ViPTree: the viral proteomic tree server

Characterization and genomic insights into bacteriophages Kpph1 and Kpph9 against hypervirulent carbapenem-resistant Klebsiella pneumoniae

The increasing incidence of infections attributed to hypervirulent carbapenem-resistant Klebsiella pneumoniae (Hv-CRKp) is of considerable concern. Bacteriophages, also known as phages, are viruses that specifically infect bacteria; thus, phage-based therapies offer promising alternatives to antibiotic treatments targeting Hv-CRKp infections. In this study, two isolated bacteriophages, Kpph1 and Kpph9, were characterized for their specificity against the Hv-CRKp K. pneumoniae NUHL30457 strain that possesses a K2 capsule serotype. Both phages exhibit remarkable environmental tolerance, displaying stability over a range of pH values (4-11) and temperatures (up to 50°C). The phages demonstrate potent antibacterial and antibiofilm efficacy, as indicated by their capacity to inhibit biofilm formation and to disrupt established biofilms of Hv-CRKp. Through phylogenetic analysis, it has been revealed that Kpph1 belongs to the new species of Webervirus genus, and Kpph9 to the Drulisvirus genus. Comparative genomic analysis suggests that the tail fiber protein region exhibits the greatest diversity in the genomes of phages within the same genus, which implies distinct co-evolution histories between phages and their corresponding hosts. Interestingly, both phages have been found to contain two tail fiber proteins that may exhibit potential depolymerase activities. However, the exact role of depolymerase in the interaction between phages and their hosts warrants further investigation. In summary, our findings emphasize the therapeutic promise of phages Kpph1 and Kpph9, as well as their encoded proteins, in the context of research on phage therapy targeting hypervirulent carbapenem-resistant Klebsiella pneumoniae.

The isolation and identification of a novel flavivirus from diseased Chinese soft-shelled turtle (Pelodiscussinensis)

In recent years, mass mortality of Pelodiscus sinensis has occurred in many Chinese turtle farms and no etiological research on this disease has been conducted to date. The main clinical manifestation of sick P. sinensis was telangiectasis induced bleeding occurred in the limbs, calipash and plastron. After dissection, we found that the blood viscosity was reduced. Typical clinical manifestations included light abdominal cavity effusion, intestine and gastric wall edema and transparency. HE staining showed distinct lesions in liver, intestine, kidney, spleen, heart and lung tissues of infected P. sinensis. TEM observation showed that the spherical virions were approximately 30 nm in diameter. Partial genome of the pathogen was obtained by Illumina sequencing and then assembled and annotated. Phylogenetic analysis of the polyprotein amino acid sequences of this pathogen and other flaviviruses showed that it was closely related to Chinese soft-shelled turtle flavivirus isolate HZ-2017. RT-PCR detection of this virus in the sick P. sinensis from turtle farms showed a high infection rate. QRT-PCR analysis of viral distribution in P. sinensis tissues indicated that the kidney contains the highest amount of virus. The virus was tentatively named "Pelodiscus sinensis flavivirus" (PSFV). In this study, the results of PSFV pathological characteristic and genome information laid a good foundation for further study of this virus.

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics

Bacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogen Streptococcus suis which causes infections in pigs and humans. Despite global efforts, the genome of only one infective S. suis phage has been described. Here, we report the isolation of two phages that infect S. suis: Bonnie and Clyde. The phages infect 58 of 100 S. suis strains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growth in vitro within two multi-strain mixes designed to simulate a polyclonal S. suis infection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices of S. suis infecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages of S. suis phages: Streptococcus thermophilus-like (Bonnie) and S. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infect S. suis, providing new data for the therapeutic application of phages in a One Health context.

Isolation, characterization and genomic analysis of the novel Listeria bacteriophage LMLPA3 as a potential antimicrobial in foods

Listeria monocytogenes (LM) is an opportunistic foodborne pathogen responsible for listeriosis in both humans and animals. The disease manifests in a variety of ways, including febrile gastroenteritis, septicemia, meningitis, and in some cases, preterm birth and spontaneous abortion. It is therefore crucial to develop effective strategies to control this bacterium. In this study, we isolated and characterized a novel Listeria phage, named LMLPA3. Morphological and genomic analyses revealed that phage LMLPA3 belongs to the class Caudovirales, family Herelleviridae, Myovirus-like. Phage LMLPA3 demonstrated remarkable stability across a range of pH values (4-10), temperatures (4-50 °C), and high NaCl concentrations (12% w/v). A total of 68 strains, comprising nine serotypes of L. monocytogenes and five other Listeria species, were found to be susceptible to lysis by phage LMLPA3. It is noteworthy that treatment with phage LMLPA3 resulted in a significant disruption of the biofilms formed by seven different serotype strains of L. monocytogenes, in comparison to the control. Furthermore, phage LMLPA3 effectively reduced the number of L. monocytogenes cells by 4 log10 CFU/mL and 2.9 log10 CFU/sample, respectively, in milk and on the surface of raw beef at an MOI of 10000. In light of these findings, it can be concluded that phage LMLPA3 has the potential to serve as an effective antimicrobial in the elimination of L. monocytogenes contamination in foodstuffs.

Characterization of a new lytic bacteriophage (vB_KpnM_KP1) targeting Klebsiella pneumoniae strains associated with nosocomial infections

A new bacteriophage, vB_KpnM_KP1, was identified and characterized, exhibiting a strong lytic effect on Klebsiella pneumoniae. Host range analysis revealed its effectiveness against 77.4% of clinical strains, achieving complete lysis of those associated with urinary tract infections (UTIs). Phage stability tests demonstrated that vB_KpnM_KP1 remained stable at neutral pH and across all tested temperatures. However, inactivation was observed at high ethanol concentrations and extreme pH levels. Transmission electron microscopy (TEM) analysis identified vB_KpnM_KP1 as a Myo-type phage with an icosahedral head and a contractile tail. Moreover, genome annotation of vB_KpnM_KP1 revealed a linear DNA genome of 174,802 bp, containing 307 open reading frames. Functional predictions suggest the presence of genes involved in DNA replication, transcription, morphogenesis, and cell lysis. Phylogenetic analysis classified vB_KpnM_KP1 within the Slopekvirus genus of the Straboviridae family, showing high sequence identity with phages that infect Enterobacter, Escherichia and Klebsiella species. These findings highlight the potential of phage vB_KpnM_KP1 as an alternative treatment for multidrug-resistant K. pneumoniae infections, particularly in UTIs, while offering valuable insights into its stability and genetic composition.

New lytic and new temperate Staphylococcus hyicus phages

A novel lytic phage with a broad host range was isolated from pig faeces and the complete genome was subsequently sequenced. The phage was found to lyse Staphylococcus hyicus, S. pseudintermedius, S. schleiferi and S. warneri, generating approximately 27 PFU per infected S. hyicus cell. The phage has an isometric head of 42 ± 2 nm in diameter and a noncontractile tail of 114 ± 9 nm long. The genome is 53,660 bp in size and consists of 79 predicted ORFs and one tRNAArg gene. The phage has been classified within the Caudoviricetes, specifically the Chaseviridae family. Its broad host range and absence of harmful genes make it suitable for use in phage therapy. In addition, a novel temperate phage was discovered that was spontaneously released from a S. hyicus isolate Pel11 from a pig with exudative epidermitis. This novel temperate phage differs from the known temperate phages in S. hyicus strains NCTC10350, MM2101 or 83/7-1B, representing a novel pathogenicity element in the S. hyicus genome.

Intestivirid Acquisition Increases Across Infancy in a Wild Primate Population

Intestivirids (order Crassvirales, family Intestiviridae), viruses that infect Bacteroidales bacteria in the mammalian gastrointestinal tract, have been identified as a highly abundant component of the healthy human virome that may shape patterns of human health and disease through direct action on the microbiome. While double-stranded DNA bacteriophages called crAssphages (Carjivirus communis) that infect bacteria in the Bacteroidales order have been identified in humans within the first month of life, the enormous variation in post-parturition infant environments and diets has inhibited a robust understanding of the physiological and environmental factors that govern acquisition patterns. We turned to a wild population of graminivorous nonhuman primates (geladas, Theropithecus gelada) under long-term study in the Simien Mountains National Park, Ethiopia, analysing faecal samples from infants and mothers in this population across the infancy period for richness and presence of crAssphage-like viruses (family Intestiviridae). Eight intestivirid genomes were identified based on terminal redundancy representing six unique variants (< 98% intergenomic similarity) closely related to the human crAssphage. The prevalence of intestivirids in gelada faecal samples begins to rise at about 10 months of age, peaks in the months surrounding weaning (~18 months), and somewhat decreases but maintains high levels into adulthood. We found a strong association between cumulative rainfall and intestivirid detection, with a higher likelihood accompanying wetter seasons with higher grass availability. In this population, the months prior to weaning have been found to be accompanied by a shift in the microbiome characterised by a decrease in glycan degrader Bacteroidales taxa and an increase in fermentative Bacteroidales taxa, and wetter seasons when the vast majority of the gelada diet comprises grasses are associated with an increase in fermentative Bacteroidales taxa. In the context of these microbiome shifts, our results suggest that the intestivirid-bacterial host relationship may interact with major developmental and seasonal dietary shifts in the mammalian host.

Amino acid residues in the tail fiber differentiate the host specificity of Cronobacter sakazakii bacteriophage

Cronobacter sakazakii is a Gram-negative pathogen that causes severe infections such as neonatal meningitis and sepsis. Bacteriophages (phages) rely on tail fibers for host recognition and infection, but the mechanisms of how phages recognize their bacterial hosts are not completely elucidated. In this study, two lytic C. sakazakii phages belonging to the Drexlerviridae family, CRES7 and CRES9, were isolated from sewage in South Korea. The genomes of both phages are almost the same, with only two nucleotide differences in the gene encoding a putative tail fiber, causing two amino acid differences at amino acid residues 400 and 550 of the tail fiber. The predicted structure of the tail fiber revealed that the two amino acid residues are located on the surface of the tail fiber, suggesting that these two amino acid residues may affect receptor binding. These amino acid differences resulted in differential host ranges, adsorption rates, and burst sizes of CRES7 and CRES9; CRES7, which could infect only the C. sakazakii serotype O1 strain, exhibited a higher adsorption rate and larger burst size compared to CRES9, whereas CRES9 could infect both serotypes O1 and O3 strains. These findings provide insights into how the mutations in the tail fiber gene contribute to the fitness of phages within natural environments and help develop phage-based strategies with expanded host range or enhanced specificity for targeted biocontrol of C. sakazakii.IMPORTANCEAccurate recognition and attachment to the bacterial host, mediated by tail fibers, are crucial for successful phage infection. Understanding the mechanisms underlying host specificity of phages is essential for developing targeted biocontrol applications. This study identified specific amino acid residues responsible for host specificity in the tail fibers of two newly isolated Cronobacter sakazakii phages, CRES7 and CRES9. Differences in these residues showed variation in O serotype recognition, leading to differences in host range, adsorption efficiency, and burst size. These findings provide valuable insights into tail fiber-mediated host specificity, facilitating the development of more effective phage-based strategies against C. sakazakii.

Efficacy of Erwinia amylovora and Xanthomonas campestris pv campestris phages to control fire blight and black rot in vivo

Phytopathogens, such as Erwinia amylovora and Xanthomonas campestris, pose significant threats to agriculture, leading to substantial economic losses. Traditional chemical pesticides can harm soil fertility, contaminate water, and impact non-target organisms such as natural predators and pollinators, highlighting the need for sustainable pest control methods. This study explores the use of bacteriophages as biocontrol agents against E. amylovora, which causes fire blight, and X. campestris pv. campestris, responsible for black rot in cruciferous vegetables. Bacteriophages were isolated from urban wastewater and tested for their lytic activity against these pathogens. Three virulent phages were identified: ɸEF1 and ɸEF2 against E. amylovora and ɸXF1 against X. campestris pv. campestris. Genetic analysis confirmed the absence of known lysogeny-related genes, indicating that these phages are ideal candidates for biocontrol applications. In vitro assays demonstrated significant bacterial population reductions. Specifically, ɸEF1 killed 92.1% of the E. amylovora population at a multiplicity of infection (MOI) of 1 after 3 h, while ɸEF2 reduced the population by 98.1%. When combined in a 1:1 ratio, the two phages reduced E. amylovora populations by 99.7%, and no regrowth of resistant cells was observed, which was not the case when the phages were applied individually. ɸXF1 killed 99.9% of X. campestris pv. campestris populations at an MOI of 1 after 5 h. In vivo experiments using pears and kohlrabi as infection models further validated the phage effectiveness. Treated pears showed reduced fire blight symptoms, and kohlrabi plants exhibited markedly less necrosis from black rot compared to untreated controls.IMPORTANCEThree new virulent phages have been isolated: two targeting Erwinia amylovora and one targeting Xanthomonas campestris pv. campestris. All phages were able to rapidly reduce the population of their corresponding phytopathogens and alleviate disease symptoms in in vivo plant models. These findings highlight the potential of these phages as biocontrol agents for managing bacterial plant diseases, offering an alternative to traditional chemical treatments.

Genomic characterization of the novel bacteriophage PfAn1 from Lake Baikal, infecting Pseudomonas fluorescens

We isolated a novel bacteriophage from Lake Baikal that infects Pseudomonas fluorescens. Transmission electron microscopy revealed that phage PfAn1 has a head with a diameter of 50 nm and a short tail. Its genome is 39,156 bp in length with a GC content of 57%. It is predicted to contain 53 open reading frames (ORFs). The results of evolutionary analysis suggest that phage PfAn1 should be considered a new member of the class Caudoviricetes.

Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections

BACKGROUND

Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in both human and veterinary medicine, presenting significant challenges in treatment because of biofilm production and its intrinsic resistance. This problem is exacerbated by the increase in acquired antimicrobial resistance. Bacteriophage (phage) therapy has emerged as a promising alternative for treating infection classically treated with antibiotics, offering a targeted approach to combat this infection. This study aimed to evaluate the therapeutic potential of 7 phages, focusing on their suitability for treating canine infections, as well as their purification and safety analysis for therapeutic use.

RESULTS

Two self-isolated phages and five provided phages were analysed. All tested phages reduced bacterial load in vitro; however, their efficacy varied across different concentrations. The host range analysis revealed a spectrum between 9.8 and 68.6% of canine clinical P. aeruginosa isolates. In our in vitro tests 3 out of 7 phages were able to significantly reduce the biofilm biomass, achieving reductions up to 93.38%. The sequence analysis did not discover known virulence factors and genes connected to antimicrobial resistance mechanisms. The self-isolated phages were classified as lysogenic, whereas the other phages had a lytic infection cycle. Through the purification of the phages, high-titre phage preparations (> 1011 PFU/ml) were generated with high stability for at least 1.5 years. The tested endotoxin units are below the regulatory limits.

CONCLUSION

Investigating phages as alternative treatment option seems promising with lytic phages covering a broad host range and a genomic potential for biofilm degradation. These findings support the development of phage cocktails as a targeted alternative for treating canine P. aeruginosa infections, particularly in cases of antibiotic resistance, and highlight the importance of selecting well-characterized lytic phages for therapeutic efficacy and safety.

Genomic characterization of a novel Pseudomonas aeruginosa bacteriophage representing the newly proposed genus Angoravirus: in vitro antimicrobial and antibiofilm activity

Multi-drug-resistant (MDR) Pseudomonas aeruginosa is an important pathogen that poses a critical threat due to its metallo-beta-lactamase (MBL)-mediated carbapenem resistance and biofilm-forming ability, making bacterial treatment very complicated and requiring alternative strategies. Bacteriophages are promising alternatives; however, the discovery of novel phages targeting MDR strains remains urgent. In this study, Pseudomonas phage Baskent_P4_1, a novel virulent siphovirus that infects clinical MDR P. aeruginosa isolates, was isolated from wastewater and characterized comprehensively. Its efficacy was tested against biofilm-forming, MDR isolates with MBL activity by spot test and efficiency of plating (EOP). Biological characterization showed that phage Baskent_P4_1 is stable at pH 4-10 and temperatures up to 50 °C, while its stability decreases  >60 °C temperature. It has a short latent period of 10 min and a high burst size of 253 phages per cell. The phage lysed 40% of the MDR P. aeruginosa isolates tested, including strong biofilm producers. In vitro assays showed significant biofilm inhibition (48.8% reduction at 10⁹ PFU/mL) and degradation of pre-formed biofilms. Transmission electron microscopy (TEM) revealed an icosahedral head (70 nm) and a long non-contractile tail (150 nm). Whole genome sequencing by Illumina demonstrated a linear dsDNA genome of 41.947 bp (62.8% GC content) with 53 predicted coding sequences. No virulence factors, antibiotic resistance genes, or tRNAs were detected, thus ensuring therapeutic safety. Along with phylogenetic and vConTACT2 analysis, these results suggested that phage Baskent_P4_1 belongs to a new genus, which was proposed here as the genus Angoravirus with three other species. Genomic analysis identified hydrolases (ORF 13/14) and 7-deazaguanine modification enzymes (ORF 46/47) that may contribute to host lysis and evasion of bacterial defenses. These findings highlight Baskent_P4_1's potential as a therapeutic candidate against MDR P. aeruginosa infections. The study underscores the importance of expanding phage diversity libraries and provides a framework for characterizing novel phages to combat antimicrobial resistance.

Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp

Background

Vibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy.

Methods

Phage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis.

Results

Phage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent.

The Arms Race Between Actinobacillus pleuropneumoniae and Its Genetic Environment: A Comprehensive Analysis of Its Defensome and Mobile Genetic Elements

Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia in swine, a highly contagious and economically significant disease. The genetic variability of A. pleuropneumoniae complicates disease control efforts, as it enables rapid adaptation to various stressors, including antimicrobial treatments. To better understand the molecular mechanisms underlying this adaptability, we investigated the role of the bacterial defensome and its relationship with mobile genetic elements (MGEs), such as prophages, plasmids, and integrative conjugative elements (ICEs). Using bioinformatic tools, we identified a diverse and rich defensome in A. pleuropneumoniae, with an average of 16 different defense systems per strain. We found that CRISPR-Cas systems, along with other defense mechanisms, are actively involved in restricting the entry of foreign genetic material, playing a crucial role in bacterial adaptation. Additionally, we characterized several novel prophages and examined their distribution across different strains, revealing their potential contribution to the bacterium's evolutionary success. Our findings underscore the complex interplay between the bacterium's defense systems and MGEs, shedding light on how A. pleuropneumoniae maintains genetic diversity while also safeguarding itself against external threats. These insights provide a better understanding of the genetic factors that influence the pathogen's adaptability and highlight potential avenues for more effective disease control strategies.

From farm effluent to biotechnological potential: pGLS, a novel and resilient temperate bacteriophage with synergistic activity and broad antibiofilm properties against Staphylococcus and Mammaliicoccus

AIMS

This study aimed to isolate and characterize a bacteriophage from dairy farm effluents capable of targeting Mammaliicoccus sciuri, a multidrug-resistant opportunistic pathogen. The biotechnological potential of the phage, including its antibiofilm activity, synergistic interactions with antibiotics, and genomic features, was also assessed.

METHODS AND RESULTS

The bacteriophage pGLS was isolated using M. sciuri GLS3 as the host strain, exhibiting extreme specificity by lysing only its host. Despite its narrow lytic spectrum, pGLS effectively disrupted biofilms formed by multiple Staphylococcaceae species, including multidrug-resistant strains, and demonstrated synergism with erythromycin, significantly reducing the minimum inhibitory concentration of both the phage and the antibiotic. The phage also displayed remarkable stability under extreme environmental conditions, such as UV exposure and a wide range of pH and temperature. Genomic analysis classified pGLS as a novel temperate phage with a 41 499 bp genome encoding 67 open reading frames, 52% of which were functionally annotated. No virulence or antimicrobial resistance genes were detected, reinforcing its safety for therapeutic applications.

CONCLUSION

The unique genomic characteristics, high environmental resilience, and antibiofilm efficacy of pGLS highlight its strong biotechnological potential for mitigating antimicrobial resistance, particularly in livestock settings. Its synergistic interactions with antibiotics further support its potential as an adjunct therapy against resistant Staphylococcaceae infections.

Telomere bacteriophages are widespread and equip their bacterial hosts with potent interbacterial weapons

Bacteriophages (phages) are viruses that can kill bacteria, thereby editing and shaping microbial communities. The telomere phages are a curious form using telomere-like structures to replicate their genomes as linear extrachromosomal elements. Here, we find that telomere phages are widely distributed in bacteria, being highly prevalent in Klebsiella species. We establish a model system to investigate telomere phage biology by isolating the virions of telomere phages and infecting naïve strains to create isogenic lines with and without a phage. We find that only a small set of telomere phage proteins is expressed in phage-host cells, including a toxin-the telocin-that kills other Klebsiella strains. We identify and validate a set of telocins in the genomes of other prevalent Klebsiella telomere phages. Thus, telomere phages are widespread elements encoding diverse antibacterial weapons and we discuss the prospect of using telocins for precision editing of microbial populations.

Characterization of novel phages KPAФ1, KP149Ф1, and KP149Ф2 for lytic efficiency against clinical MDR Klebsiella pneumoniae infections

Phage therapy offers a promising approach to the increasing antimicrobial resistance of Klebsiella pneumoniae. This study highlights three novel lytic bacteriophages-KPAФ1, KP149Ф1, and KP149Ф2- targeting multidrug-resistant (MDR) K. pneumoniae. These phages belong to the Myoviridae and Podoviridae family and demonstrate their efficacy and stability across a wide range of temperatures (up to 60°C) and pH levels (pH 4 to 11). Genomic analysis reveals that they are free from virulence, toxicity, and antimicrobial resistance genes, making them promising candidates for therapeutic use. Among these phages, KPAФ1 showed the highest lytic activity with a 26.15% lysis against MDR K. pneumoniae isolates. Additionally, a phage cocktail comprising all three phages improved lytic efficacy to 32.30%. This study also examined the antimicrobial resistance profiles of K. pneumoniae isolates, emphasizing the critical need for alternative treatments. By effectively targeting resistant strains, these phages offer a potential candidacy to be used as a viable alternative or a complementary antimicrobial agent to traditional antibiotics, opening up the possibility for advanced phage-based therapies. The promising results from this study pave the way for developing new treatments that could significantly improve patient care and outcomes from the growing issue of resistant bacterial infections.

Antimicrobial potential of a novel K5-specific phage and its recombinant strains against Klebsiella pneumoniae in milk

The nutrient-rich composition of milk creates an optimal environment for bacterial proliferation, making the inhibition of microbial growth essential for maintaining dairy product quality and ensuring consumer safety. Klebsiella pneumoniae is an important contaminant of milk and a leading cause of bovine mastitis. Although the increasingly serious antibiotic resistance has led to a renewed interest in phage therapy, research on antimicrobial potential of Klebsiella phages in milk remains scarce. The K5 serotype of K. pneumoniae is a major concern due to its high virulence and prevalence in dairy farming operations. Despite its clinical and economic importance, the availability of phages specifically targeting this serotype remains substantially limited. Here, we successfully isolated and sequenced 2 K1-specific Klebsiella phages, P284 and P287, and one K5-specific Klebsiella phage P252. We identified the receptor-binding proteins with depolymerization activity in these phages. The phage library against K5 K. pneumoniae was enriched by phage genome modification. Specifically, we replaced the receptor-binding protein of K1-specific phage P284 with that of K5-specific phage P252, resulting in the generation of recombinant phages T and F, which exhibit specific lytic activity against K5 K. pneumoniae. Compared with phage P252, recombinant phages T and F exhibited better and more prolonged antibacterial potential in planktonic assay. In addition, all these K5-specific phages could significantly inhibit bacterial growth and reduce bacterial populations in milk at 4°C and 38°C. In summary, this study provided K5-specific phages with potential application in managing K. pneumoniae contamination and infection in the dairy industry.

Acinetobacter baumannii and Klebsiella pneumoniae Isolates Obtained from Intensive Care Unit Patients in 2024: General Characterization, Prophages, Depolymerases and Esterases of Phage Origin

Acinetobacter baumannii and Klebsiella pneumoniae are significant nosocomial pathogens worldwide. In this study, the general characterization of A. baumannii and K. pneumoniae isolates obtained from the blood of intensive care unit patients of the multidisciplinary scientific and practical center of emergency medicine from January to September 2024 was performed. Prophage regions and prophage-derived tailspike polysaccharide-depolymerizing or -modifying enzymes within these isolates were identified and characterized in detail using a refined workflow. The protocol, encompassing a comprehensive survey of all predicted bacterial proteins, revealed an average of 6.0 prophage regions per Acinetobacter baumannii genome, including regions putatively derived from filamentous phages, and 4.8 prophage regions per Klebsiella pneumoniae isolate. Analysis of these putative prophage regions indicated that most were related to previously isolated, yet unclassified, temperate phages infecting A. baumannii and K. pneumoniae. However, certain identified sequences likely originated from phages representing novel groups comparatively distant from known phages.

Biological characteristics and genome analysis of Citrobacter freundii phage K1M

Bacteriophages that infect specific bacteria and cause their lysis are potentially useful for preventing and treating bacterial infections and controlling microbes in the environment. Citrobacter freundii is an opportunistic pathogen that is commonly present in the environment, food, animals, and human intestines. It also causes aquatic animal diseases in aquaculture. In this study, using Citrobacter freundii as the target host, a novel lytic phage, vB_CfrS_K1M (K1M), was isolated. Morphologically, K1M is a long-tailed phage with a head diameter of 68 ± 2 nm and a tail length of 130 ± 2 nm. The phage encodes a polysaccharide depolymerase and demonstrates stable biological activity. The genome of K1M is 47,995 bp in length, with 45.12% G + C content and 97 putative open reading frames (ORFs), only 36 of which encode proteins. The results of phylogenetic analysis based on TerL sequences suggest that K1M represents a new viral genus, for which we propose the name "Fredivirus".

Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages

The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.

Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome

Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.

Characterization and therapeutic potential of phage vB_Eco_ZCEC08 against multidrug-resistant uropathogenic Escherichia coli

BACKGROUND

Urinary tract infections (UTIs) caused by antibiotic-resistant bacteria have become a significant public health concern. The increasing ineffectiveness of antibiotics has led to a renewed focus on investigating other strategies, such as bacteriophages, to target specific pathogenic bacteria and prevent future resistance.

RESULTS

This study reports the isolation and characterization of bacteriophage vB_Eco_ZCEC08 targeting uropathogenic Escherichia coli (UPEC). Phage vB_Eco_ZCEC08 is morphologically a non-contractile tailed phage that exhibits strong lytic activity against UPEC with a short latent period of less than 15 min and a lysis time of 20 min to produce a high burst of around 900 phage particles per host cell. vB_Eco_ZCEC08 phage activity demonstrated exceptional stability against temperature [-80-60 ̊C], pH [2-11], UV exposure and incubation in artificial human urine. The phage effectively reduced UPEC counts over a range of infection rates, with MOI 1 the most effective, and which resulted in the limited emergence of phage-insensitive bacteria. A whole-genome study of the 47.926 bp vB_Eco_ZCEC08 phage identified one tRNA gene and 84 predicted genes. Comparative genomics and phylogenetic analysis suggest that the vB_Eco_ZCEC08 phage belongs to the same genus as the Salmonella phage vB_SenS_ST1 but represents a new species. Phage vB_Eco_ZCEC08 showed minimal cytotoxicity against human urinary bladder cancer and skin fibroblast cell lines.

CONCLUSION

vB_Eco_ZCEC08 phage demonstrates strong selective lytic activity against UPEC in the absence of any lysogenic behavior. These properties coupled with inherent physiochemical stability and low cytotoxicity support the development of vB_Eco_ZCEC08 as an alternative treatment for multidrug-resistant UPEC.

Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation

Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.

Weberviruses are gut-associated phages that infect Klebsiella spp

Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life, and associated depolymerases. In this study, we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome, and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n = 258 from isolates, n = 65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n = 330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%), and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.

Novel strategies for vancomycin-resistant Enterococcus faecalis biofilm control: bacteriophage (vB_EfaS_ZC1), propolis, and their combined effects in an ex vivo endodontic model

BACKGROUND

Endodontic treatment failures are predominantly attributed to Enterococcus faecalis (E. faecalis) infection, a Gram-positive coccus. E. faecalis forms biofilms, resist multiple antibiotics, and can withstand endodontic disinfection protocols. Vancomycin-resistant strains, in particular, are challenging to treat and are associated with serious medical complications.

METHODS

A novel phage, vB_EfaS_ZC1, was isolated and characterized. Its lytic activity against E. faecalis was assessed in vitro through time-killing and biofilm assays. The phage's stability under various conditions was determined. Genomic analysis was conducted to characterize the phage and its virulence. The phage, propolis, and their combination were evaluated as an intracanal irrigation solution against a 4-week E. faecalis mature biofilm, using an ex vivo infected human dentin model. The antibiofilm activity was analyzed using a colony-forming unit assay, field emission scanning electron microscopy, and confocal laser scanning microscopy.

RESULTS

The isolated phage, vB_EfaS_ZC1, a siphovirus with prolate capsid, exhibited strong lytic activity against Vancomycin-resistant strains. In vitro assays indicated its effectiveness in inhibiting planktonic growth and disrupting mature biofilms. The phage remained stable under wide range of temperatures (- 80 to 60 °C), tolerated pH levels from 4 to 11; however the phage viability significantly reduced after UV exposure. Genomic analysis strongly suggests the phage's virulence and suitability for therapeutic applications; neither lysogeny markers nor antibiotic resistance markers were identified. Phylogenetic analysis clustered vB_EfaS_ZC1 within the genus Saphexavirus. The phage, both alone and in combination with propolis, demonstrated potent antibiofilm effects compared to conventional root canal irrigation.

CONCLUSION

Phage vB_EfaS_ZC1 demonstrates a promising therapy, either individually or in combination with propolis, for addressing challenging endodontic infections caused by E. faecalis.

Potential of vB_Pa_ZCPS1 phage embedded in situ gelling formulations as an ocular delivery system to attenuate Pseudomonas aeruginosa keratitis in a rabbit model

Pseudomonas aeruginosa keratitis (or pink eye) is a challenging ocular infection that causes serious complications due to the deficiency of effective antibiotic treatment. Thus, in this study we isolated and characterized a specific bacteriophage, phage vB_Pa_ZCPS1, to be used to formulate an in situ- gel loaded bacteriophage for an in vivo rabbit infection treatment model. Phage vB_Pa_ZCPS1 is a double-stranded DNA bacterial virus, of 46,135 bp encoding 75 open reading frames (ORFs) with no antibiotic resistance genes detected. Moreover, it has a podoviral morphotype from the Caudoviricetes class with a 62.4 nm capsid and a short inflexible tail of around 18.8 nm, as indicated by the transmission electron microscope (TEM). Phage vB_Pa_ZCPS1 presented good stability to the UV exposure and a wide range of pH values from 3.0 to 11.0. In addition, the phage-bacteria dynamics study showed that phage vB_Pa_ZCPS1 was effective against P. aeruginosa, especially at low multiplicities of infections (MOIs), including 0.001, 0.01, and 0.1. Respectively, it was loaded to the characterized in situ gel composed of 14 % Pluronic F-127 and 1.5 % HPMC K4M polymer. The in situ-gel has a gelling time of 30 s ± 1, and a temperature of 33 °C ± 1, where the viscosity of the gel increases 10-fold. For the in vivo trial, the infected group treated with phage presented improved clinical outcomes, where the histopathological analysis revealed normal corneal thickness and intact corneal stratified squamous epithelium. Thus, the in situ-gel loaded phage vB_Pa_ZCPS1 could be a potential candidate approach to treat P. aeruginosa keratitis.

Fully resolved genome assembly of a Macrococcus bovicus isolated from a human skin infection

The complete circular genome of Macrococcus bovicus LI0213 isolated from a human skin lesion was obtained using a hybrid assembly of Nanopore and Illumina reads. The genome consisting of a 2,082,488-bp chromosome and three plasmids, contains phage-related sequences and represents the first fully resolved genome of M. bovicus from human origin.

Isolation, characterization, and genomic analysis of phage MY02 targeting extended-spectrum beta-lactamase-producing Klebsiella pneumoniae

Abuse of antibiotics has led to increased rates of resistance in extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae and an acceleration in the emergence of drug-resistant strains, which can have serious consequences for nosocomial infections. In this study, phage MY02, which infects ESBL-producing Klebsiella pneumoniae, was isolated from sewage and characterized. Phage MY02 was found to have an optimal multiplicity of infection of 0.001, with a lysis period of up to 40 minutes and an average burst of about 80 plaque-forming units per cell. The phage was found to be stable over a temperature range of -20 to 60°C and a pH range of 3-11 and to have a broad host range. Whole-genome sequencing showed that the genome of phage MY02 is ??171,821?? bp in length and contains 293 open reading frames. Sequence comparisons and phylogenetic analysis showed that phage MY02 belongs to the genus Marfavirus in the class Caudoviricetes. This novel broad-spectrum Klebsiella pneumoniae phage has potential applications against bacterial infections.

Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome

Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.

Extra peptidase of a cyanophage confers its stronger lytic effect on bloom-forming Microcystis aeruginosa

Microcystis covers important cyanobacteria species that causes harmful algal blooms. Cyanophages are viruses that infect and lyse cyanobacteria and have been considered as potential cyanobacteria control strategy. Present study isolated two cyanophage strains, MaMV-CH01 (CH01) and MaMV-CH02 (CH02), infecting M. aeruginosa. Growth curves showed that CH01 has a stronger proliferation ability and host cell lysis capability than CH02. Combined with genomic, gene structure and function analysis, as well as biologic testing including infectivity, we confirmed that there is widespread horizontal gene transfer between the cyanophages and cyanobacteria, enabling the cyanophages to carry a series of auxiliary metabolic genes (AMG) related to host's metabolism. Moreover, compared with CH02, the cyanophage CH01 carrying extra AMG, a peptidase encoding gene (82R), exhibited stronger lytic activity against its host. Expression of CH01 82R in vitro showed strong bacteriostatic activity. Further, testing the cyanophage's ability to form plaques showed that the CH01(AMG+), which encodes the aforementioned peptidase, can form larger plaques, with an area of about threefold than that formed by CH02(AMG-). Above results indicated that the cyanophages with specific peptidase possessed stronger algicidal efficiency, which provided a direction for finding efficient cyanophages to regulate the population of bloom-forming cyanobacteria.

Responding to exogenous quorum-sensing signals promotes defense against phages by repressing OmpV expression in Pseudomonas syringae pv. actinidiae

Bacteriophages as viral predators can restrict host strains and shape the bacterial community. Conversely, bacteria also adopt diverse strategies for phage defense. Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of bacterial canker on kiwifruit. Though Psa lacks quorum sensing signaling molecule synthase LuxI, two (PsaR1 and PsaR3) of three LuxR homologous were confirmed to bind with exogenous N-acyl homoserine lactone (AHL), OXO-C8-HSL. The adsorption and infection efficiency of phage KBC54 to Psa significantly reduced by adding OXO-C8-HSL or heterologous expression of traI of Agrobacterium tumefaciens in Psa. By generating PsaR1 and PsaR3 mutants, as well as PsaR-AHL MST assays, we specified that the two PsaRs can recruit AHL to enhance bacterial resistance against phage. Absence of PsaR1 and PsaR3 resulted in up-regulation of the outer membrane protein OmpV, and knockout of ompV led to impaired phage adsorption efficiency. Given that OmpV specifically interacted with the phage tail fiber protein Tp3 in pull-down assay, we deduced that OmpV serves as a cell surface receptor recognized by phage. This study highlights the remarkable ability of Psa recruiting QS signals to inhibit phage infection. This may be a common strategy for non-AHL producing bacteria that evolved to take control of phage infection and promote host fitness by orchestrating QS signals in living niches.

Isolation, complete characterization and phylogeography of the first bacteriophage against Vibrio neocaledonicus, which encodes a pyruvate phosphate dikinase and represents a novel viral family

Vibrio are widely distributed in aquatic environments and are major pathogens commonly found in aquaculture environments, playing a significant role in human production activities and maintaining ecological stability. Here, a novel phage, vB_VneS_J26, which infects Vibrio neocaledonicus, was isolated from coastal seawater in Qingdao, China. Transmission electron microscopy revealed that vB_VneS_J26 exhibits siphovirus morphotype, with a linear double-stranded DNA genome of 82,477 bp in length and G+C content of 45.11 mol%, encoding 122 putative ORFs. Three auxiliary metabolic genes related to carbon metabolism and host cell redox processes were identified, including a pyruvate phosphate dikinase, which catalyses the reversible conversion between phosphoenolpyruvate and pyruvate and is rarely detected in viruses. Whole-genome phylogenetic and comparative genomic analyses suggested that vB_VneS_J26 represents a potential novel viral family, comprising six isolated vibriophages, proposed as Modirecodeviridae. Phylogeographic analysis indicated that Modirecodeviridae is primarily distributed in epipelagic and mesopelagic zones of the Arctic and temperate tropical oceans.

Identifying phage Lysins through genomic analysis of prophages from Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative opportunistic pathogen, responsible for nosocomial infections worldwide. In recent years, this microorganism has acquired resistance to various antibiotics, prompting the World Health Organization (WHO) to declare carbapenem-resistant A. baumannii (CRAB) a critical priority microorganism requiring urgent attention and the development of new therapeutic options. Here, we screened for prophages in 158 genomes of A. baumannii, comprising 139 complete genomes from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), and 19 newly sequenced clinical isolates. Additionally, we conducted phylogenetic analyses of prophages, highlighting their diversity and local clustering. The analyzed genomes harbored at least two prophage regions, resulting in the identification of a total of 950 prophage regions, of which 348 were considered complete prophages through software analysis and manual curation, while the remainder may represent prophage remnants. The complete prophages ranged from 28.6 to 103.9 kbp, with an average GC content of 39%. Based on genomic similarity, only 18 complete prophages were taxonomically classified to the genus Vieuvirus. Among all identified complete prophages, we identified 166 genes encoding for putative lysins, while prophage regions that were not considered complete could also harbor putative lysins. These findings highlight the abundance of prophage-encoded lysins in A. baumannii genomes, which are promising therapeutic agents for combating A. baumannii infections, particularly in the face of rising antibiotic resistance.

Characterization and therapeutic potential of newly isolated bacteriophages targeting the most common Salmonella serovars in Europe

Despite meticulous monitoring of Salmonella spp. throughout the food chain to ensure safer animal food products for consumers, the number of salmonellosis cases in humans continues to rise annually in Europe. Phage therapy emerges as a promising tool for controlling and eradicating Salmonella in primary production. This study aimed to fully characterize new phage therapy candidates isolated from animal sources. To achieve this, a phenotypic and genetic characterization of five phage isolates was conducted. The five phages demonstrated physical stability across a wide range of temperatures and pH levels, effectively lysing 12 different Salmonella serovars, including the most prevalent ones in the European Union in recent years, as well as multidrug-resistant strains isolated from the field. Additionally, four of the phages exhibited depolymerase production in the host range, with genomic analysis confirming that all five possessed sequences encoding for this activity, suggesting their potential as surface-disinfecting agents. Genetic analysis further revealed that the phages belong to distinct genera: Felixounavirus, Cornellvirus, Skatevirus, Agtevirus and Berlinvirus. Notably, none of the phages contained harmful sequences that could compromise their future application, such as virulence factors, antibiotic resistance genes or temperate markers. Overall, these five phages show promise as suitable candidates for phage therapy applications or phage-based Salmonella eradication strategies, where their integration in the existing biocontrol measures may enhance both food safety and public health.

Isolation, characterization, and genomic analysis of three novel Herelleviridae family lytic bacteriophages against uropathogenic isolates of Staphylococcus saprophyticus

BACKGROUND

Staphylococcus saprophyticus (S. saprophyticus) is the second most prevalent etiological agent of urinary tract infections (UTIs) in young women. However, there is a paucity of data regarding its bacteriophage (phage). Therefore, this study was conducted to isolate and identify new lytic phages from municipal wastewater with the objective of increasing knowledge about phages and their genomes.

METHODS

A total of 11 clinical isolates of S. saprophyticus and 30 wastewater samples were used to isolate three lytic phages (vB_SsapH-Golestan-100, vB_SsapH-Golestan101-M, and vB_SsapH-Golestan-105-M). The morphology, behavioral characteristics, and complete DNA genomes of these phages were analyzed.

RESULTS

The microscopic images of the phages revealed that the sizes of their heads and tail lengths fell within the ranges of 90-111 nm and 234-266 nm, respectively. All phages exhibited high adsorption rates (99.5% in 15 min) and burst sizes (150-210 PFU per infected cell), with a potential for a narrow host range. Genomic analysis of Staphylococcus phages indicated a size of 136,433 base pairs (bp) with a guanine-cytosine (GC) content of 33.7% and 192 open reading frames (ORFs) for vB_SsapH-Golestan-100, 144,081 bp with a GC content of 29.6% and 205 ORFs for vB_SsapH-Golestan101-M, and 142,199 bp with a GC content of 30.6% and 203 ORFs for vB_SsapH-Golestan-105-M. A bioinformatics analysis indicated that all three phages belong to the Twortvirinae subfamily of Herelleviridae. Among the three phages, vB_SsapH-Golestan-100 exhibited the least similarity to previously known phages, with less than 21% similarity with its closest counterparts in genomic databases.

CONCLUSIONS

This study identified new phages that have the ability to destroy a broad range of S. saprophyticus isolates and may potentially be classified as a new genus and species within the Herelleviridae family in future studies.

The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures

BACKGROUND

The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS

In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS

The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS

Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.

Description of two novel bacteriophages of the class Caudoviricetes that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum

Here, we describe the isolation and characterization of two novel phages from Brazilian soil that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum, which we have named "RS phage AB1 and RS phage CA1. Genome sequencing and phylogenetic analysis revealed that RS phage AB1 is a novel member of the family Peduoviridae, while RS phage CA1 could not be classified as part of any established family. Thus, we propose a new viral family, "Anamaviridae", with two subfamilies, "Kantovirinae" and "Mascarenevirinae", with the latter including RS phage CA1. We propose the species names "Cocadavirus alagoinhas" and "Acarajevirus bahia" for RS phage CA1 and RS phage AB1, respectively. These findings increase our understanding of the diversity of phages infecting plant pathogens of the genus Ralstonia.

Genome-guided development of a bacterial two-strain system for low-temperature soil biocementation

Degradation and erosion of soil is a significant threat to global food security and overall agricultural productivity. This issue is exacerbated by climate change and intensive human activity, meaning that the development of sustainable solutions for those problems is critical. Microbially induced calcite precipitation (MICP) offers a promising approach to stabilise soil particles; however, its applicability at low temperatures remains limited. In our study, we introduce a novel two-strain system combining the type strain for biocementation experiments, Sporosarcina pasteurii DSM 33, and Sporosarcina sp. ANT_H38, a novel, psychrotolerant strain obtained from the Antarctic. The novel strain enabled enhanced biocementation performance when combined with the type strain. Biocementation experiments showed a 3.5-fold increase in soil cohesion, while maintaining a similar internal friction angle compared to the type strain alone (10.7 kPa vs 34.12 kPa; 0.55 kPa for untreated soil). The increased cohesion significantly reduces susceptibility to erosion, offering a practical and sustainable solution. Furthermore, to better understand the mechanisms driving this process, we conducted a comprehensive bioinformatic analysis of the ANT_H38 genome, revealing unique cold-adaptive genes, as well as urease genes, which are evolutionarily distant from other Sporosarcina ureases. Those results provide valuable insights into the strain's functional adaptations, particularly under low-temperature conditions. Overall, our study addresses a critical issue, offering a robust, nature-based solution that enhances soil resilience through MICP. Performed laboratory work confirms the potential of the system for real-world applications, while the comprehensive bioinformatic analysis provides the much needed context and information regarding the possible mechanisms behind the process. KEY POINTS: • Antarctic Sporosarcina sp. ANT_H38 contains unique urease genes • Two-strain ANT_H38/DSM33 system effectively stabilises soil at low temperatures • Two-strain system has potential for stopping soil erosion and desertification.

Synergistic antibacterial activity of curcumin and phage against multidrug-resistant Acinetobacter baumannii

Acinetobacter baumannii is a priority bacterial pathogen and leading cause of nosocomial infections, particularly in intensive care units (ICUs). The average incidence of carbapenem-resistant A. baumannii infections in ICUs is 41.7 cases/1,000 patients, highlighting the urgent need for more effective alternative therapies to replace carbapenems. Thus, this study aimed to investigate for the first time the antibacterial activity of curcumin in combination with the novel phage vB_AbaSI_1 to combat multidrug-resistant (MDR) A. baumannii in vitro. Phage vB_AbaSI_1 (capsid diameter 91 nm, contractile tail 94/20 nm) was isolated from sewage and infects ~ 29% of the 131 bacterial isolates examined. The 52,783 kb phage genome has 75 ORFs, encodes an integrase, lacks tRNAs/virulence genes, and belongs to the Caudoviricetes. Commercially sourced curcumin (400 µg/mL), combined with phage vB_AbaSI_1 (MOI 100) reduced MDR A. baumannii 131 to undetectable levels 1 h post-treatment at 37 °C, and this efficacy was further extended for 5 h in double-dosed phage/curcumin-treated cultures. In contrast, treatment with just phage vB_AbaSI_1 reduced bacterial growth but rebounded within 3 h, while curcumin-only treated cultures showed only 1-log bacterial reduction compared to untreated control. The phage/curcumin synergy occurred exclusively with phage-susceptible strains pre-curcumin exposure. This suggests the potential disruption of bacterial cell membrane during phage infection allowing curcumin entry, as no synergy was observed with phage-resistant strains. This innovative strategy of combining phage and curcumin showed great efficacy at controlling MDR A. baumannii and has a potential for therapeutic deployment. Future work will focus on engineering the phage to make it therapeutically acceptable.

Characterization of Newly Isolated Rosenblumvirus Phage Infecting Staphylococcus aureus from Different Sources

Staphylococcus aureus is a globally significant pathogen associated with severe infections, foodborne illnesses, and animal diseases. Its control has become increasingly challenging due to the spread of antibiotic-resistant strains, highlighting the urgent need for effective alternatives. In this context, bacteriophages have emerged as promising biocontrol agents. This study aimed to characterize the newly isolated Staphylococcus phage CapO46 and evaluate its efficacy in reducing S. aureus in milk. Identified as a new species within the Rosenblumvirus genus, CapO46 exhibited a podovirus-like structure and a small linear dsDNA genome (17,107 bp), with no lysogeny-related, antimicrobial resistance, or virulence genes. Host range assays demonstrated its ability to infect all 31 S. aureus isolates from two different countries and in diverse environmental contexts, achieving high efficiency of plating (EOP > 0.5) in 64.5% of cases. Kinetic analyses revealed rapid adsorption and a short latent period, with a burst size of approximately 30 PFU/cell. In UHT whole-fat milk, CapO46 achieved a maximum reduction of 7.2 log10 CFU/mL in bacterial load after 12 h, maintaining significant suppression (1.6 log10 CFU/mL) after 48 h. Due to its genetic safety, high infectivity across multiple isolates, and antimicrobial activity in milk, CapO46 can be considered a promising candidate for S. aureus biocontrol applications.

Analysis of a novel phage as a promising biological agent targeting multidrug resistant Klebsiella pneumoniae

The rise of deaths by resistant bacteria is a global threat to public health systems. Klebsiella pneumoniae is a virulent pathogen that causes serious nosocomial infections. The major obstacle to bacterial treatment is antibiotic resistance, which necessitates the introducing of alternative therapies. Phage therapy has been regarded as a promising avenue to fight multidrug-resistant (MDR) pathogens. In the current study, a novel phage vB_KpnP_KP17 was isolated from sewage, and its lytic potential was investigated against K. pneumoniae. The isolated phage vB_KpnP_kP17 was lytic to 17.5% of tested K. pneumoniae isolates. One step growth curve indicated a virulent phage with a short latent period (20 min) and large burst size (331 PFU/cell). Additionally, vB_KpnP_kP17 maintained its activity against planktonic cells over a wide range of pH, temperature and UV irradiation intervals. The potential of vB_KpnP_KP17 as antibiofilm agent was revealed by the biofilm inhibition assay. The isolated phage vB_KpnP_KP17 at multiplicity of infection (MOI) of 10 inhibited more than 50% of attached biofilms of tested K. pneumoniae isolates. The genome of vB_KpnP_kP17 was characterized and found to be a linear dsDNA of 39,936 bp in length and GC content of 52.85%. Additionally, the absence of toxicity, virulence and antibiotic resistance genes further confirms the safety of vB_KpnP_KP17 for clinical applications. These characteristics make vB_KpnP_KP17 of a potential therapeutic value to manage MDR K. pneumoniae infections. Additionally, the formulation of vB_KpnP_KP17 in a cocktail with other lytic phages or with antibiotics could be applied to further limit biofilm-producing K. pneumoniae infections.

Enhanced suppression of Stenotrophomonas maltophilia by a three-phage cocktail: genomic insights and kinetic profiling

Stenotrophomonas maltophilia is an understudied, gram-negative, aerobic bacterium that is widespread in the environment and increasingly a cause of opportunistic infections. Treating S. maltophilia remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with cystic fibrosis, cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there remains a great need for well-characterized phages, especially against S. maltophilia. In response to an oncology patient with a sepsis infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against S. maltophilia host strain B28B. We hypothesized that, when combined into a cocktail, genetically diverse phages would give rise to distinct lytic infection kinetics that would enhance bacterial killing when compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was further investigated and screened for potential therapeutic use. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared with individual phages when observed for 48 h. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 S. maltophilia strains to determine if a multi-phage cocktail has an expanded host range. Our phages remained strain-specific and infected >50% of tested strains. In six clinically relevant S. maltophilia strains, the multi-phage cocktail has enhanced suppression of bacterial growth. These findings suggest that specialized phage cocktails may be an effective avenue of treatment for recalcitrant S. maltophilia infections resistant to current antibiotics.

VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .

Pseudomonas Phage Lydia and the Evolution of the Mesyanzhinovviridae Family

Phage Lydia, a newly isolated siphovirus infecting Pseudomonas aeruginosa, was characterized with respect to its basic kinetic properties and subjected to comparative bioinformatic analysis with related phages. The phage exhibited a restricted host range, with lytic activity observed against 7 of 30 tested isolates. The genome of phage Lydia consists of a 61,986 bp dsDNA molecule and contains 89 predicted genes. Bioinformatic analysis suggests the presence of a DNA modification system, but no apparent genes associated with lysogeny or antibiotic resistance were identified. Taxonomic classification places Lydia within the Mesyanzhinovviridae family, Rabinowitzvirinae subfamily, and Yuavirus genus, with the closest relation to Pseudomonas virus M6. Comprehensive bioinformatic studies, including structural modelling and analysis of phage proteins, as well as comparative taxonomic, phylogenomic, and pangenomic analyses of the Mesyanzhinovviridae family, revealed relationships between proteins of Mesyanzhinovviridae phages, proteins from other phage groups, encapsulins, and a gene transfer agent (GTA) particle from Rhodobacter capsulatus. These analyses uncovered patterns of evolutionary history within the family, characterized by genetic exchange events alongside the maintenance of a common genomic architecture, leading to the emergence of new groups within the family.

Characterization of Pseudomonas phage MME: a novel tool for combatting multidrug-resistant Pseudomonas aeruginosa and disinfection

AIM

Combatting Pseudomonas aeruginosa, known for its robust biofilm formation, presents significant challenges in healthcare, food, and industry. Phages offer promising alternatives against this resilient pathogen. We aim to demonstrate their viability as alternative therapeutic and decontamination options.

METHODS AND RESULTS

We introduce the lytic activity and decontamination efficacy of Pseudomonas phage MME, isolated from sewage, on solid surfaces, as well as on its biological and genomic characterization. The phage showed lytic activity against both antibiotic-resistant clinical strains and reference strains. About 90% of the phage adsorbed to its host within 20 min, with an average burst size of ∼53 PFU per infected cell. The bactericidal effect on the host at the 8th hour showed a 95% killing efficiency. Additionally, phage MME effectively reduced bacterial loads on glass, plastic, and metal surfaces, simulating hospital environments. Confocal laser scanning microscopy demonstrated the phage's bactericidal activity on glass surfaces at the 8th and 12th hours, preventing biofilm formation. Bioinformatic analysis confirmed that phage MME represents a new species within the Bruynoghevirus genus. Comparative genomic analysis revealed no virulence factors within the phage MME genome.

CONCLUSIONS

These findings highlight the potent lytic activity of phage MME against P. aeruginosa, underscoring its potential as a valuable tool in combatting this pathogen and its suitability for diverse applications, including as a decontaminating agent.

Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages-ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)-when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage-host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host.

Genomic and phenotypic characterization of staphylococci isolated from the skin of non-human primates

The growth of wildlife tourism coupled with continued deforestation has resulted in increased contact between non-human primates (NHPs) and humans. Such events may promote the transmission of potentially pathogenic bacteria such as Staphylococcus spp. However, the presence and associated virulence of staphylococci associated with NHPs remain poorly characterized. To help address this, we isolated staphylococci from the skin of four NHP species housed at a UK zoo and characterized their antimicrobial resistance, virulence factors and prophage. We recovered 82 isolates from mannitol salt agar, of which 28 were tentatively confirmed as staphylococci by 16S rRNA gene sequencing. Fourteen isolates were determined to be unique, based on differences in their 16S rRNA gene sequences and origins of isolation. Whole-genome sequencing of the 14 isolates and subsequent genomic analysis identified 5 species, belonging to the genus Staphylococcus (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus pasteuri, Staphylococcus saprophyticus and Staphylococcus warneri). Bioinformatic prediction of antimicrobial resistance genes identified a total of 85 resistance determinants across all 14 isolates, potentially rendering them resistant to a range of antibiotic classes. However, phenotypic testing revealed only a single case of clinical resistance. Isolates belonging to the species S. pasteuri were identified as the most proficient biofilm formers. Potentially complete prophages were identified in 11 of the sequenced isolates. Prophage JCT0104_p1, identified within the genome of S. aureus JCT0104, was found to encode the virulence factor staphylokinase, which is associated with pathogenesis in humans. Our findings contribute to the limited knowledge of the diversity and characteristics of staphylococci residing on the skin of captive NHPs.

Characterization and anti-biofilm potentiality of an isolated novel Aeromonas hydrophila-infecting bacteriophage AHPMCC11, belonging to the genus Ahphunavirus

Aeromonas hydrophila is a major aquatic habitat pathogen responsible for huge economic losses in the aquaculture and food industries. In this study, a lytic bacteriophage AHPMCC11 was isolated by using A. hydrophila MTCC 1739. AHPMCC11 showed a short latent period of 10 min and the burst size was 215 PFU/cell. AHPMCC11 had potent bacteriolytic activity within 2 h in liquid culture inhibition assay and exhibited biofilm scavenging activity against A. hydrophila MTCC 1739. AHPMCC11 was found stable at a wide range of pH levels (3-12), temperature ranges (4-37 °C), and salinity conditions (0-40 ppt). The AHPMCC11 genome was determined to be 42,439 bp in length with 58.9 % G + C content, 51 CDS, and no tRNA. Comparative genome study suggested that AHPMCC11 may represent a novel species within the Autographiviridae family, belonging to the Ahphunavirus genus. In conclusion, AHPMCC11 might be used as a biocontrol agent in aquaculture and the food industry.

taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level

Background

Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee on the Taxonomy of Viruses. With the rapid increase in phage genomic data there is a growing need for automated classification systems that can handle large-scale genome analyses and place phages into new or existing genera and species.

Materials and Methods

We developed taxMyPhage, a tool system for the rapid automated classification of dsDNA bacteriophage genomes. The system integrates a MASH database, built from ICTV-classified phage genomes to identify closely related phages, followed by BLASTn to calculate intergenomic similarity, conforming to ICTV guidelines for genus and species classification. taxMyPhage is available as a git repository at https://github.com/amillard/tax_myPHAGE, a conda package, a pip-installable tool, and a web service at https://phagecompass.ku.dk.

Results

taxMyPhage enables rapid classification of bacteriophages to the genus and species level. Benchmarking on 705 genomes pending ICTV classification showed a 96.7% accuracy at the genus level and 97.9% accuracy at the species level. The system also detected inconsistencies in current ICTV classifications, identifying cases where genera did not adhere to ICTV's 70% average nucleotide identity (ANI) threshold for genus classification or 95% ANI for species. The command line version classified 705 genomes within 48 h, demonstrating its scalability for large datasets.

Conclusions

taxMyPhage significantly enhances the speed and accuracy of bacteriophage genome classification at the genus and species levels, making it compatible with current sequencing outputs. The tool facilitates the integration of bacteriophage classification into standard workflows, thereby accelerating research and ensuring consistent taxonomy.