorhabditis elegans expressing A{beta}1-42, -synuclein, and polyglutamine tracts. Here, we reveal the first comprehensive analysis of the human microbiome for its effect on proteins associated with neurodegenerative diseases. Our results suggest that bacteria affect the aggregation of metastable proteins by modulating host proteostasis rather than selectively targeting specific disease-associated proteins. These results reveal bacteria that potentially influence the pathogenesis of PCDs and open new promising prevention and treatment opportunities by altering the abundance of beneficial and detrimental microbes.

microbiology↗

bioRxiv2017

Brucella abortus Induces A Warburg Shift In Host Metabolism That Enhances Intracellular Replication Of The Pathogen

Intracellular bacterial pathogens exploit host cell resources to replicate and survive inside the host. Targeting these host systems is one promising approach to developing novel antimicrobials to treat intracellular infections. We show that human macrophage-like cells infected with Brucella abortus undergo a metabolic shift characterized by attenuated tricarboxylic acid cycle metabolism, reduced amino acid consumption, altered mitochondrial localization, and increased lactate production. This shift to an aerobic glycolytic state resembles the Warburg effect, a change in energy production that is well-described in cancer cells, and also occurs in activated inflammatory cells. B. abortus efficiently uses lactic acid as its sole carbon and energy source and requires the ability to metabolize lactate for normal survival in human macrophage-like cells. We demonstrate that chemical inhibitors of host glycolysis and lactate production do not affect in vitro growth of B. abortus in axenic culture, but decrease its survival in the intracellular niche. Our data support a model in which infection shifts host metabolism to a Warburg-like state, and B. abortus uses this change in metabolism to promote intracellular survival. Pharmacological perturbation of these features of host cell metabolism may be a useful strategy to inhibit infection by intracellular pathogens.\n\nIMPORTANCEBrucella spp. are intracellular bacterial pathogens that cause disease in a range of mammals, including livestock. Transmission from livestock to humans is common and can lead to chronic human disease. Human macrophage-like cells infected with Brucella abortus undergo a Warburg-like metabolic shift to an aerobic glycolytic state where the host cells produce lactic acid and have reduced amino acid catabolism. We provide evidence that the pathogen can exploit this change in host metabolism to support growth and survival in the intracellular niche. Drugs that inhibit this shift in host cell metabolism inhibit intracellular replication and decrease the survival of B. abortus in an in vitro infection model; these drugs may be broadly useful therapeutics for intracellular infections.

microbiology↗