Search Results (249)

CRISPR-Cas systems are best known as adaptive immune defenses in prokaryotes, but they also function as versatile regulators bridging bacterial immunity with host-related processes. Beyond neutralizing invasive phages and plasmids, these systems influence core aspects of bacterial physiology, such as modulating gene expression, stress responses, biofilm formation, quorum sensing, and virulence. Notably, CRISPR-mediated regulation can facilitate immune evasion at the host-pathogen interface, underscoring these systems as central orchestrators of microbial survival and host interactions. In addition, CRISPR-Cas has rapidly become a cornerstone of synthetic biology and microbiome engineering. Recent strategies repurpose native and engineered CRISPR systems to precisely modulate microbiome composition or deliver sequence-specific antimicrobials, underscoring the expanding translational potential of this system. Collectively, emerging insights highlight both the canonical immune function and non-canonical regulatory roles of CRISPR-Cas, as well as their broad biological and biotechnological relevance. This review provides a critical synthesis of these developments, illustrating how CRISPR-Cas bridges adaptive immunity and microbial physiology, and outlines future directions for harnessing this duality to deepen understanding of microbial physiology and inform new translational applications. Full article

Objectives: To explore the genetic basis of phage resistance in sequentially generated capsular mutants of phage-resistant Klebsiella pneumoniae using an established phage library. Methods: Sequential induction strategies were employed to obtain phage-resistant K. pneumoniae capsular mutants by exposing ST11-K64 K. pneumoniae Kp2325 to different single phages. Whole genome sequencing and bioinformatic analysis were used to elucidate the capsular-related genetic changes in phage-resistant mutants. Phenotypic changes were assessed through gene complementation, growth assays, phage cleavage spectrum analysis, TEM for phage morphology, CPS analysis, biofilm formation, and virulence assays. Results: Three sequentially generated phage-resistant K. pneumoniae capsular mutants were obtained, designated R1, R2 and R3. The narrowing of the phage cleavage spectrum and the evolutionary trade-offs of biological phenotypes were observed. Key genetic changes included: (1) ISKpn26 insertion disrupting wcaJ in R1; (2) combined wcaJ insertion and 9-bp deletion in waaH in R2; and (3) CPS gene cluster deletion in R3 were identified as key mechanisms of phage resistance in K. pneumoniae mutants R1, R2 and R3, respectively. Conclusions: Sequential exposure to different single phages led to rapid evolution of phage resistance in K. pneumoniae via genetic mutations that disrupt capsular synthesis. These findings highlight the critical role of bacterial capsule in phage–host interactions and emphasize the need to use phage cocktails targeting different types of receptors to counteract the evolution of bacterial defense mechanisms in phage therapy. Full article

Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we report the characterization of the lytic bacteriophage vB_EfaS_LOK1, isolated from urban sewage using E. faecalis strain IIH-74.4 as the host. Transmission electron microscopy revealed morphological features consistent with the phages formerly classified within the Siphoviridae family. The phage exhibited high thermal and pH stability, remaining viable up to 70 °C and within a pH range of 4–11. It displayed a latent period of 20 min and a burst size of 72 PFU/cell. Notably, vB_EfaS_LOK1 exhibited a narrow host range, lysing only the strain used for their isolation. Genomic analysis revealed a 41.2 kb double-stranded DNA genome devoid of known virulence or antibiotic resistance genes. Phylogenomic analysis classified the phage within the genus Efquatrovirus (Caudoviricetes), suggesting it represents a newly isolated bacteriophage species. Functional annotation identified genes related to DNA replication, host interaction, and bacterial lysis, including endolysins and holins with putative antimicrobial properties. Long-term stability assays demonstrated that tryptic soy broth (TSB) with CaCl₂/MgCl₂ at 4 °C maintained viability for at least 90 days. Collectively, these findings support the potential of vB_EfaS_LOK1 as a potential candidate for the development of phage-based therapies targeting E. faecalis. Full article

Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment. Full article

Bacteriophages, or phages, are sophisticated nanomachines that efficiently infect bacteria. Their infection of lactic acid bacteria (LAB) used in fermentation can lead to significant industrial losses. Among phages that infect monoderm bacteria, those with siphovirion morphology characterized by a long, non-contractile tail are predominant. The initial stage of phage infection involves precise host recognition and binding. To achieve this, phages feature host adhesion devices (HADs) located at the distal end of their tails, which have evolved to recognize specific proteinaceous or saccharidic receptors on the host cell wall. Ceduovirus represents a group of unique lytic siphophages that specifically infect the LAB Lactococcus lactis by targeting proteinaceous receptors. Despite having compact genomes, most of their structural genes are poorly annotated and the architecture and function of their HADs remain unknown. Here we used AlphaFold3 to explore the Ceduovirus HADs and their interaction with the host. We show that Ceduovirus HADs exhibit unprecedented features among bacteriophages infecting Gram⁺, share structural similarities with bacterial secretion system VI, and combine both saccharide and protein-binding modules. Moreover, we could annotate the majority of Ceduovirus genes encoding structural proteins by leveraging their predicted structures, highlighting AlphaFold’s significant contribution to phage genome annotation. Full article

Cyanobacterial blooms are increasingly becoming more intense and frequent, posing a public health threat globally. Drinking water treatment plants that rely on algal bloom-affected waters may create waste (water treatment residuals, WTRs) that concentrates contaminants. Source waters may contain harmful cyanobacteria, cyanophages (bacteriophages that infect cyanobacteria), and bacteria. Cyanophages are known to affect bloom formation and growth dynamics, so there is a need to understand viral-host dynamics between phage and bacteria in these ecosystems for managing cyanobacteria. This study isolated and characterized lytic cyanophages from WTRs of a HAB-affected lake in Ohio that infect toxic bloom-forming filamentous cyanobacteria Planktothrix agardhii. Phage infections in the Lake Erie cyanobacteria culture were examined visually and via microscopy and fluorometry. Whole genome sequencing and metagenomic analyses were also conducted. Observed changes in Planktothrix included sheared and shriveled filaments, reduced clumping, and buoyancy changes. Photosynthetic pigmentation was unexpectedly more apparent during phage infection. Metagenomic analyses identified nineteen phages and seven other co-existing bacterial genera. Annotated bacterial genomes contained metabolic pathways that may influence phage infection efficiency. Viral genomes were successfully tied to microbial hosts, and annotations identified important viral infection proteins. This study examines cyanobacterial-phage interactions that may have potential for bioremedial applications. Full article

Bacteriophages (phages) play a pivotal role in shaping microbial communities and driving bacterial evolution. Among the diverse mechanisms governing phage–host interactions, the Arbitrium (ARM) communication system represents a recently discovered paradigm in phage decision-making between the lytic and lysogenic cycles. Initially identified in Bacillus-infecting phages, the ARM system employs a quorum-sensing-like peptide signaling mechanism to modulate infection dynamics and optimize population-level survival strategies. Recent studies have elucidated the structural and functional basis of ARM regulation, highlighting its potential applications in antimicrobial therapy, microbiome engineering, and synthetic biology. The significance of ARM systems lies in their ability to regulate bacterial population stability and influence the evolutionary trajectories of microbial ecosystems. Despite being a relatively recent discovery, ARM systems have garnered considerable attention due to their role in decoding phage population dynamics at the molecular level and their promising biotechnological applications. This review synthesizes current advancements in understanding ARM systems, including their molecular mechanisms, ecological implications, and translational potential. By integrating recent findings, we provide a comprehensive framework to guide future research on phage–host communication and its potential for innovative therapeutic strategies. Full article

The spread of antibiotic-resistant pathogenic Escherichia coli poses a serious threat to calf health on livestock farms. With the decline in antibiotic therapy effectiveness, alternative approaches such as phage therapy are urgently needed. This study aimed to isolate lytic E. coli bacteriophages, characterize their properties, and evaluate the synergistic effects of their combined use with veterinary antibiotics against colibacillosis pathogens in calves. As a result of the work, 4 bacteriophages were isolated from wastewater from various cities of Kazakhstan: vB_EcoS_ABO/4, vB_EcoM_PL/4, vB_Eco_CWW/26, vB_EcoM_ShWW/46. Morphological, biological, and genomic analyses showed that the phages belong to different genera of the Caudoviricetes class, possess high lytic activity, broad host range, environmental stability, and lack genes associated with lysogeny, antibiotic resistance, or virulence. Interaction studies with antibiotics revealed synergistic or additive effects in over 75% of cases. These findings highlight the strong potential of the isolated bacteriophages for independent or adjunctive use in the treatment and prevention of colibacillosis in calves. However, further in vivo studies are required to definitively confirm their therapeutic efficacy. Full article

Colorectal cancer (CRC), a prevalent malignancy, is a significant global health concern. The intricate interplay of genetic mutations, inflammatory processes, and environmental factors underscores the complexity of CRC’s etiology. The human gut harbors a diverse microbial community that plays a key role in maintaining homeostasis and influencing various aspects of host physiology. Perturbations in the gut microbiome (GM) composition and function have been implicated in CRC carcinogenesis. This bidirectional relationship involves microbial contributions to inflammation, DNA damage, and immune modulation, shaping the tumor microenvironment (TME). Bacteriophages, viruses that infect bacteria, contribute to the microbiome’s diversity and function by influencing bacterial abundance and composition. These phages can impact host–microbiome interactions, potentially influencing CRC risk. Furthermore, they can be manipulated to transport targeted medication, without being metabolized. Antibiotics exert selective pressures on the gut microbiome, leading to shifts in bacterial populations and potential dysbiosis. Probiotics can modulate the composition and activity of the GM and could be considered adjunctive therapy in the treatment of CRC. Understanding the intricate balance between bacteriophages, antibiotics–probiotics, and the GM is essential for comprehending CRC etiology and progression. Full article

Bacteriophages of the order Crassvirales are highly abundant and near-universal members of the human gut microbiome worldwide. Zeta crAss-like phages comprise a separate group in the order Crassvirales, and their genomes exhibit greater variability than genomes of crAss-like phages from other families within the order. Zeta crAss-like phages employ multiple adaptation mechanisms, ensuring their survival despite host defenses and environmental pressure. Some Zeta crAss-like phages use alternative genetic coding and exploit diversity-generating retroelements (DGRs). These features suggest complex evolutionary relationships with their bacterial hosts, sustaining parasitic coexistence. Mutations in tail fiber proteins introduced by DGR can contribute to their adaptation to changes in the host cell surface and even expand the range of their hosts. In addition, the exchange of DNA polymerases via recombination makes it possible to overcome the bacterial anti-phage protection directed at these enzymes. Zeta crAss-like phages continuously adapt due to genetic diversification, host interaction tweaks, and counter-defense innovations, driving an evolutionary arms race with hosts. Based on the genome characteristics of the Zeta crAss-like phages, we propose to separate them into the Echekviridae family (“эчәк”—“intestines” in Tatar) following the tradition of using the word “intestines” in different languages, suggested previously. Full article

This review addresses the urgent need for alternative strategies to combat drug-resistant mycobacterial infections, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, as well as non-tuberculous mycobacterial (NTM) diseases. Traditional antibiotics are increasingly limited by resistance, toxicity, and poor efficacy, particularly in immunocompromised patients. A comprehensive literature search was conducted using PubMed, Scopus, and Google Scholar, covering publications primarily from 2000 to 2025. Only articles published in English were included to ensure consistency in data interpretation. Search terms included “mycobacteriophages,” “phage therapy,” “drug-resistant mycobacteria, “diagnostic phages,” and “phage engineering.” The review examines the therapeutic and diagnostic potential of mycobacteriophages—viruses that specifically infect mycobacteria—focusing on their molecular biology, engineering advances, delivery systems, and clinical applications. Evidence suggests that mycobacteriophages offer high specificity, potent bactericidal activity, and adaptability, positioning them as promising candidates for targeted therapy. Although significant obstacles remain—including immune interactions, limited host range, and regulatory challenges—rapid progress in synthetic biology and delivery platforms continues to expand their clinical potential. As research advances and clinical frameworks evolve, mycobacteriophages are poised to become a valuable asset in the fight against drug-resistant mycobacterial diseases, offering new precision-based solutions where conventional therapies fail. Full article

Background: Heparan sulfate (HS) is widely implicated as a receptor for Chlamydia cell attachment and infectivity. However, the enzymatic modification of HS modified by the 3-O sulfotransferase-3 (3-OST-3) enzyme in chlamydial cell entry remains unknown. Methodology: To rule out the possibility that host cell 3-O sulfated heparan sulfate (3-OS HS) plays a significant role in C. muridarum entry, a Chinese hamster ovary (CHO-K1) cell model lacking endogenous 3-OST-3 was used. In addition, we further tested the efficacy of the phage-display-derived cationic peptides recognizing heparan sulfate (G1 peptide) and the moieties of 3-O sulfated heparan sulfate (G2 peptide) against C. muridarum entry using human cervical adenocarcinoma (HeLa 229) and human vaginal epithelial (VK2/E6E7) cell lines. Furthermore, molecular dynamics simulations were conducted to investigate the interactions of the Chlamydia lipid bilayer membrane with the G1 and G2 peptides, focusing on their binding modes and affinities. Results: The converse effect of 3-OST-3 expression in the CHO-K1 cells had no enhancing effect on C. muridarum entry. The G2 peptide significantly (>80%) affected the cell infectivity of the elementary bodies (EBs) at all the tested concentrations, as evident from the reduced fluorescent staining in the number of inclusion bodies. The observed neutralization effect of G2 peptide on C. muridarum entry suggests the possibility of sulfated-like domains being present on the EBs. In addition, data generated from our in silico computational structural modeling indicated that the G2 peptide ligand had significant affinity towards the C. muridarum lipid bilayer. Conclusions: Taken together, our findings show that the pretreatment of C. muridarum with 3-O sulfated heparan sulfate recognizing G2 peptide significantly prevents the entry of EBs into host cells. Full article

Pseudomonas aeruginosa is a major opportunistic pathogen with high levels of antibiotic resistance. Phage therapy represents a promising alternative for the treatment of difficult infections both alone and in combination with antibiotics. Here, we isolated and characterized three novel lytic myoviruses, Cisa, Nello, and Moonstruck. Genomic analysis revealed that Cisa and Nello belong to the Pbunavirus genus, while Moonstruck is a novel Pakpunavirus species. All lacked lysogeny, virulence, or resistance-associated genes, supporting their therapeutic suitability. Phage Nello and Moonstruck were active against P. aeruginosa Pa3GrPv, isolated from a patient with lung infection candidate for phage therapy. Moonstruck exhibited superior lytic activity with ciprofloxacin sub-MIC value (0.125 µg/mL), achieving bacterial suppression for 48 h. However, to improve the lytic efficacy of the phages on the clinical isolate, phage adaptation via serial passage was investigated. The killing efficacy of Nello was enhanced, whereas Moonstruck showed a less consistent improvement, suggesting phage-specific differences in evolutionary dynamics. Sequencing of the evolved phages revealed point mutations in tail-associated genes, potentially linked to a better phage–host interaction. These results support the use of phage–antibiotic combinations and directed evolution as strategies to enhance phage efficacy against drug-resistant infections. Overall, these findings support the therapeutic potential of the newly isolated phages in treating P. aeruginosa lung infections. Full article

Protein kinases and phosphatases are essential for post-translational regulation, enabling bacteria to adapt to environmental stresses and modulate virulence. While prior reviews have broadly covered their roles in stress response, antibiotic resistance, and virulence, this article updates specifically on the roles of histidine kinases (HKs) and serine/threonine kinases (STKs) in mediating phage-bacteria interactions. A key aspect is phage-encoded kinases, which hijack bacterial signalling by phosphorylating and disrupting host processes to promote infection. Despite their importance, significant gaps remain in understanding these regulatory networks. This microreview highlights both the unresolved mechanisms and the therapeutic potential of targeting kinase pathways—for instance, by disrupting phage evasion strategies or enhancing phage-based antimicrobial therapies. Full article

Multidrug-resistant (MDR) bacterial infections present a major challenge in cancer therapy, particularly for immunocompromised patients undergoing chemotherapy, radiation, or surgery. These infections often arise from prolonged antibiotic use, hospital-acquired pathogens, and weakened immune defenses, leading to increased morbidity and mortality. As conventional antibiotics become less effective against MDR strains, there is an urgent need for alternative treatment options. This review highlights phage therapy as a promising approach to managing MDR bacterial infections in cancer patients. Once widely used, phage therapy has recently regained attention as a targeted antimicrobial strategy that can specifically eliminate harmful bacteria while preserving the beneficial microbiota. Phages work by directly lysing bacteria, disrupting biofilms, and synergizing with antibiotics to restore bacterial susceptibility. These mechanisms make phage therapy especially appealing for treating infections that complicate cancer treatments. However, the clinical application of phage therapy faces challenges such as variability in phage–host interactions, regulatory hurdles, and immune responses in patients. This review identifies gaps in current research regarding the use of phage therapy for MDR infections in cancer patients. By examining recent innovations, therapeutic mechanisms, and associated limitations, we provide valuable insights into the potential of phage therapy for improving infection management in oncology. Future research should focus on refining phage delivery methods, assessing long-term safety, and exploring combination therapies to maximize clinical efficacy. Overcoming these challenges could position phage therapy as a valuable complement to existing antimicrobial strategies in cancer care. Full article