A multivalent adsorption apparatus explains the broad host range of phage phi92: a comprehensive genomic and structural analysis

Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections, and strains that are resistant to antibiotics are a major problem in treating these infections. Phage therapy is a promising alternative approach that can be used to treat infections caused by polyresistant bacterial strains. In the present study, 16 bacteriophages isolated from sewage and surface water were investigated. Phage host specificity was tested on a collection of 77 UPEC strains. The phages infected 2-44 strains, and 80% of the strains were infected by at least one phage. The susceptible E. coli strains belonged predominantly to the B2 phylogenetic group, including strains of two clones, CC131 and CC73, that have a worldwide distribution. All of the phages belonged to class Caudoviricetes and were identified as members of the families Straboviridae, Autographiviridae, and Drexlerviridae and the genera Kagunavirus, Justusliebigvirus, and Murrayvirus. A phage cocktail composed of six phages - four members of the family Straboviridae and two members of the family Autographiviridae - was prepared, and its antibacterial activity was tested in liquid medium. Complete suppression of bacterial growth was observed after 5-22 hours of cultivation, followed by partial regrowth. At 24 hours postinfection, the cocktail suppressed bacterial growth to 43-92% of control values. Similar results were obtained when testing the activity of the phage cocktail in LB and in artificial urine medium. The results indicate that our phage cocktail has potential to inhibit bacterial growth during infection, and they will therefore be preserved in the national phage bank, serving as valuable resources for therapeutic applications.

Prediction of Klebsiella phage-host specificity at the strain level

Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use. We present PhageHostLearn, a machine learning system that predicts strain-level interactions between receptor-binding proteins and bacterial receptors for Klebsiella phage-bacteria pairs. We evaluate this system both in silico and in the laboratory, in the clinically relevant setting of finding matching phages against bacterial strains. PhageHostLearn reaches a cross-validated ROC AUC of up to 81.8% in silico and maintains this performance in laboratory validation. Our approach provides a framework for developing and evaluating phage-host prediction methods that are useful in practice, which we believe to be a meaningful contribution to the machine-learning-guided development of phage therapeutics and diagnostics.

Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages

Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.

Diverse bacteriophages for biocontrol of ESBL- and AmpC-β-lactamase-producing E. coli

Novel solutions are needed to reduce the risk of transmission of extended spectrum β-lactamase (ESBL) and AmpC β-lactamase producing Escherichia coli (ESBL/AmpC E. coli) from livestock to humans. Given that phages are promising biocontrol agents, a collection of 28 phages that infect ESBL/AmpC E. coli were established. Whole genome sequencing showed that all these phages were unique and could be assigned to 15 different genera. Host range analysis showed that 82% of 198 strains, representing the genetic diversity of ESBL/AmpC E. coli, were sensitive to at least one phage. Identifying receptors used for phage binding experimentally as well as in silico predictions, allowed us to combine phages into two different cocktails with broad host range targeting diverse receptors. These phage cocktails efficiently inhibit the growth of ESBL/AmpC E. coli in vitro, thus suggesting the potential of phages as promising biocontrol agents.

Host range and cell recognition of archaeal viruses

Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.

Phage fibers and spikes: a nanoscale Swiss army knife for host infection

Bacteriophages are being rediscovered as potent agents for medical and industrial applications. However, finding a suitable phage relies on numerous factors, including host specificity, burst size, and infection cycle. The host range of a phage is, besides phage defense systems, initially determined by the recognition and attachment of receptor-binding proteins (RBPs) to the target receptors of susceptible bacteria. RBPs include tail (or occasionally head) fibers and tailspikes. Owing to the potential flexibility and heterogeneity of these structures, they are often overlooked during structural studies. Recent advances in cryo-electron microscopy studies and computational approaches have begun to unravel their structural and fundamental mechanisms during phage infection. In this review, we discuss the current state of research on different phage tail and head fibers, spike models, and molecular mechanisms. These details may facilitate the manipulation of phage-host specificity, which in turn will have important implications for science and society.

An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano

A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.

High niche specificity and host genetic diversity of groundwater viruses

Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.

Prokaryotic virus host prediction with graph contrastive augmentaion

Prokaryotic viruses, also known as bacteriophages, play crucial roles in regulating microbial communities and have the potential for phage therapy applications. Accurate prediction of phage-host interactions is essential for understanding the dynamics of these viruses and their impacts on bacterial populations. Numerous computational methods have been developed to tackle this challenging task. However, most existing prediction models can be constrained due to the substantial number of unknown interactions in comparison to the constrained diversity of available training data. To solve the problem, we introduce a model for prokaryotic virus host prediction with graph contrastive augmentation (PHPGCA). Specifically, we construct a comprehensive heterogeneous graph by integrating virus-virus protein similarity and virus-host DNA sequence similarity information. As the backbone encoder for learning node representations in the virus-prokaryote graph, we employ LGCN, a state-of-the-art graph embedding technique. Additionally, we apply graph contrastive learning to augment the node representations without the need for additional labels. We further conducted two case studies aimed at predicting the host range of multi-species phages, helping to understand the phage ecology and evolution.

Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers

Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.

Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups

BACKGROUND

The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups.

METHODS

Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution.

RESULTS

We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages.

CONCLUSION

The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.

The structure of Klebsiella pneumoniae K108 capsular polysaccharide is similar to Escherichia coli colanic acid

The clinical isolate of Klebsiella pneumoniae 1333/P225 was revealed as containing a KL108 K. pneumoniae K locus for capsule biosynthesis. The gene cluster demonstrated a high level of sequence and arrangement similarity with that of the E. coli colanic acid biosynthesis gene cluster. The KL108 gene cluster includes a gene of WcaD polymerase responsible for joining oligosaccharide K units into capsular polysaccharide (CPS), acetyltransferase, pyruvyltransferasefive and genes for glycosyltransferases (Gtrs), four of which have homologues in genetic units of the colanic acid synthesis. The fifth Gtr is specific to this cluster. The work involved the use of sugar analysis, Smith degradation and one- and two-dimensional ¹H and ¹³C NMR spectroscopy to establish the structure of the K108 CPS. The CPS repetitive K unit is composed of branched pentasaccharide with three monosaccharides in the backbone and a disaccharide side chain. The main chain is the same as for colanic acid but the side chain differs. Two bacteriophages infecting K. pneumoniae strain 1333/P225 were isolated and structural depolymerase genes were determined; depolymerases Dep108.1 and Dep108.2 were cloned, expressed and purified. It was demonstrated that both depolymerases specifically cleave the β-Glcp-(1→4)-α-Fucp linkage between K108 units in the CPS.

Isolation and Characterization of a Novel Phage Collection against Avian-Pathogenic Escherichia coli

The increase in antibiotic-resistant avian-pathogenic Escherichia coli (APEC), the causative agent of colibacillosis in poultry, warrants urgent research and the development of alternative therapies. This study describes the isolation and characterization of 19 genetically diverse, lytic coliphages, 8 of which were tested in combination for their efficacy in controlling in ovo APEC infections. Genome homology analysis revealed that the phages belong to nine different genera, one of them being a novel genus (Nouzillyvirus). One phage, REC, was derived from a recombination event between two Phapecoctavirus phages (ESCO5 and ESCO37) isolated in this study. Twenty-six of the 30 APEC strains tested were lysed by at least one phage. Phages exhibited varying infectious capacities, with narrow to broad host ranges. The broad host range of some phages could be partially explained by the presence of receptor-binding protein carrying a polysaccharidase domain. To demonstrate their therapeutic potential, a phage cocktail consisting of eight phages belonging to eight different genera was tested against BEN4358, an APEC O2 strain. In vitro, this phage cocktail fully inhibited the growth of BEN4358. In a chicken lethality embryo assay, the phage cocktail enabled 90% of phage-treated embryos to survive infection with BEN4358, compared with 0% of nontreated embryos, indicating that these novel phages are good candidates to successfully treat colibacillosis in poultry. IMPORTANCE Colibacillosis, the most common bacterial disease affecting poultry, is mainly treated by antibiotics. Due to the increased prevalence of multidrug-resistant avian-pathogenic Escherichia coli, there is an urgent need to assess the efficacy of alternatives to antibiotherapy, such as phage therapy. Here, we have isolated and characterized 19 coliphages that belong to nine phage genera. We showed that a combination of 8 of these phages was efficacious in vitro to control the growth of a clinical isolate of E. coli. Used in ovo, this phage combination allowed embryos to survive APEC infection. Thus, this phage combination represents a promising treatment for avian colibacillosis.

Function of the bacteriophage P2 baseplate central spike Apex domain in the infection process

The contractile tail of bacteriophage P2 functions to drive the tail tube across the outer membrane of its host bacterium, a prerequisite event for subsequent translocation of phage genomic DNA into the host cell. The tube is equipped with a spike-shaped protein (product of P2 gene V , gpV or Spike) that contains a membrane-attacking Apex domain carrying a centrally positioned Fe ion. The ion is enclosed in a histidine cage that is formed by three symmetry-related copies of a conserved HxH (histidine, any residue, histidine) sequence motif. Here, we used solution biophysics and X-ray crystallography to characterize the structure and properties of Spike mutants in which the Apex domain was either deleted or its histidine cage was either destroyed or replaced with a hydrophobic core. We found that the Apex domain is not required for the folding of full-length gpV or its middle intertwined β-helical domain. Furthermore, despite its high conservation, the Apex domain is dispensable for infection in laboratory conditions. Collectively, our results show that the diameter of the Spike but not the nature of its Apex domain determines the efficiency of infection, which further strengthens the earlier hypothesis of a drill bit-like function of the Spike in host envelope disruption.

Bacteriophages as Biotechnological Tools

Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.

Functionalized biological metal-organic framework with nanosized coronal structure and hierarchical wrapping pattern for enhanced targeting therapy

Inefficient tumor-targeted delivery and uncontrolled drug release are the major obstacles in cancer chemotherapy. Herein, inspired by the targeting advantage of coronavirus from its size and coronal structure, a coronal biological metal-organic framework nanovehicle (named as corona-BioMOF) is constructed for improving its precise cancer targeting ability. The designed corona-BioMOF is constructed as the carriers-encapsulated carrier model by inner coated with abundant protein-nanocaged doxorubicin particles and external decorated with high-affinity apoferritin proteins to form the spiky surface for constructing the specific coronal structure. The corona-BioMOF shows a higher affinity and an enhanced targeting ability towards receptor-positive cancer cells compared to that of MOF-drug composites without spiky surface. It also exhibits the hierarchical wrapping pattern-endowed controlled lysosome-specific drug release and remarkable tumor lethality in vivo. Moreover, water-induced surface defect-based protein handle mechanism is first proposed to shape the coronal-BioMOF. This work will provide a better inspiration for nanovehicle construction and be broadly useful for clinical precision nanomedicine.

Phage-encoded carbohydrate-interacting proteins in the human gut

In the human gastrointestinal tract, the gut mucosa and the bacterial component of the microbiota interact and modulate each other to accomplish a variety of critical functions. These include digestion aid, maintenance of the mucosal barrier, immune regulation, and production of vitamins, hormones, and other metabolites that are important for our health. The mucus lining of the gut is primarily composed of mucins, large glycosylated proteins with glycosylation patterns that vary depending on factors including location in the digestive tract and the local microbial population. Many gut bacteria have evolved to reside within the mucus layer and thus encode mucus-adhering and -degrading proteins. By doing so, they can influence the integrity of the mucus barrier and therefore promote either health maintenance or the onset and progression of some diseases. The viral members of the gut - mostly composed of bacteriophages - have also been shown to have mucus-interacting capabilities, but their mechanisms and effects remain largely unexplored. In this review, we discuss the role of bacteriophages in influencing mucosal integrity, indirectly via interactions with other members of the gut microbiota, or directly with the gut mucus via phage-encoded carbohydrate-interacting proteins. We additionally discuss how these phage-mucus interactions may influence health and disease states.

High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.

The Specific Capsule Depolymerase of Phage PMK34 Sensitizes Acinetobacter baumannii to Serum Killing

The rising antimicrobial resistance is particularly alarming for Acinetobacter baumannii, calling for the discovery and evaluation of alternatives to treat A. baumannii infections. Some bacteriophages produce a structural protein that depolymerizes capsular exopolysaccharide. Such purified depolymerases are considered as novel antivirulence compounds. We identified and characterized a depolymerase (DpoMK34) from Acinetobacter phage vB_AbaP_PMK34 active against the clinical isolate A. baumannii MK34. In silico analysis reveals a modular protein displaying a conserved N-terminal domain for anchoring to the phage tail, and variable central and C-terminal domains for enzymatic activity and specificity. AlphaFold-Multimer predicts a trimeric protein adopting an elongated structure due to a long α-helix, an enzymatic β-helix domain and a hypervariable 4 amino acid hotspot in the most ultimate loop of the C-terminal domain. In contrast to the tail fiber of phage T3, this hypervariable hotspot appears unrelated with the primary receptor. The functional characterization of DpoMK34 revealed a mesophilic enzyme active up to 50 °C across a wide pH range (4 to 11) and specific for the capsule of A. baumannii MK34. Enzymatic degradation of the A. baumannii MK34 capsule causes a significant drop in phage adsorption from 95% to 9% after 5 min. Although lacking intrinsic antibacterial activity, DpoMK34 renders A. baumannii MK34 fully susceptible to serum killing in a serum concentration dependent manner. Unlike phage PMK34, DpoMK34 does not easily select for resistant mutants either against PMK34 or itself. In sum, DpoMK34 is a potential antivirulence compound that can be included in a depolymerase cocktail to control difficult to treat A. baumannii infections.

Enterococcus faecalis Bacteriophage vB_EfaS_efap05-1 Targets the Surface Polysaccharide and ComEA Protein as the Receptors

Enterococcus faecalis is a Gram-positive opportunistic pathogen that causes nosocomial infections in humans. Due to the growing threat of antibiotic resistance of E. faecalis, bacteriophage therapy is a promising option for treating of E. faecalis infection. Here, we characterized a lytic E. faecalis bacteriophage vB_EfaS_efap05-1 with a dsDNA genome of 56,563 bp. Phage vB_EfaS_efap05-1 had a prolate head and a tail, and belongs to Saphexavirus which is a member of Siphoviridae. Efap05-1 uses either surface polysaccharide or membrane protein ComEA as the receptor because the mutation of both genes (ComEA and UDP-glucose 4-epimerase galE) prevents phage adsorption and leads to phage resistance, and complementation of ComEA or galE could recover its phage sensitivity. Our results provided a comprehensive analysis of a new E. faecalis phage and suggest efap05-1 as a potential antimicrobial agent.

Bacteriophage therapy as an alternative biocontrol against emerging multidrug resistant E. coli in broilers

Avian pathogenic Escherichia coli (APEC) is considered a severe issue to both poultry business and health of the general public. In that context, 50 samples from 250 diseased broiler chickens in 10 chicken farms were employed to Escherichia coli isolation. Microbiological techniques were employed to detect isolates of E. coli from 250 diseased broiler chickens which were examined by antimicrobial susceptibility profiles against 11 antimicrobial agents using disc diffusion technique as well as their biofilm forming capacity were detected. In addition to, study the isolation and purification of phages based on spot technique to verify that lytic phages are present in E. coli isolates and plaque assay for titration of bacteriophages. In the present research, we also looked at the ability of bacteriophages to inhibit and dissolve previously formed biofilms by E. coli O78 isolate. Moreover, experimental testing of E. coli O78 bacteriophages for colibacillosis prevention and control in one day old broiler chicks were done. The obtained results showed that twenty-six E. coli isolates out of 50 examined samples were isolated (10.4%). The most prevalent serotypes were O78, O121:H7, O146:H2, O124, O113:H4, O112:H2, O1:H7, O55:H7, O2:H6, O91:H21, O26:H11. Antibiogram results demonstrated the resistance of E. coli isolates with high percentage 100% were against, Ampicillin, Amoxicillin and Tetracycline. Biofilm quantification analysis showed that 24/26 (92.3%) isolates were considered biofilm producer isolates. The characterization and the lytic activity of bacteriophage were performed based on Transmission electron microscopy and showed the greatest lytic activity against the evaluated host strains with effective activity at concentration of 10⁷ at 24 h and strong significant reduction of the established E. coli O 78 biofilm within 12 h. The result of experimental infection showed that the performance indicators of phage in treated and challenged group showed high significant increase in body weight, weight gain and improved FCR than infected –antibiotic treated and infected bacteriophage and antibiotic treated. Total viable cell counts of E. coli in the lungs of birds revealed that there is highly significant difference between the six groups count results. We concluded that phage therapy found to be an attractive option to prevent and control multidrug resistant colibacillosis in broilers.

Novel Klebsiella pneumoniae virulent bacteriophage KPPK108.1 capable of infecting the K108 serotype strains

Multidrug-resistant Klebsiella pneumoniae strains are one of the major causes of nosocomial infections caused by the antibiotic-resistant bacteria. There are different options for dealing with this threat, among which is the clinical application of bacteriophages. The study was aimed to isolate and describe a virulent bactriophage, having the potential for therapeutic use. The standard phage biology and bioinformatic methods were used, which included the advanced techniques for protein structure prediction (AlphaFold software), and electron microscopy. The virulent podovirus KPPK108.1, being the member of genus Drulisvirus, which is able to specifically infect the K. pneumoniae strains with the KL108 type capsular polysaccharide, has been isolated from the wastewater. The sequence of the bactriophage genome has been defined, the biological properties have been investigated, and the genetic features have been described.

Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

PHIDA: A High Throughput Turbidimetric Data Analytic Tool to Compare Host Range Profiles of Bacteriophages Isolated Using Different Enrichment Methods

Bacteriophages are viruses that infect bacteria and are present in niches where bacteria thrive. In recent years, the suggested application areas of lytic bacteriophage have been expanded to include therapy, biocontrol, detection, sanitation, and remediation. However, phage application is constrained by the phage's host range-the range of bacterial hosts sensitive to the phage and the degree of infection. Even though phage isolation and enrichment techniques are straightforward protocols, the correlation between the enrichment technique and host range profile has not been evaluated. Agar-based methods such as spotting assay and efficiency of plaquing (EOP) are the most used methods to determine the phage host range. These methods, aside from being labor intensive, can lead to subjective and incomplete results as they rely on qualitative observations of the lysis/plaques, do not reflect the lytic activity in liquid culture, and can overestimate the host range. In this study, phages against three bacterial genera were isolated using three different enrichment methods. Host range profiles of the isolated phages were quantitatively determined using a high throughput turbidimetric protocol and the data were analyzed with an accessible analytic tool "PHIDA". Using this tool, the host ranges of 9 Listeria, 14 Salmonella, and 20 Pseudomonas phages isolated with different enrichment methods were quantitatively compared. A high variability in the host range index (HRi) ranging from 0.86-0.63, 0.07-0.24, and 0.00-0.67 for Listeria, Salmonella, and Pseudomonas phages, respectively, was observed. Overall, no direct correlation was found between the phage host range breadth and the enrichment method in any of the three target bacterial genera. The high throughput method and analytics tool developed in this study can be easily adapted to any phage study and can provide a consensus for phage host range determination.

Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages

Phages belonging to the Ackermannviridae family encode up to four tail spike proteins (TSPs), each recognizing a specific receptor of their bacterial hosts. Here, we determined the TSPs diversity of 99 Ackermannviridae phages by performing a comprehensive in silico analysis. Based on sequence diversity, we assigned all TSPs into distinctive subtypes of TSP1, TSP2, TSP3 and TSP4, and found each TSP subtype to be specifically associated with the genera (Kuttervirus, Agtrevirus, Limestonevirus, Taipeivirus) of the Ackermannviridae family. Further analysis showed that the N-terminal XD1 and XD2 domains in TSP2 and TSP4, hinging the four TSPs together, are preserved. In contrast, the C-terminal receptor binding modules were only conserved within TSP subtypes, except for some Kuttervirus TSP1s and TSP3s that were similar to specific TSP4s. A conserved motif in TSP1, TSP3 and TSP4 of Kuttervirus phages may allow recombination between receptor binding modules, thus altering host recognition. The receptors for numerous uncharacterized phages expressing TSPs in the same subtypes were predicted using previous host range data. To validate our predictions, we experimentally determined the host recognition of three of the four TSPs expressed by kuttervirus S117. We confirmed that S117 TSP1 and TSP2 bind to their predicted host receptors, and identified the receptor for TSP3, which is shared by 51 other Kuttervirus phages. Kuttervirus phages were thus shown encode a vast genetic diversity of potentially exchangeable TSPs influencing host recognition. Overall, our study demonstrates that comprehensive in silico and host range analysis of TSPs can predict host recognition of Ackermannviridae phages.

How Broad Is Enough: The Host Range of Bacteriophages and Its Impact on the Agri-Food Sector

Novel bacteriophages (phages) possessing a broad host range are consistently and routinely reported, yet there is presently no consensus on the definition of “broad host range.” As phages are increasingly being used in the development of methods for the detection and biocontrol of human pathogens, it is important to address the limitations associated with the host range. For instance, unanticipated host range breadth may result in the detection of nonpathogenic targets, thereby increasing the false-positive rate. Moreover, a broad host range is generally favored in biocontrol applications despite the risk of undesirable ancillary effects against nontarget species. Here, we discuss the research progress, applications, and implications of broad host range phages with a focus on tailed broad host range phages infecting human pathogens of concern in the Agri-Food sector.

A Novel Broad Host Range Phage Infecting Alteromonas

Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.

Engineering the Modular Receptor-Binding Proteins of Klebsiella Phages Switches Their Capsule Serotype Specificity

The high specificity of bacteriophages is driven by their receptor-binding proteins (RBPs). Many Klebsiella bacteriophages target the capsular exopolysaccharide as the receptor and encode RBPs with depolymerase activity. The modular structure of these RBPs with an N-terminal structural module to attach the RBP to the phage tail, and a C-terminal specificity module for exopolysaccharide degradation, supports horizontal transfer as a major evolutionary driver for Klebsiella phage RBPs. We mimicked this natural evolutionary process by the construction of modular RBP chimeras, exchanging N-terminal structural modules and C-terminal specificity modules. All chimeras strictly follow the capsular serotype specificity of the C-terminal module. Transplanting chimeras with a K11 N-terminal structural RBP module in a Klebsiella phage K11 scaffold results in a capsular serotype switch and corresponding host range modification of the synthetic phages, demonstrating that horizontal transfer of C-terminal specificity modules offers Klebsiella phages an evolutionary highway for rapid adaptation to new capsular serotypes.

Making sense of virus size and the tradeoffs shaping viral fitness

Viruses span an impressive size range, with genome length varying a thousandfold and virion volume nearly a millionfold. For cellular organisms the scaling of traits with size is a pervasive influence on ecological processes, but whether size plays a central role in viral ecology is unknown. Here, we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We outline hypotheses within a quantitative framework, and analyse data where available, to consider how size affects the primary components of viral fitness. We argue that larger viruses have fewer offspring per infection and slower contact rates with host cells, but a larger genome tends to increase infection efficiency, broaden host range, and potentially increase attachment success and decrease decay rate. These countervailing selective pressures may explain why a breadth of sizes exist and even coexist when infecting the same host populations. Oligotrophic ecosystems may be enriched in "giant" viruses, because environments with resource-limited phagotrophs at low concentrations may select for broader host range, better control of host metabolism, lower decay rate and a physical size that mimics bacterial prey. Finally, we describe where further research is needed to understand the ecology and evolution of viral size diversity.

Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches

Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.

Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichiacoli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae,Drexlerviridae,Chaseviridae,Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.

Phage S144, A New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii

Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent.

Fitness Trade-Offs Resulting from Bacteriophage Resistance Potentiate Synergistic Antibacterial Strategies

Bacteria that cause life-threatening infections in humans are becoming increasingly difficult to treat. In some instances, this is due to intrinsic and acquired antibiotic resistance, indicating that new therapeutic approaches are needed to combat bacterial pathogens. There is renewed interest in utilizing viruses of bacteria known as bacteriophages (phages) as potential antibacterial therapeutics. However, critics suggest that similar to antibiotics, the development of phage-resistant bacteria will halt clinical phage therapy. Although the emergence of phage-resistant bacteria is likely inevitable, there is a growing body of literature showing that phage selective pressure promotes mutations in bacteria that allow them to subvert phage infection, but with a cost to their fitness. Such fitness trade-offs include reduced virulence, resensitization to antibiotics, and colonization defects. Resistance to phage nucleic acid entry, primarily via cell surface modifications, compromises bacterial fitness during antibiotic and host immune system pressure. In this minireview, we explore the mechanisms behind phage resistance in bacterial pathogens and the physiological consequences of acquiring phage resistance phenotypes. With this knowledge, it may be possible to use phages to alter bacterial populations, making them more tractable to current therapeutic strategies.

Genome-wide screens reveal Escherichia coli genes required for growth of T1-like phage LL5 and V5-like phage LL12

The host factor requirements of phages and mechanisms of mutational phage insensitivity must be characterized for rational design of phage cocktails. To characterize host dependencies of two novel Escherichia coli phages, the T1-like siphophage LL5 and the V5-like myophage LL12, forward genetic screens were conducted against the Keio collection, a library of single non-essential gene deletions in E. coli str. BW25113. These screens and subsequent experiments identified genes required by phages LL5 and LL12. E. coli mutants deficient in heptose II and the phosphoryl substituent of heptose I of the inner core lipopolysaccharide (LPS) were unable to propagate phage LL5, as were mutants deficient in the outer membrane protein TolC. Mutants lacking glucose I of the LPS outer core failed to propagate LL12. Two additional genes encoding cytoplasmic chaperones, PpiB and SecB, were found to be required for efficient propagation of phage LL5, but not LL12. This screening approach may be useful for identifying host factors dependencies of phages, which would provide valuable information for their potential use as therapeutics and for phage engineering.

Broad-host-range Salmonella bacteriophage STP4-a and its potential application evaluation in poultry industry

Salmonella is regarded as the predominant cause of foodborne illnesses worldwide, and the increase of these antimicrobial-resistant strains makes it more difficult to prevent. On this occasion, bacteriophages (phages) stand out as an alternative biocontrol agent with high efficiency and low mutation rates. Salmonella phages have confronted challenges to counteract with more than 2,500 serovars of Salmonella spp. and overcome the universality of antibiotics to different species, and thus, broad-host-range phages infecting Salmonella spp. are urgently required to realize precise poultry treatment or clinical therapy. First, phage STP4-a was screened to have a broad host range through bioinformatics analysis, and then the host range assay proved that phage STP4-a could inhibit 88 out of 91 Salmonella strains. Then, in silico analysis excluded the possibility of phage STP4-a possessing any known lysogeny factors, toxins, pathogen-related genes, or foodborne allergens, and oral toxicity studies further ensured the safety of unknown factors or suspected risks. In addition, strong inhibition effects of phage STP4-a were seen on both single Salmonella strain and multiple Salmonella strains in vitro, reducing 3-5 log in 30 min. Phage STP4-a could survive and keep more than 50% activity in simulated stomach or intestine environments in vitro. In terms of antimicrobial activities in chickens, pretreatment with phage STP4-a was the most efficient approach to Salmonella biocontrol, non-detectable in feces during the 14-day experimental period. Therefore, phage STP4-a was an extremely broad-host-range and safe biocontrol agent, performing its potential as a food additive or therapeutic drug in poultry industry.

The arms race between bacteria and their phage foes

Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.

Modeling the Architecture of Depolymerase-Containing Receptor Binding Proteins in Klebsiella Phages

Klebsiella pneumoniae carries a thick polysaccharide capsule. This highly variable chemical structure plays an important role in its virulence. Many Klebsiella bacteriophages recognize this capsule with a receptor binding protein (RBP) that contains a depolymerase domain. This domain degrades the capsule to initiate phage infection. RBPs are highly specific and thus largely determine the host spectrum of the phage. A majority of known Klebsiella phages have only one or two RBPs, but phages with up to 11 RBPs with depolymerase activity and a broad host spectrum have been identified. A detailed bioinformatic analysis shows that similar RBP domains repeatedly occur in K. pneumoniae phages with structural RBP domains for attachment of an RBP to the phage tail (anchor domain) or for branching of RBPs (T4gp10-like domain). Structural domains determining the RBP architecture are located at the N-terminus, while the depolymerase is located in the center of protein. Occasionally, the RBP is complemented with an autocleavable chaperone domain at the distal end serving for folding and multimerization. The enzymatic domain is subjected to an intense horizontal transfer to rapidly shift the phage host spectrum without affecting the RBP architecture. These analyses allowed to model a set of conserved RBP architectures, indicating evolutionary linkages.

The "fighting wisdom and bravery" of tailed phage and host in the process of adsorption

In the process of bacteriophage and bacteria struggle, adsorption is the key factor to determine who is the winner. In this paper, the molecular mechanism of tailed bacteriophage recognition and adsorption to host and the strategy of "fighting wisdom and courage" between them are reviewed.

Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail

Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.

Two Phages of the Genera Felixounavirus Subjected to 12 Hour Challenge on Salmonella Infantis Showed Distinct Genotypic and Phenotypic Changes

Salmonella Infantis is considered in recent years an emerging Salmonella serovar, as it has been associated with several outbreaks and multidrug resistance phenotypes. Phages appear as a possible alternative strategy to control Salmonella Infantis (SI). The aims of this work were to characterize two phages of the Felixounavirus genus, isolated using the same strain of SI, and to expose them to interact in challenge assays to identify genetic and phenotypic changes generated from these interactions. These two phages have a shared nucleotide identity of 97% and are differentiated by their host range: one phage has a wide host range (lysing 14 serovars), and the other has a narrow host range (lysing 6 serovars). During the 12 h challenge we compared: (1) optical density of SI, (2) proportion of SI survivors from phage-infected cultures, and (3) phage titer. Isolates obtained through the assays were evaluated by efficiency of plating (EOP) and by host-range characterization. Genomic modifications were characterized by evaluation of single nucleotide polymorphisms (SNPs). The optical density (600 nm) of phage-infected SI decreased, as compared to the uninfected control, by an average of 0.7 for SI infected with the wide-host-range (WHR) phage and by 0.3 for SI infected with the narrow-host-range (NHR) phage. WHR phage reached higher phage titer (7 × 1011 PFU/mL), and a lower proportion of SI survivor was obtained from the challenge assay. In SI that interacted with phages, we identified SNPs in two genes (rfaK and rfaB), which are both involved in lipopolysaccharide (LPS) polymerization. Therefore, mutations that could impact potential phage receptors on the host surface were selected by lytic phage exposure. This work demonstrates that the interaction of Salmonella phages (WHR and NHR) with SI for 12 h in vitro leads to emergence of new phenotypic and genotypic traits in both phage and host. This information is crucial for the rational design of phage-based control strategies.

Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells

Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.

Molecular and Evolutionary Determinants of Bacteriophage Host Range

The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.

Identification and characterization of new broad host-range rV5-like coliphages C203 and P206 directed against enterobacteria

We isolated and characterized two novel rV5-like lytic bacteriophages from independently collected food samples. Nucleotide sequence analysis revealed that these phages have linear double-stranded DNA genomes comprising 138,073 bp with 213 CDS and 5 tRNA genes. The two genomes contain completely identical nucleotide sequence, albeit there is a 10,718 bp-long shift in the sequence. The GC content of the phage genomes was 43.7% and they showed high general homology to rV5-like phages. The new phages were termed C203 and P206. The genome of both phages contains a unique ORF that encodes for a putative phage homing endonuclease. The phage produced clear plaques with a burst size of approx. 1000 viral particles and a latent period of 60 min. Morphological investigation indicated that the new phages are members of the family Myoviridae with an approximate head length of 85 nm, tail length of 75 nm, and a head width of 96 nm. C203 and P206 exhibit a broad and uniform host range, which included enterohemorrhagic Escherichia coli strains of serogroup O157, multi drug resistant (MDR) E. coli strains of various sero- and pathotypes, and both Shigella sonnei and S. dysenteriae strains. C203 and P206 both effectively reduced the number of living EHEC O157:H7 Sakai in experimentally inoculated minced meat. The same broad host range, the lack of any virulence related genes, the stability and its short latent period suggest that these newly found phages could be suitable candidates as a bio-control agents against food-borne pathogenic Enterobacteria.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.

The human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.

Cryo-EM reconstruction of Type VI secretion system baseplate and sheath distal end

The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate assembles around a tip complex with associated effectors and connects to the membrane complex by TssK. The baseplate assembly initiates sheath-tube polymerization, which in some organisms requires TssA. Here, we analyzed both ends of isolated non-contractile Vibrio cholerae sheaths by cryo-electron microscopy. Our analysis suggests that the baseplate, solved to an average 8.0 Å resolution, is composed of six subunits of TssE/F₂/G and the baseplate periphery is decorated by six TssK trimers. The VgrG/PAAR tip complex in the center of the baseplate is surrounded by a cavity, which may accommodate up to ~450 kDa of effector proteins. The distal end of the sheath, resolved to an average 7.5 Å resolution, shows sixfold symmetry; however, its protein composition is unclear. Our structures provide an important step toward an atomic model of the complete T6SS assembly.