Phage Research Articles

RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses

RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts.

Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity-proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.

Explorations of Post-DLI Low-Dose Cyclophosphamide for Preventing Severe aGVHD

Background Relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a serious life-threatening complication. The granulocyte colony-stimulated factor mobilized donor lymphocyte infusions (gDLI) combined with chemotherapy is currently a commonly used treatment method. Nevertheless, gDLI may cause so severe acute graft-versus-host disease (aGVHD) as to impact prognosis. Posttransplant cyclophosphamide (PTCy) has been the backbone for GVHD prophylaxis by inducing tolerance to minor histocompatibility antigens in recipients, while the application of post-gDLI low-dose cyclophosphamide (PDCy) for GVHD prophylaxis has not yet been attempted. Methods To explore this possibility, a retrospective study was conducted. 20 patients relapsing after HSCT were administered 20 mg/kg/d cyclophosphamide（Cy）on day 3 (for matched related transplantation) or on days 3 and 4 (for haplo-identical or unrelated transplantation) after gDLI to prevent aGVHD (the PDCy group). Furthermore, through propensity score matching, 58 matched controls received other (for HID and URD) or no (for MSD) immunosuppressive therapy for GVHD prophylaxis (the Non-Cy group). Patients from the PDCy and the Non-Cy group were matched by transplantation type, CD3+ T cell counts, and age and gender of recipients and donors. An MRD complete response was undetectable MRD lower than 0.01% with qPCR, and a reduction of at least one-log fold in MRD load post gDLI was defined as an MRD response. Results The PDCy group comprised 9 and 11 men and women, respectively, with a median age of 38 (34-52, IQR) years. The Non-Cy group comprised 34 and 24 men and women, respectively, with a median age of 40 (29-47, IQR) years. The infused CD3+T cell dose in the PDCy and Non-Cy group was 3.0 *10^7/kg and 2.9 *10^7/kg, respectively (p=1.0). The interval between HSCT and gDLI was longer in the PDCy group when compared to the Non-Cy group (30.8 vs 6.5 months, p<0.01). And first recurrence accounted for a higher percentage in the Non-Cy group (93% vs 45%, p<0.01). Other transplant- and DLI-specific data did not exhibit any significant difference between the groups. With a median follow-up of 4.8 (0-37.1) months, the PDCy group had lower cumulative incidence of severe aGVHD (III-IV, 5% vs 31%, p=0.02; II-IV, 25% vs 52%, p=0.04, figure 1A, B), but no significant differences existed in 4-month OS (64% vs 59%, p=0.51, figure 1E) and NRM (20% vs 19%, p=0.5, figure 1D). Among 49 patients undergoing salvage treatment (PDCy group, n=16; Non-Cy group, n=33), there was no statistical difference in 4-month CIR (20% vs 47%, p=0.11, figure 1C) and rates of objective response (PR+CR, 68.8% vs 54.5%, p=0.6). Among 29 patients undergoing preemptive treatment (PDCy group, n=4; Non-Cy group, n=25), there was no statistical difference in the rates of MRD complete response (25% vs 42%, p=1) and MRD response (25% vs 50%, p=0.6) between the PDCy group and the Non-Cy group. The PDCy regimen didn't increase the incidence of severe bacterial infection (45% vs 33%, p=0.3), bacteremia (25% vs 16%, p=0.11), fungus infection (20% vs 29.3%, p=0.4), virus infection (5% vs 19%, p=0.1), hemorrhagic cystitis (n=1 vs n=1), and cardiac events (n=0 vs n=0). Conclusions In conclusion, on the premise of safety, the PDCy regimen could effectively protest against severe aGVHD after gDLI while preserving therapeutic response rates. However, the research results still require verification through longer follow-up and large prospective randomized studies.

Phage Therapy-Challenges, Opportunities and Future Prospects.

The increasing drug resistance of bacteria to commonly used antibiotics creates the need to search for and develop alternative forms of treatment. Phage therapy fits this trend perfectly. Phages that selectively infect and kill bacteria are often the only life-saving therapeutic option. Full legalization of this treatment method could help solve the problem of multidrug-resistant infectious diseases on a global scale. The aim of this review is to present the prospects for the development of phage therapy, the ethical and legal aspects of this form of treatment given the current situation of such therapy, and the benefits of using phage products in persons for whom available therapeutic options have been exhausted or do not exist at all. In addition, the challenges faced by this form of therapy in the fight against bacterial infections are also described. More clinical studies are needed to expand knowledge about phages, their dosage, and a standardized delivery system. These activities are necessary to ensure that phage-based therapy does not take the form of an experiment but is a standard medical treatment. Bacterial viruses will probably not become a miracle cure-a panacea for infections-but they have a chance to find an important place in medicine.

Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure

An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.

Detection and Quantification of Bacteriophages in Wastewater Samples by Culture and Molecular Methods.

Bacteriophages are promising tools for the detection of fecal pollution in water bodies and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages are perfect surrogates for the study of the fate and transport of enteric viruses, generally better than any other group of indicators.Different groups of bacteriophages, such as somatic coliphages, F-specific RNA bacteriophages, and bacteriophages infecting selected strains of Bacteroides, have been comprehensively tested as indicators of fecal pollution. Somatic coliphages and F-specific RNA bacteriophages can be used as indicators of general fecal contamination, whereas Bacteroides phages can be used to detect a particular fecal source, for instance, human, bovine, porcine, or poultry fecal contamination.Feasible and cost-effective protocols standardized by the International Standardization Organization and the United States Environmental Protection Agency for the detection of infectious bacteriophages belonging to these three groups are available. Molecular methods for the detection of some particular phages have also been developed. Here we introduce those methods for the detection, enumeration, and isolation of bacteriophages in wastewater samples.

Bacterial cGAS senses a viral RNA to initiate immunity

Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. Since mammalian oligoadenylate synthetases also bind viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.

Discovery of tryptanthrin analogues bearing F and piperazine moieties as novel phytopathogenic antibacterial and antiviral agents.

Plant bacterial infections and plant viruses seriously affect the yield and quality of crops. Based on the various activities of tryptanthrin, a series of tryptanthrin analogues bearing F and piperazine moieties were designed, synthesized, and evaluated for their biological activities against three plant bacteria and tobacco mosaic virus (TMV). Bioassay results indicated that compounds 6a-6l displayed excellent antibacterial activities in vitro and 6a-6c and 6g exhibited better antiviral activities against TMV than commercial ribavirin. In particular, 6b showed the most effect on Xanthomonas oryzae pv. oryzae (Xoo) with a half-maximal effective concentration (EC50 ) of 1.26 μg mL-1 , compared with the commercial pesticide bismerthiazol (BT; EC50 = 34.3 μg mL-1 ) and thiodiazole copper (TC; EC50 = 73.3 μg mL-1 ). Meanwhile, 6a also had the best antiviral activity at 500 μg mL-1 for curative, protection, and inactivation purposes, compared with ribavirin in vivo. Compound 6b could cause changes in bacterial morphology, induce the accumulation of reactive oxygen species, promote apoptosis of bacterial cells, inhibit the formation of biofilm, and block the growth of Xoo cells. Proteomic analysis revealed major differences in the bacterial secretory system pathways T2SS and T6SS, which inhibited membrane transport. Molecular docking revealed that 6a and 6g could interact with TMV coat protein preventing virus assembly. These results suggest that tryptanthrin analogues bearing F and piperazine moieties could be promising candidate agents for antibacterial and antiviral use in agricultural production. © 2023 Society of Chemical Industry.

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top‐down proteomic analysis

RationalePathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes.MethodsProtein biomarkers of two strains of Shiga toxin–producing Escherichia coli (STEC) were identified using antibiotic induction, matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF‐TOF) tandem mass spectrometry (MS/MS) with post‐source decay (PSD), top‐down proteomic (TDP) analysis, and plasmid sequencing. Alphafold2 was also used to compare predicted in silico structures of the identified proteins to prominent fragment ions generated using MS/MS‐PSD. Strain samples were also analyzed with and without chemical reduction treatment to detect the attachment of pendant groups bound by thioester or disulfide bonds.ResultsShiga toxin was detected and/or identified in both STEC strains. For the first time, we also identified the osmotically inducible protein (OsmY) whose sequence unexpectedly had two forms: a full and a truncated sequence. The truncated OsmY terminates in the middle of an α‐helix as determined by Alphafold2. A plasmid‐encoded colicin immunity protein was also identified with and without attachment of an unidentified cysteine‐bound pendant group (~307 Da). Plasmid sequencing confirmed top‐down analysis and the identification of a promoter upstream of the immunity gene that is activated by antibiotic induction, that is, SOS box.ConclusionsTDP analysis, coupled with other techniques (e.g., antibiotic induction, chemical reduction, plasmid sequencing, and in silico protein modeling), is a powerful tool to identify proteins (and their modifications), including prophage‐ and plasmid‐encoded proteins, produced by pathogenic microorganisms.

THE REVIEW ARTICLE OF BACTERIOPHAGE THERAPY AND ANTIBIOTIC RESISTANCE

Antibiotic resistance is now one of the biggest challenges which has arised in the medical world. Scientist are working day and night non stop to deal with this challenge. Antibiotic resistance is when the bacteria develop characteristics and modify in its features that it is no longer affected bythe antibiotic which once worked and were effective on them. Resistance occur due to mutation of the bacteria were the bacteria modifies the antibiotic target site that when exposed to antibiotics it can no longer get affected, also by reduced permeability, the bacterial wall becomes hard and impermeable to antibiotic agents. The antibiotic resistance has read to over production and development of different antibiotics which becomes useless in a shortperiod of time , so energy resources and financial resource are lost in the way but without giving permanent solution. To deal with the problem of antibiotic resistance alternative methods for treatment of bacterial infection are developed, the development read to the rediscovery of bacteriophage therapy, which treat those bacterial infections which are antibiotic resistance .Bacteriophage therapy is the use of bacterial viruses to kill the bacteria. Phagesare the viruses that attacks specific target bacteria and burst it or kill it. The bacteriophage attack and attaches to the bacterium, then draw its DNA into the cell and destroy the bacterium to function or replicate. The bacteriophage can be used to treat different deadly bacterial infections , research are still going on to improve the effectiveness of the bacteriophage so that it can be the permanent solution to antibiotic resistance and the treatment to deadly bacterial infections. greek word which means ‘to eat’ ,then bacteriophage means to eat bacteria , bacteriophage are bacterial viruses which attacks the bacterial cells and kills or breakthe bacterium. Bacteriophages are very highly specific, theyonly affect the bacteria of a specific strain. This specificity and killing capability makesthem enermies of bacteria.

MS2 Virus-like Particles as a Versatile Peptide Presentation Platform: Insights into the Deterministic Abilities for Accommodating Heterologous Peptide Lengths.

Virus-like particles (VLPs) are nanostructures with the potential to present heterologous peptides at high density, thereby triggering heightened immunogenicity. RNA bacteriophage MS2 VLPs are a compelling delivery platform among them. However, a notable hurdle arises from the immune response toward MS2 coat protein, swiftly eliminating subsequent vaccinations via the same vector. Although larger inserts effectively mask carrier epitopes, current research predominantly focuses on displaying short conserved peptides (<30 aa). A systematic evaluation regarding the deterministic ability of MS2 VLPs as a platform for presenting heterologous peptides remains a gap. In light of this, we employed the "single-chain dimer" paradigm to scrutinize the tolerance of MS2 VLPs for peptide/protein insertions. The results unveiled functional MS2 VLP assembly solely for inserts smaller than 91 aa. Particularly noteworthy is the largest insertion achieved on the MS2 VLPs to date: the RNA helicase A (RHA) dsRNA-binding domains (dsRBD1). Attempts to introduce additional linkers or empty coat subunits fail to augment the expression level or assembly of the MS2 VLPs displaying dsRBD1, affirming 91 aa as the upper threshold for exogenous protein presentation. By illuminating the precise confines of MS2 VLPs in accommodating distinct peptide lengths, our study informs the selection of appropriate peptide and protein dimensions. This revelation not only underscores the scope of MS2 VLPs but also establishes a pivotal reference point, facilitating the strategic manipulation of MS2 VLPs to design next-generation epitope/antibody-based therapeutics.

Phage Milagro: a platform for engineering a broad host range virulent phage for Burkholderia.

Burkholderia infections are a significant concern in people with CF and other immunocompromising disorders, and are difficult to treat with conventional antibiotics due to their inherent drug resistance. Bacteriophages, or bacterial viruses, are now seen as a potential alternative therapy for these infections, but most of the naturally occurring phages are temperate and have narrow host ranges, which limit their utility as therapeutics. Here we describe the temperate Burkholderia phage Milagro and our efforts to engineer this phage into a potential therapeutic by expanding the phage host range and selecting for phage mutants that are strictly virulent. This approach may be used to generate new therapeutic agents for treating intractable infections in CF patients.

Dopamine alters phage morphology to exert an anti-infection effect.

Antiviral drug development is important for human health, and the emergence of novel COVID-19 variants has seriously affected human lives and safety. A bacteriophage-a bacterial virus with a small and simple structure-is an ideal experimental candidate for studying the interactions between viruses and their hosts. In this study, the effects and mechanisms of catecholamines on phages were explored, and dopamine (DA) was found to have general and efficient anti-infection effects. A clear dose-dependent effect was observed when different phages were treated with DA, with higher DA concentrations exhibiting stronger anti-phage activity. The half maximal inhibitory concentration values of DA for vB-EcoS-IME167, T4 Phage, and VMY22 were determined as 0.26, 0.12, and 0.73 mg mL-1, respectively. The anti-phage effect of DA increased with treatment duration. In addition, the anti-infection activities of DA against vB-EcoS-IME167, T4 Phage, and VMY22 were increased by 105, 104, and 104 folds compared to that of the control. This ability of DA was observed only in phages and not in the host bacteria. Morphological changes of phages were observed under transmission electron microscopy following their treatment with DA, and considerable changes in adsorption were confirmed via quantitative reverse transcription polymerase chain reaction. These results suggest that the anti-phage effect of DA is primarily due to the destruction of the external structure of the phage. This study, to the best of our knowledge, is the first to report the universal anti-phage infection effect of dopamine, which provides novel information regarding DA and forms a basis for further research and development of antiviral drugs. Moreover, it provides a new perspective for the research about the defense and counter-defense of bacteria and bacteriophages.

Abstract 11918: Simultaneous Presentation of Pyogenic Pericarditis, Coronavirus Infection, and Endocarditis: A Challenging Triad in a Single Patient

Background: Pyogenic pericarditis is a rapidly progressive infection with high mortality near 100%. In the present antibiotic age, bacterial pericarditis is an uncommon cause of acute pericarditis. The reported incidence of pyogenic pericarditis is less than 1% of all pericarditis cases. Case: 54 year-old male patient that presented with complaints of generalized weakness, fatigue, and fever. He was diagnosed with Coronavirus 229E by PCR. He was in respiratory distress, and CT chest showed concern for large pericardial effusion. Transthoracic echocardiogram showed large pericardial effusion (Image) without tamponade effect. Patient decompensated overnight and bedside point of care ultrasound overnight showed concern for tamponade effect. Pericardial window was performed and 800 ml thick purulent drainage evacuated. While in the ICU patient underwent transesophageal echocardiogram that showed Small hyper-mobile echo-density on the aortic valve concerning for endocarditis (image). Patient also had Type 1 Bicuspid aortic valve with heavily calcified raphe. Cultures on the pericardial effusion grew methicillin sensitive Staphylococcus Aureus. Patient will need 6 weeks of IV antibiotics and aortic valve replacement. Infectious disease recommended lifelong suppression therapy for MSSA. Decision-making: It is not uncommon for bacterial endocarditis and viruses to cause pericardial effusions. It is uncommon for a patient to have bacterial endocarditis, Coronavirus, and be diagnosed with pyogenic pericardial effusion. Cardiac tamponade is a clinical emergency, and evacuation of pericardial fluid to assist reduce the pressure surrounding the heart is used to treat cardiac tamponade. Conclusion: Here we present a case to our knowledge that has never been described before. This is a case of a patient that had infective endocarditis with confirmed Coronavirus that resulted in a pyogenic pericardial effusion.

An IoT based Tree Specific Soil Nutrient Management System Using Neural Network for Cashew Cultivation

Anacardium occidentale commonly known as Cashew was introduced into India by Portuguese in 16th century. Farmers of Cuddalore District, Tamil Nadu in India, are interested in Cashew Cultivation due to its export market values. To achieve better yield from cashew cultivation, farmers need to supply balanced nutrition to the soil and by following intercropping method. In literature, Recent Technologies like Artificial Intelligence and IOT are widely used to predict dosage of the fertilizer to be applied. By examining the numerous connected ascribe success locations of Cashew orchards, it was possible to determine how much macronutrients like Nitrogen (N), Phosphorus (P), and Potassium (K) were present in the soil and it will be helpful for the understanding of soil fertility level of the area. In our work, using IOT set up which includes Arduino UNO, NPK sensor and OLED display, we identified NPK values of soil for various cashew trees in a particular area. Along with NPK values of soil, inputs include the local soil type, PH and Tree age. Based on the input factors, DL trained model will provide suggestions of fertilizer dose to be applied for a specific tree for the Cashew cultivating farmers for better yield. In our proposed work, LSTM based Recurrent Neural Network (RNN) Algorithm is used to provide a better prediction of fertilizer. With the help of this research, we can be provided with what intercrop to plant and how much fertilizer to use, in what ratio to supply and fertilizer shop suggestion to enhance agricultural knowledge across the globe using the Internet of Things (IoT) and Artificial Intelligence. The result of RNN model was compared with Random Forest, Linear Regression, Linear Random Classifier, Decision Tree Classifier with proving accuracy of 98.7 %. Together with a decrease in the farmers' input efforts, these strategies will increase the productivity of the fields.

How Simple Maths Can Inform Our Basic Understanding of Phage Therapy.

Phage therapy is the application of bacterial viruses to control and, ideally, to eliminate problematic bacteria from patients. Usually employed are so-called strictly lytic phages, which upon adsorption of a bacterium should give rise to both bacterial death and bacterial lysis. This killing occurs with single-hit kinetics, resulting in relatively simple ways to mathematically model organismal-level, phage-bacterium interactions. Reviewed here are processes of phage therapy as viewed from these simpler mathematical perspectives, starting with phage dosing, continuing through phage adsorption of bacteria, and then considering the potential for phage numbers to be enhanced through in situ phage population growth. Overall, I suggest that a basic working knowledge of the underlying "simple maths" of phage therapy can be helpful toward making dosing decisions and predicting certain outcomes. This especially is during controlled in vitro experimentation but is relevant to thinking about in vivo applications as well.

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

BackgroundViruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.ResultsWe identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.ConclusionTaken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.2RJdjcjTGzDNGfvgvrWr_YVideo

Broad-range capsule-dependent lytic Sugarlandvirus against Klebsiella sp.

The emergence of antibiotic-resistant bacteria has become a serious global health threat requiring the development of novel treatments. Klebsiella pneumoniae is an encapsulated bacterium considered a major concern due to its high resistance, prevalence, and mortality rates. Phage therapy has been proposed as a very promising alternative to combat infections by Klebsiella sp. infections. However, most of the Klebsiella phages described so far present a high specificity, infecting one or a few capsular types due to the presence of depolymerases in their genomes, which limits their therapeutic potential. Here, we present three new Klebsiella phages isolated from the environment, vB_Kpn_K7PH164C4, vB_Kpn_K30λ2.2, and vB_Kpl_K32PH164C1, belonging to the family Demerecviridae and the genus Sugarlandvirus. The most important feature of these new Klebsiella phages is their broad host range, especially vB_Kpn_K7PH164C4 and vB_Kpn_K30λ2.2, which infects strains of more than 20 different capsular types, representing the broadest infection range observed for Klebsiella phages. Genomic analysis revealed the presence of three receptor-binding proteins lacking depolymerase domains. Nevertheless, capsule expression is suggested to be a determining factor in phage infectivity, despite the absence of depolymerase activity against capsular components. Our findings hold potential for the development of promising phage-based therapeutics directed against K. pneumoniae.IMPORTANCEThe emergence of multi-drug resistant bacteria is a global health problem. Among them, Klebsiella pneumoniae is considered a high-priority pathogen, making it necessary to develop new therapeutic tools to reduce the bacterial burden in an effective and sustainable manner. Phages, bacterial viruses, are very promising tools. However, phages are highy specific, rendering large-scale therapeutics costly to implement. This is especially certain in Klebsiella, a capsular bacterium in which phages have been shown to be capsular type dependent, infecting one or a few capsular types through specific enzymes called depolymerases. In this study, we have isolated and characterized novel phages with lytic ability against bacteria from a wide variety of capsular types, representing the Klebsiella phages with the widest range of infection described. Remarkably, these broad-range phages showed capsule dependency, despite the absence of depolymerases in their genomes, implying that infectivity could be governed by alternative mechanisms yet to be uncovered.

Bacterial outer membrane vesicles bound to bacteriophages modulate neutrophil responses to bacterial infection.

Pseudomonas aeruginosa is a major human pathogen, particularly effective at colonizing the airways of patients with cystic fibrosis. Bacteriophages are highly abundant at infection sites, but their impact on mammalian immunity remains unclear. We previously showed that Pf4, a temperate filamentous bacteriophage produced by P. aeruginosa, modifies the innate immune response to P. aeruginosa infections via TLR3 signaling, but the underlying mechanisms remained unclear. Notably, Pf4 is a single-stranded DNA and lysogenic phage, and its production does not typically result in lysis of its bacterial host. We identified previously that internalization of Pf4 by human or murine immune cells triggers maladaptive viral pattern recognition receptors and resulted in bacterial persistence based on the presence of phage RNA. We report now that Pf4 phage dampens inflammatory responses to bacterial endotoxin and that this is mediated in part via bacterial vesicles attached to phage particles. Outer membrane vesicles (OMVs) are produced by Gram-negative bacteria and play a key role in host pathogen interaction. Recently, evidence has emerged that OMVs differentially package small RNAs. In this study, we show that Pf4 are decorated with OMVs that remain affixed to Pf4 despite of purification steps. These phages are endocytosed by human cells and delivered to endosomal vesicles. We demonstrate that short RNAs within the OMVs form hairpin structures that trigger TLR3-dependent type I interferon production and antagonize production of antibacterial cytokines and chemokines. In particular, Pf4 phages inhibit CXCL5, preventing efficient neutrophil chemotaxis in response to endotoxin. Moreover, blocking IFNAR or TLR3 signaling abrogates the effect of Pf4 bound to OMVs on macrophage activation. In a murine acute pneumonia model, mice treated with Pf4 associated with OMVs show significantly less neutrophil infiltration in BAL fluid than mice treated with purified Pf4. These changes in macrophage phenotype are functionally relevant: conditioned media from cells exposed to Pf4 decorated with OMVs are significantly less effective at inducing neutrophil migration in vitro and in vivo. These results suggest that Pf4 phages alter innate immunity to bacterial endotoxin and OMVs, potentially dampening inflammation at sites of bacterial colonization or infection.

Comparing the decay of human wastewater-associated markers and enteric viruses in laboratory microcosms simulating estuarine waters in a temperate climatic zone using qPCR/RT-qPCR assays

This study investigated the decay rates of wastewater-associated markers and enteric viruses in laboratory microcosms mimicking estuarine water environments in temperate Sydney, NSW, Australia using qPCR and RT-qPCR assays. The results demonstrated the reduction in concentrations of Bacteroides HF183, Lachnospiraceae Lachno3, cross-assembly phage (crAssphage), pepper mild mottle virus (PMMoV), human adenovirus (HAdV 40/41), and enterovirus (EV) over a span of 42 days under spring/summer temperatures, presence/absence of microbiota, and different light conditions. The study found that HF183, Lachno3, crAssphage, PMMoV, HAdV 40/41, and EV exhibited varying decay rates depending on the experimental conditions. The average T90 values ranged from a few days to several months, indicating the rapid decay or prolonged persistence of these markers and enteric viruses in the estuarine environment. Furthermore, the study examined the effects of indigenous microbiota and spring/summer temperatures on wastewater-associated markers and enteric viruses decay rates. It was found that the presence of microbiota and temperature significantly influenced the decay rates of HF183 and PMMoV. Additionally, the study compared the effects of artificial sunlight and spring/summer temperatures on marker decay rates. Bacterial markers decayed faster than viral markers, although among viral markers crAssphage decay rates were relatively faster when compared to PMMoV. The exposure to artificial sunlight significantly accelerated the decay rates of bacterial markers, viral markers, and enteric viruses. Temperature also had an impact on the decay rates of Lachno3, crAssphage, and HAdV 40/41. In conclusion, this study provides valuable insights into the decay rates of wastewater-associated markers and enteric viruses under different experimental conditions that mimicked temperate environmental conditions. The findings contribute to our understanding of the fate and persistence of these markers in the environment which is crucial for assessing and managing risks from contamination by untreated human wastewater.