Abstract Shiga toxin-converting bacteriophages play a critical role in the emergence and virulence of pathogenic Escherichia coli strains. Despite their significance, detailed structural information on these phages remains scarce. Here we present a high-resolution cryo-electron microscopy and proteomic analysis of the phi24B bacteriophage, revealing an icosahedral capsid with T=9 symmetry, decorated by a processed esterase protein (gp84) and stabilized by cementing proteins. The tail assembly comprises a dodecameric portal, two rings of adapter proteins sharing a common fold, a hexameric nozzle, six lateral tail fibers, and a flexible central needle fiber. The binding sites of the fibers are described. Comparative analysis indicates conservation of the tail structure with related podoviruses but very different peripheral features.

The global virome (virosphere; unformal domain Viraea) has evolved over at least three billion years through continuous co-evolution with the major domains of life, including Archaea, Bacteria, and Eukarya. All viral pathogens known to cause human infectious diseases are of zoonotic origin, having entered human populations at different stages of human evolution and societal development. This process remains ongoing today. The global virome constitutes an immense reservoir of viruses with pandemic potential. Continuous shaping of viral population gene pools under environmental selective pressures drives the emergence of novel human infections. Certain zoonotic viruses have adapted to sustained human-to-human transmission, becoming anthroponotic or zooanthroponotic pathogens, whereas others remain primarily zoonotic. To date, more than 500 viruses (representing over 180 species) have been identified as causative agents of human infectious diseases. Collectively, viral infections affect nearly the entire global population annually: acute intestinal viral infections account for approximately 6 billion cases, acute respiratory viral infections for 1–5 billion cases, vector-borne viral fevers for 450 million cases, parenterally transmitted viral hepatitis for 3 million new cases, and HIV infection for 1.5 million new cases, resulting in an estimated 10–15 million deaths annually, excluding long-term sequelae. Viruses transmitted via the aerosol route periodically give rise to pandemics associated with millions of deaths. At the time of emergence, humanity is typically unprepared, lacking effective means for prevention and treatment. The annual economic burden attributable to major viral infections–including HIV, parenteral viral hepatitis, and influenza–is estimated at hundreds of billions to trillions of U.S. dollars, while the COVID-19 pandemic alone inflicted global economic losses estimated at USD 8.8 trillion, with long-term consequences projected to reach USD 16 trillion (roughly 10–15% of annual global economic output). Persistent, centuries-long pandemics caused by herpesviruses, papillomaviruses, polyomaviruses, and parvoviruses are associated with oncogenesis and a broad spectrum of systemic diseases, for which preventive and therapeutic options remain limited. Ensuring biological security requires continuous genomic surveillance of the virome across both natural and anthropogenically altered ecosystems. Such surveillance will improve the capacity to predict pandemic emergence and inform strategic approaches to prevention, including vaccine development, as well as antiviral therapies targeting multiple stages of viral life cycle. Fundamental research into virus–host interactions and the pathogenesis of viral infections remains essential for advancing preparedness against current and future viral threats.

Background: The majority of bacteriophages stop replicating once the host culture approaches the stationary phase. Only a few bacteriophages are able to replicate in host cells at the transition to, or already in, the early stationary phase of growth (early stationary phase infective, eSPI phages) have been characterized so far. Materials and Methods: The coliphage DH23 was isolated from the river water using an enrichment procedure with a stationary phase culture of the host. Genomic sequencing, epigenetic modifications detection, and morphological and biological characterization were performed. Results: DH23 is a small siphovirus with a genome of 44,682 b.p. Phylogenetic analysis suggests that DH23 may be considered as a new species within the Dhillonvirus genus, closely related to Sodalis phage SO-1 and coliphage TheodorHerzl. Phage DH23 plaques continue to expand for several days of incubation and it is able to form plaques when applied to already mature 24 h-old host lawn. Conclusions: Bacteriophage DH23 features an eSPI phenotype very similar to phage T7. Expanding the number of characterized eSPI coliphages may facilitate deciphering the molecular basis of eSPI phenotype and development of new eSPI platforms for phage therapy or other applications.

The emergence of antibiotic resistance among bacterial pathogens poses a significant threat to aquaculture and public health. This study presents the characterization of a novel bacteriophage, designated as Ursula, specifically targeting Citrobacter, a prominent pathogen affecting fish populations. We isolated Ursula from aquatic environments during a search for novel phages active against fish pathogens, and conducted a comprehensive analysis of its morphological, genomic, and lytic properties. Transmission electron microscopy revealed that Ursula has a myovirus morphology, being a rather large T4-like phage. Genomic sequencing identified a double-stranded linear DNA genome of approximately 183 kb, containing unique genes associated with lytic activity and host recognition. This phage is related to other T4-like Citrobacter phages, being a new species.

Despite the difficult and turbulent history of Russia and the USSR during the period from the 1917 revolution until the end of World War II, in 1945, research on bacteriophage therapy (PT) and basic bacteriophage biology developed in the country starting in the 1920s, concurrently with the development of this field in the West. While practical achievements in PT made in the USSR are quite well known to the scientific community, the efforts of Soviet scientists to discover the nature of phages and PT mechanisms in the 1930s have essentially fallen out of scholarly discourse. Here, I introduce a valuable source of historical information and a beautiful piece of early bacteriophage and PT conceptualization: the monograph by Prof. M.I. Lurie "Twort-d'Hérelle Phenomenon," which appeared days before the beginning of the devastating Great Patriotic War (1941) and was totally obscured by the war events, escaping the attention of historians of science.

Bacteria of the genus Aeromonas, especially A. hydrophila and A. veronii are recognized as important fish pathogens that cause significant economic losses in aquaculture. Environmentally friendly bacteriophage-based solutions for the treatment of fish and for the reduction of colonization by pathogenic bacteria in production facilities are currently in high demand. The bacteriophage Gekk3-15 was isolated during a search for novel phage strains potentially suitable for Aeromonas biocontrol applications. Genome sequencing revealed that this virus is a relatively small myovirus with a 64847 bp long dsDNA genome, which is consistent with virion electron microscopy data. Bacteriophage Gekk3-15 is distinct in its nucleotide and encoded aa sequences from all other sequenced bacteriophage genomes, and may represent a new viral taxon at the genus or subfamily level.

Escherichia coli and its bacteriophages are among the most studied model microorganisms. Bacteriophages for various E. coli strains can typically be easily isolated from environmental sources, and many of these viruses can be harnessed to combat E. coli infections in humans and animals. However, some relatively rare E. coli strains pose significant challenges in finding suitable phages. The uropathogenic strain E. coli UPEC124, isolated from a patient suffering from neurogenic bladder dysfunction, was found to be resistant to all coliphages in our collections, and initial attempts to isolate new phages failed. Using an improved procedure for phage enrichment, we isolated the N4-related phage Mimir124, belonging to the Gamaleyavirus genus, which was able to lyse this “difficult” E. coli strain. Although Mimir124 is a narrow-spectrum phage, it was effective in the individualized treatment of the patient, leading to pathogen eradication. The primary receptor of Mimir124 was the O antigen of the O101 type; consequently, Mimir124-resistant clones were rough (having lost the O antigen). These clones, however, gained sensitivity to some phages that recognize outer membrane proteins as receptors. Despite the presence of nine potential antiviral systems in the genome of the UPEC124 strain, the difficulty in finding effective phages was largely due to the efficient, non-specific cell surface protection provided by the O antigen. These results highlight the importance of an individualized approach to phage therapy, where narrow host-range phages—typically avoided in pre-fabricated phage cocktails—may be instrumental. Furthermore, this study illustrates how integrating genomic, structural, and functional insights can guide the development of innovative therapeutic strategies, paving the way for broader applications of phage therapy in combating multidrug-resistant bacterial pathogens.

A modified method for culturing, concentrating, and purifying phage ϕ24B preparations was developed. In particular, a new lysogenic phage-producing strain lacking flagella was used, induction conditions were optimized, and purification in a sucrose gradient followed by concentration by deposition on a Freon 113 cushion were used. Using this method, a preparation of the Stx-converting bacteriophage ϕ24B was obtained, suitable for CryoEM direct analysis. Based on CryoEM data for this phage, the first primary three-dimensional reconstruction of its virions was performed. The structure of the phage ϕ24B tail is described. It was shown that the adsorption apparatus of this virus is represented by six thin lateral fibrils, and an axial fibril located at the end of the tail. This arrangement of the tail structure is consistent with the previously proposed hypothesis based on analysis of the receptor binding proteins (RBPs) of this bacteriophage.

Bacteria of the genus Aeromonas, especially A. hydrophila and A. veronii are recognized as important fish pathogens that cause significant economic losses in aquaculture. Environmentally friendly bacteriophage-based solutions for the treatment of fish and for the reduction of colonization by pathogenic bacteria in production facilities are currently in high demand. The bacteriophage Gekk3-15 was isolated during a search for novel phage strains potentially suitable for Aeromonas biocontrol applications. Genome sequencing revealed that this virus is a relatively small myovirus with a 64847 bp long dsDNA genome, which is consistent with virion electron microscopy data. Bacteriophage Gekk3-15 is distinct in its nucleotide and encoded aa sequences from all other sequenced bacteriophage genomes, and may represent a new viral taxon at the genus or subfamily level.

Erwinia amylovora bacteriophages are of interest as fire blight control agents. This paper presents data on the biology and molecular genetic properties of 12 E. amylovora tailed bacteriophages. Genome sequences of seven of them were determined and the phages were identified as the representatives of Caudoviricetes; Vequintavirinae, Ounavirinae and Autographiviridae families. The bacteriophages studied were active against E. amylovora, Pantoea agglomerans and Pantoea ananatis strains. The myovirus Hena1 had the narrowest host range lysing 12

The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.

Symbiotic associations are dynamic systems influenced by both intrinsic and extrinsic factors. Here we describe for the first time the developmental and seasonal changes of the funicular bodies in the bryozoan Dendrobeania fruticosa, which are unique temporary organs of cheilostome bryozoans containing prokaryotic symbionts. Histological and ultrastructural studies showed that these organs undergo strong seasonal modification in the White Sea during the ice-free period. Initially (in June) they play a trophic function and support the development of a large population of bacteria. From June to September, both funicular bodies and bacteria show signs of degradation accompanied by development of presumed virus-like particles (VLPs); these self-organize to hollow spheres inside bacteria and are also detected outside of them. Although the destruction of bacteria coincides with the development of VLPs and spheres, the general picture differs considerably from the known instances of bacteriophagy in bryozoans. We broadly discuss potential routes of bacterial infection in Bryozoa and question the hypothesis of vertical transfer, which, although widely accepted in the literature, is contradicted by molecular, morphological and ecological evidence.

Starter culture lysis by Lactococcus lactis bacteriophages is one of the leading causes of the fermentation failure in dairy industry. In the present work we performed a PCR grouping of lactophages identified in 73 samples of milk whey obtained from industrial facilities located in Russia. From these samples we isolated 10 novel L. lactis bacteriophages associated with the fermentation failure in different regions of the Russian Federation. The genomes of these bacteriophage isolates are closely related and similar to the known c2-like phages ( Ceduovirus genus). However, the allelic variants of the receptor recognition proteins found in these genomes were different.

Bacteriophages are often considered as possible agents of biological control of unwanted bacterial populations in medicine, agriculture and food industry. Although the virulent phages can efficiently kill the infected host cells but at the population level phage attack not always leads to the host population collapse but may result in establishment of a more or less stable co-existence. The mechanism of the long-term stabilization of the mixed phage-host cultures is poorly understood. Here we describe bacteriophages VyarbaL and Hena2, the members of the Molineuxvirinae and the Ounavirinae subfamilies, respectively, that are able to form the pseudolysogenic associations (PA) with their host Erwinia amylovora 1/79Sm on solid media. These PAs were stable through multiple passages. The phenomenon of the PA formation between a bacterial culture and bacteriophages decreases the effectiveness of bacteriophage-mediated biological control agents based on lytic bacteriophages.

Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems that recognize former invaders using memorized (captured) pieces of their DNA as pathogen signatures. Mammals possess a vast repertoire of antibodies and T-cell receptor variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells that express matching antibodies or receptors. These cells proliferate to fight the infection and form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. We propose a hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. In this study, we test this hypothesis with the methods of bioinformatics and identify several candidate defense systems based on diversity-generating retroelements.