PHROG: families of prokaryotic virus proteins clustered using remote homology

AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes

Anti-CRISPR (Acr) proteins play a key role in phage-host interactions and hold great promise for advancing genome-editing technologies. However, finding new Acrs has been challenging due to their low sequence similarity. Recent advances in protein structure prediction have opened new pathways for Acr discovery by using 3D structure similarity. This study presents an updated AcrDB, with the following new features not available in other databases: (1) predicted Acrs from human gut virome databases, (2) Acr structures predicted by AlphaFold2, (3) a structural similarity search function to allow users to submit new sequences and structures to search against 3D structures of experimentally known Acrs. The updated AcrDB contains predicted 3D structures of 795 candidate Acrs with structural similarity (TM-score ≥0.7) to known Acrs supported by at least two of the three non-sequence similarity-based tools (TM-Vec, Foldseek, AcrPred). Among these candidate Acrs, 121 are supported by all three tools. AcrDB also includes 3D structures of 122 experimentally characterized Acr proteins. The 121 most confident candidate Acrs were combined with the 122 known Acrs and clustered into 163 sequence similarity-based Acr families. The 163 families were further subject to a structure similarity-based hierarchical clustering, revealing structural similarity between 44 candidate Acr (cAcr) families and 119 known Acr families. The bacterial hosts of these 163 Acr families are mainly from Bacillota, Pseudomonadota, and Bacteroidota, which are all dominant gut bacterial phyla. Many of these 163 Acr families are also co-localized in Acr operons. All the data and visualization are provided on our website: https://pro.unl.edu/AcrDB.

Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models

Protein sequence analysis examines the order of amino acids within protein sequences to unlock diverse types of a wealth of knowledge about biological processes and genetic disorders. It helps in forecasting disease susceptibility by finding unique protein signatures, or biomarkers that are linked to particular disease states. Protein Sequence analysis through wet-lab experiments is expensive, time-consuming and error prone. To facilitate large-scale proteomics sequence analysis, the biological community is striving for utilizing AI competence for transitioning from wet-lab to computer aided applications. However, Proteomics and AI are two distinct fields and development of AI-driven protein sequence analysis applications requires knowledge of both domains. To bridge the gap between both fields, various review articles have been written. However, these articles focus revolves around few individual tasks or specific applications rather than providing a comprehensive overview about wide tasks and applications. Following the need of a comprehensive literature that presents a holistic view of wide array of tasks and applications, contributions of this manuscript are manifold: It bridges the gap between Proteomics and AI fields by presenting a comprehensive array of AI-driven applications for 63 distinct protein sequence analysis tasks. It equips AI researchers by facilitating biological foundations of 63 protein sequence analysis tasks. It enhances development of AI-driven protein sequence analysis applications by providing comprehensive details of 68 protein databases. It presents a rich data landscape, encompassing 627 benchmark datasets of 63 diverse protein sequence analysis tasks. It highlights the utilization of 25 unique word embedding methods and 13 language models in AI-driven protein sequence analysis applications. It accelerates the development of AI-driven applications by facilitating current state-of-the-art performances across 63 protein sequence analysis tasks.

Distinct effects of mucin on phage-host interactions in model systems of beneficial and pathogenic bacteria

Phage-host interactions that occur in host-associated microbiomes are influenced by a plethora of environmental factors. Mucins are glycoproteins that represent the main component of mucus, which is found in the animal digestive tract and on the surface of certain organs, serving as the first line of defense against toxins and pathogens. Previous studies have shown that lytic phages have an important influence on the microbial composition in mucosal areas. Our study expands this knowledge to interactions between previously untested lytic phages targeting probiotic and pathogenic bacteria, as well as temperate phages targeting probiotic bacteria. These interactions could be important in shaping microbial communities and affecting the well-being of their host. This study demonstrates that mucins enhance the adherence of Vibrio anguillarum lytic phages and Bacillus subtilis lytic and temperate phages, as well as B. subtilis and V. anguillarum cells, to solid surfaces. Our results also show that mucins positively affect the attachment of B. subtilis cells even in the presence of phages. This positive effect was not observed in the case of V. anguillarum. This suggests that mucin may shield certain bacteria from phage infections. We also found that mucin influenced the metabolic activity of the two tested bacterial species differently, with strong positive effects on V. anguillarum but not on B. subtilis. This work supports previous findings that phages adhere efficiently to mucus and extends these studies to include other beneficial and pathogenic bacterial species. It also reveals that mucins have different effects on phage-host interactions in different phage-host systems, which may have implications for phage therapies or probiotic treatment strategies.

Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy

Chrysochromulina parva (C. parva) is a eukaryotic freshwater haptophyte algae found in lakes and rivers worldwide. It is known to be infected by viruses, yet knowledge of the diversity and activity of these viruses is still very limited. Based on sequences of PCR-amplified DNA polymerase B (polB) gene fragments, Chrysochromulina parva virus BQ1 (CpV-BQ1) was the first known lytic agent of C. parva, and was considered a member of the virus family Phycodnaviridae, order Algavirales. However, the genome of a different C. parva-infecting virus (CpV-BQ2, or Tethysvirus ontarioense) from another virus family, the Mesomimiviridae, order Imitervirales, was the first sequenced. Here, we report the complete genome sequence of the putative phycodnavirus CpV-BQ1, accession PQ783904. The complete CpV-BQ1 genome sequence is 165,454 bp with a GC content of 32.32% and it encodes 193 open reading frames. Phylogenetic analyses of several virus hallmark genes including the polB, the late gene transcription factor (VLTF-3), and the putative A32-like virion packaging ATPase (Viral A32) all demonstrate that CpV-BQ1 is most closely related to other viruses in the phylum Megaviricetes within the order Algavirales, family Phycodnaviridae.

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

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

Complete genome sequence of bacteriophages infecting Escherichia, Enterobacter, and Pseudomonas isolates

We reported six new species of bacteriophages belonging to the genus Drulisvirus, Mosigvirus, Kayfunavirus, and Kagunavirus, with a shared genome similarity of 77.2% to 94.5%. Seven isolates are suitable candidates for phage therapy, thereby expanding our knowledge about biocontrol alternatives against infections caused by multidrug-resistant bacteria.

Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail

Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promise in treating P. aeruginosa infections, the development of bacteriophage-insensitive mutants (BIMs) in the presence of bacteriophages has been described. The aim of this study was to examine the genetic changes associated with the BIM phenotype. Biofilms of three genetically distinct P. aeruginosa strains, including PAO1 (ATCC 15692), and two clinical respiratory isolates (one CF and one non-CF) were grown for 7 days and treated with either a cocktail of four bacteriophages or a vehicle control for 7 consecutive days. BIMs isolated from the biofilms were detected by streak assays, and resistance to the phage cocktail was confirmed using spot test assays. Comparison of whole genome sequencing between the recovered BIMs and their respective vehicle control-treated phage-sensitive isolates revealed structural variants in two strains, and several small variants in all three strains. These variations involved a TonB-dependent outer membrane receptor in one strain, and mutations in lipopolysaccharide synthesis genes in two strains. Prophage deletion and induction were also noted in two strains, as well as mutations in several genes associated with virulence factors. Mutations in genes involved in susceptibility to conventional antibiotics were also identified in BIMs, with both decreased and increased antibiotic sensitivity to various antibiotics being observed. These findings may have implications for future applications of lytic phage therapy.IMPORTANCELytic bacteriophages are viruses that infect and kill bacteria and can be used to treat difficult-to-treat bacterial infections, including biofilm-associated infections and multidrug-resistant bacteria. Pseudomonas aeruginosa is a bacterium that can cause life-threatening infections. Lytic bacteriophage therapy has been trialed in the treatment of P. aeruginosa infections; however, sometimes bacteria develop resistance to the bacteriophages. This study sheds light on the genetic mechanisms of such resistance, and how this might be harnessed to restore the sensitivity of multidrug-resistant P. aeruginosa to conventional antibiotics.

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems

Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.

Complete genome sequence analysis of a new Escherichia phage, GaoY1-9D

In this study, a new Escherichia phage, GaoY1-9D, was isolated from farm sewage samples and sequenced. Its genome length is 50,368 bp, and its G + C content is 46.46%. The genome of phage GaoY1-9D is a double-stranded circular DNA that has 127-bp terminal repeats at both ends and does not contain any tRNA genes. Based on the results of genome sequence comparisons, Escherichia phage GaoY1-9D represents a new species in the family Drexlerviridae.

Genome sequences of two phages active against cystic fibrosis isolates of Pseudomonas aeruginosa

We describe the genomes of two Pseudomonas aeruginosa phages of the genus Bruynoghevirus, WRAIR_EPa83 and WRAIR_EPa87. They consist of 45,622 and 45,077 bp, with 52.52% and 52.11% guanine-cytosine content, contain 81 and 80 coding sequences, two and three tRNA genes, and direct terminal repeats of 183 and 184 bp, respectively.

Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

Prophages are bacteriophages that integrate their genomes into the bacterial chromosome. This research aimed to analyze and characterize prophages integrated into 44 Pseudomonas aeruginosa strains isolated from tertiary hospitals in Saudi Arabia. A total of 97 intact prophages were identified among clinical strains, with 16 prophages found present in more than one strain simultaneously. All prophages were found to have lengths ranging from 7.7 kb to 74.1 kb, and their GC content was found to be between 49.91% and 64.9%. Our findings show that prophages are present in the majority of the isolated P. aeruginosa strains (41 out of 44). Additionally, several proteins related to viral defense (toxin/antitoxin modules and proteins against restriction-modification enzymes) were identified, supporting the idea that prophages influence bacterial pathogenesis and anti-phage defenses.

Bakta Web - rapid and standardized genome annotation on scalable infrastructures

The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of command line software tools and the interpretation of result files in various formats might be challenging and pose technical barriers. Here, we present the recent updates on the Bakta web server, a user-friendly web interface for conducting and visualizing annotations using Bakta without requiring command line expertise or local computing resources. Key features include interactive visualizations through circular genome plots, linear genome browsers, and searchable data tables facilitating the interpretation of complex annotation results. The web server generates standard bioinformatics outputs (GFF3, GenBank, EMBL) and annotates diverse genomic features, including coding sequences, non-coding RNAs, small open reading frames (sORFs), and many more. The development of an auto-scaling cloud-native architecture and improved database integration led to substantially faster processing times and higher throughputs. The system supports FAIR principles via extensive cross-reference links to external databases, including RefSeq, UniRef, and Gene Ontology. Also, novel features have been implemented to foster sharing and collaborative interpretation of results. The web server is freely available at https://bakta.computational.bio.

Engineering bacteriophages through deep mining of metagenomic motifs

Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where these motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to find sequence motifs in metagenomic datasets to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to mine metagenomes for functional motifs invisible to other searches. We experimentally tested ~17,000 Meta-SIFT-derived sequence motifs in the receptor binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with motifs sourced from distant families. Position, substitution, and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen Escherichia coli O121. Meta-SIFT is a powerful tool to unlock the potential encoded in phage metagenomes to engineer bacteriophages.

Characterization and genome analysis of the novel virulent Burkholderia phage Bm1, which is active against pan-drug-resistant Burkholderia multivorans

The escalating challenges of antibiotic resistance in bacterial pathogens have necessitated the exploration of alternative therapeutic strategies. Among these, bacteriophage therapy has regained attention as a promising approach to combat multidrug-resistant bacteria. Bacteriophages are viruses that infect and lyse specific bacterial strains, making them attractive candidates for targeted antimicrobial treatment. Burkholderia multivorans, a Gram-negative bacterium, is known to cause opportunistic infections, particularly in individuals with a compromised immune system or with cystic fibrosis. The prevalence of antibiotic-resistant Burkholderia strains has raised concerns about treatment options. In this study, we characterized the Burkholderia phage Bm1, a virulent bacteriophage isolated from an environmental source. Electron microscopy revealed that Bm1 phage particles have myovirus morphology, with an icosahedral head of 72 nm in diameter and a contractile tail of 100 nm in length and 18 nm in width. The genome of phage Bm1 consists of a double-stranded DNA of 67,539 bp with a terminal repeat region at each end. Comparative analysis indicated that the closest relative of phage Bm1 is Burkholderia phage BCSR129, with a calculated VIRIDIC identity of 57.7%. The apparent absence of an integrase gene suggests that the Burkholderia phage Bm1 has a strictly lytic life cycle.

A complete genome of an obligately lytic Pseudomonas aeruginosa bacteriophage, Minga-mokiny 4

We report the isolation of a bacteriophage with obligately lytic activity against Pseudomonas aeruginosa from wastewater. The reported phage, Minga-mokiny 4, appears to belong to the Schitoviridae family, is of the Litunavirus genus, and has a 72,362-bp genome. No known genes associated with lysogeny, bacterial resistance, or virulence were predicted.

Lytic activity, stability, biofilm disruption capabilities, and genomic characterization of two bacteriophages active against respiratory MRSA

AIMS

This study aimed to characterize bacteriophages for potential therapeutic use against Staphylococcus aureus, focusing on clinical respiratory isolates of methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) strains. Specifically, it sought to evaluate phage lytic activity, host range, stability, biofilm disruption capabilities, and overall safety for therapeutic use.

METHODS AND RESULTS

Novel phages, Koomba kaat 1 and Biyabeda mokiny 1, were identified and characterized using microbiological assays and bioinformatics. They exhibited lytic activity against clinical MSSA and MRSA isolates, disrupted biofilms from airway isolates, remained stable for at least one year in storage, and could be aerosolized without significant reductions in activity. Bioinformatic tools were used to assess safety, lifecycle, virulence, and prophage contamination when grown using their original isolation host. Receptor binding proteins within their genomes were also predicted, providing insight into their mechanisms of action. Both phages demonstrated strong efficacy against the clinical isolates tested and demonstrated robust stability under storage and delivery conditions.

CONCLUSIONS

Koomba kaat 1 and Biyabeda mokiny 1 are promising candidates for phage therapy. Their efficacy against clinical S. aureus isolates, ability to break down biofilm, and stability for airway implementation, positions them as valuable tools for addressing persistent airway infections caused by S. aureus.

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory), which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity has remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains, and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. Our results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

Isolation and characterization of a roseophage representing a novel genus in the N4-like Rhodovirinae subfamily distributed in estuarine waters

BACKGROUND

Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.

RESULTS

In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.

CONCLUSIONS

Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

BACKGROUND

Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS

Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS

This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.

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

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

Characterization and therapeutic potential of newly isolated bacteriophages against Staphylococcus species in bovine mastitis

Bovine mastitis, primarily caused by Staphylococcus aureus, significantly affects the dairy industry by reducing milk production and quality. The rise of antibiotic-resistant bacteria has prompted the need for alternative treatments. The three newly isolated bacteriophages, OPT-SA02, OPT-SC01, and OPT-SX11, were isolated from chicken fecal and sewage samples in South Korea. These bacteriophages were characterized via physiological and genomic analyses, identifying their therapeutic potential against S. aureus-induced mastitis. The bacteriophages were identified as members of the Herelleviridae family, exhibiting stability across broad pH (2-12) and temperature (37-70°C) ranges, as well as strong antibacterial activity at low multiplicity of infection (MOI) levels. Genomic analysis revealed that the conservation of lysis-related genes (holin and endolysin) is responsible for their lytic capabilities. Additionally, protein structural predictions revealed multi-domain structures in their endolysins, enhancing their lytic potential. These findings suggest that OPT-SA02, OPT-SC01, and OPT-SX11 show significant promise as alternative treatments for bovine mastitis.IMPORTANCEBovine mastitis, caused by pathogens such as Staphylococcus aureus and Staphylococcus xylosus, remains a major challenge in dairy farming, leading to significant economic losses and reduced milk quality. The increasing prevalence of antibiotic-resistant strains further complicates treatment, emphasizing the need for alternative strategies. This study identifies three newly isolated bacteriophages with effective antibacterial activity against these pathogens and provides comprehensive genomic and structural insights into their mechanisms. Genomic characterization revealed conserved lytic cassettes and genetic diversity within related bacteriophages, offering a deeper understanding of their evolutionary relationships and potential applications. Furthermore, protein structure analysis of the endolysin derived from these bacteriophages identified multi-domain architectures with preserved catalytic cores, underscoring their lytic efficacy against bacterial cell walls. These findings advance the understanding of the genetic and structural mechanisms of bacteriophage-mediated lysis and highlight their potential as sustainable tools for managing bovine mastitis and improving milk quality in dairy farming.

Complete genome sequences of three Pseudomonas aeruginosa phages of the genus Phikmvvirus

We describe the genomes of three lytic Pseudomonas aeruginosa phages of the genus Phikmvvirus. The genomes of phages vB_Pae4841-AFR43, vB_Pae10145-KEN1, and vB_Pae9718-KEN10 consist of 43,426, 43,406, and 43,118 bp, with 62.4%, 62.3%, and 62.2% GC content, contain 63, 66, and 64 coding sequences, respectively, and no tRNA genes.

Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats

Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-enriched and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles

Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization. The source code is available at the GitHub page: github.com/art-egorov/lovis4u. Detailed documentation that includes an example-driven guide is available from the software home page: art-egorov.github.io/lovis4u.

Six Novel Pseudomonas aeruginosa Phages: Genomic Insights and Therapeutic Potential

Introduction

Pseudomonas aeruginosa is an opportunistic pathogen that causes health care-associated infections. The rise of antibiotic-resistant bacterial strains necessitates alternative treatment strategies, with bacteriophage therapy being a promising approach.

Methods

Six bacteriophages were isolated from sewage samples. Phage isolation involved centrifugation, filtration, and plaque assays. The morphology of each sample was examined using transmission electron microscopy (TEM). Genomic DNA was sequenced and compared among the isolates. The phages' lytic activities were assessed using growth curve analysis.

Results

The phages displayed distinct genomic characteristics, grouping into three genomic clusters. No known virulence or antibiotic resistance genes were detected, indicating their safety for therapeutic use. Taxonomic analysis identified the phages as belonging to the genera Pbunavirus, Nipunavirus, Abidjanvirus, and a novel genus. TEM analysis revealed their diverse morphologies. Temperate phages showed less effective lytic activities.

Conclusion

Several of the isolated bacteriophages show potential as candidates for phage therapy research and could be effective against P. aeruginosa infections.

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

New Morganella morganii Phage vB_Mm5 with Tolerance to Cu2+ Ions

Background

Research on phages targeting Morganella morganii is still emerging, with limited studies compared with other phage-host systems. Interest in these phages has increased due to rising antibiotic resistance and their potential for controlling M. morganii spread in the environment.

Materials and Methods

This study investigates the biology and genetics of the novel M. morganii-infecting myophage vB_Mm5 and evaluates its stability under Cu2+ exposure.

Results

Phage vB_Mm5 has a 10-min latent period and a burst size of 30 (±5). It shows high tolerance to elevated temperatures and Cu2+. The phage genome, comprising 163,232 bp dsDNA with 229 open reading frames, encodes genes that not only enhance the phage's predatory capabilities but also confer resistance to host defense mechanisms.

Conclusions

vB_Mm5 is highly distinct from other sequenced M. morganii phages, does not contain any known virulence genes, and holds potential as a therapeutic agent against M. morganii infections.

Self-splicing introns in genes of Bastillevirinae bacteriophages

Group I introns are self-splicing ribozymes that can be found in eukaryotes, prokaryotes, and quite often in their viruses. The distribution, structure, and splicing of group I introns in genes of some phage taxa like the Tevenvirinae or Twortwirinae was extensively studied. On the other hand, the prevalence of intervening sequences in most other clades of bacterial viruses remains mostly unexplored. In this paper, we describe group I autocatalytic introns in genes of phages from the Bastillevirinae subfamily. This taxon belongs to the Herelleviridae family and consists of 15 genera and 37 species, including viruses with strong antimicrobial potential. A bioinformatic search for intron-related RNA structures revealed the presence of 45 intervening sequences within 37 genes that belong to four gene families. Eight of the nine genes selected for experimental validation were spliced-four only in an infected bacteria but additional four self-spliced in vitro. Interestingly, one of the studied genes undergoes alternative splicing. To sum up, our findings expand the knowledge on the distribution and diversity of group I introns and shed new light on this neglected aspect of phage transcriptomics. Additionally, in the course of our study, we demonstrated the effectiveness of nanopore sequencing in elucidating prokaryotic splicing mechanisms.

Complete genome sequence of Salmonella enterica bacteriophage SeKF_80, isolated from wastewater in British Columbia

Salmonella enterica is a Gram-negative inhabitant of the gastrointestinal tract of warm-blooded animals and commonly implicated in foodborne illness. Here, we describe the isolation of Salmonella enterica phage SeKF_80. The 89,965 bp genome contains 174 predicted coding sequences with 44 predicted functions. Phage SeKF_80 shares species-level similarity with Salmonella phages 7-11.

An Actively Homing Insertion Element in a Phage Methylase Contains a Hidden HNH Endonuclease

Background/Objectives: The ShiLan domain was previously identified as an insertion sequence in a phage DNA methylase gene that exhibited similar evolutionary patterns to that of an active intein or self-splicing intron but could not be identified as either. It produces no internal stop codons when read in frame with its host methylase gene, leading to the thought that it may not be an intron and rather be an abnormal type of intein. However, the sequence has no detectable self-splicing domains, which are essential for intein persistence, as preventing an intein from successfully splicing is often detrimental to proper host protein function. Methods: The analysis of alternate open reading frames for the full nucleotide sequence of this insertion element revealed the insertion to be an out-of-frame histidine-asparagine-histidine (HNH) endonuclease. A GTG start codon is located 18 bp into the insertion, and a TAA stop codon within the last four bases of the insertion (TAAC). When this frame is read, an HNH endonuclease is revealed. In-depth computational analysis could not retrieve support for this element being any known type of self-splicing element, neither intein nor intron. When read in-frame with the methylase gene, this insertion is predicted to take on a looping structure that may be able to avoid interference with the DNA methylase activity. We performed searches for sequences similar in nature to the inserted out-of-frame HNH and found several in other phages and prokaryotes. We present our survey of these out-of-frame endonuclease insertion elements as well as some speculation on how these endonucleases are getting translated to facilitate their homing activity. Conclusions: These findings expand our understanding of the possible arrangements for and prevalence of unorthodox mobile genetic elements and overlapping open reading frames in phages.

Identification of Diverse Bacteriophages Associated with Bees and Hoverflies

Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies.

Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

Motivation

Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive and time-consuming, hindering rapid clinical deployment.

Results

We developed Sphae, an automated bioinformatics pipeline designed to streamline the therapeutic potential of a phage in under 10 minutes. Using Snakemake workflow manager, Sphae integrates tools for quality control, assembly, genome assessment, and annotation tailored specifically for phage biology. Sphae automates the detection of key genomic markers, including virulence factors, antimicrobial resistance genes, and lysogeny indicators such as integrase, recombinase, and transposase, which could preclude therapeutic use. Among the 65 phage sequences analyzed, 28 showed therapeutic potential, 8 failed due to low sequencing depth, 22 contained prophage or virulent markers, and 23 had multiple phage genomes. This workflow produces a report to assess phage safety and therapy suitability quickly. Sphae is scalable and portable, facilitating efficient deployment across most high-performance computing and cloud platforms, accelerating the genomic evaluation process.

Availability and implementation

Sphae source code is freely available at https://github.com/linsalrob/sphae, with installation supported on Conda, PyPi, Docker containers.

Klebsiella pneumoniae Phage M198 and Its Therapeutic Potential

The rapid worldwide spread of antibiotic resistance is quickly becoming an increasingly concerning problem for human healthcare. Non-antibiotic antibacterial agents are in high demand for many Gram-negative bacterial pathogens, including Klebsiella pneumoniae. Klebsiella-targeting phages are among the most promising alternative therapy options. They have already been successfully applied in a number of cases, and it is expected that the need for anti-Klebsiella phages will only increase in the future. This prospect highlights the need for well-characterized therapeutic phages. In this work, we describe a K. pneumoniae phage, which also infects strains of Klebsiella oxytoca. Here, we characterize phage M198 in terms of its biological and genetic properties. Since in some phage therapy cases, phages are administered in combination with antibiotics, here, we also screen for possible synergistic effects of combining phage M198 with six different antibiotics. We found that phage M198 has good lytic activity against clinical isolates; it does not have any indications of a temperate lifestyle, and it has synergistic potential when combined with some therapeutically relevant antibiotics.

PhageDive: the comprehensive strain database of prokaryotic viral diversity

Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, Félix d'Hérelle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ.

BFVD-a large repository of predicted viral protein structures

The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences, severely limiting their study. To address this, we created the Big Fantastic Virus Database (BFVD), a repository of 351 242 protein structures predicted by applying ColabFold to the viral sequence representatives of the UniRef30 clusters. By utilizing homology searches across two petabases of assembled sequencing data, we improved 36% of these structure predictions beyond ColabFold's initial results. BFVD holds a unique repertoire of protein structures as over 62% of its entries show no or low structural similarity to existing repositories. We demonstrate how a substantial fraction of bacteriophage proteins, which remained unannotated based on their sequences, can be matched with similar structures from BFVD. In that, BFVD is on par with the AFDB, while holding nearly three orders of magnitude fewer structures. BFVD is an important virus-specific expansion to protein structure repositories, offering new opportunities to advance viral research. BFVD can be freely downloaded at bfvd.steineggerlab.workers.dev and queried using Foldseek and UniProt labels at bfvd.foldseek.com.

Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island

In this study, we identify and characterize a novel phage-inducible chromosomal island (PICI) found in commensal Escherichia coli MP1. This novel element, EcCIMP1, is induced and mobilized by the temperate helper phage vB_EcoP_Kapi1. EcCIMP1 contributes to superinfection immunity against its helper phage, impacting bacterial competition outcomes. Genetic analysis of EcCIMP1 led us to uncover a putative transcriptional repressor, which silences virulence gene expression in the murine pathogen Citrobacter rodentium. We also found a putative excisionase encoded by EcCIMP1 which paradoxically does not promote excision of EcCIMP1 but rather supports excision of the helper phage. Another putative excisionase encoded by a presumed integrative conjugative element can also support the excision of vB_EcoP_Kapi1, demonstrating crosstalk between excisionases from multiple classes of mobile genetic elements within the same cell. Although phylogenetically distant from other characterized PICIs, EcCIMP1 and EcCIMP1-like elements are prevalent in both pathogenic and commensal isolates of E. coli from around the world, underscoring the importance of characterizing these abundant genetic elements.

Insights from Shigella bacteriophage genomes analysis

Shigella species, a major cause of shigellosis, remain a substantial global health issue and the emergence of antibiotic-resistant Shigella strains has aggravated the situation. Hence, four Shigella phages were investigated to provide insights into the evolutionary trajectories and genomic properties of Shigella-infecting bacteriophages using comparative genome analysis. Analysis shows that these four phages belong to the Tequatrovirus genus and include a considerable number of proteins for 'Tail' and "DNA, RNA and Nucleotide Metabolism," indicating their aptitude for specialized host interaction and replication efficiency. The identification of 10 tRNAs further support that, these phages have high replication efficiency. Thus, this study improves our understanding of phage evolution by exposing the genetic mechanisms that drive phage adaptability and host specificity. This also highlights the significance of phage genomic research in developing viable therapies for antibiotic-resistant Shigella infections.

PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

MOTIVATION

Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.

RESULTS

We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence thresholds and sequence similarity settings. The margin in performance is most pronounced when the sequence similarity between the training and test sets drops below 40%, wherein, at a relatively high-confidence threshold of above 50%, PHIStruct presents a 7%-9% increase in class-averaged F1 over machine learning tools that do not directly incorporate structure information, as well as a 5%-6% increase over BLASTp.

AVAILABILITY AND IMPLEMENTATION

The data and source code for our experiments and analyses are available at https://github.com/bioinfodlsu/PHIStruct.

Genome sequences of five Klebsiella bacteriophages that belong to the genus Jiaodavirus

We describe the genomes of five lytic Klebsiella pneumoniae myophages, therapeutic candidates, that belong to the family Straboviridae and genus Jiaodavirus. The genomes ranged from 165,574 to 169,768 bp, with ca. 40% GC content, contained 289-300 coding sequences, had 15-16 tRNA genes, and no terminal repeats.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (~1:100), but a much larger ratio of phage genomes to bacterial genomes (~4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occurs at a low average rate (~0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone, while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

Sxt1, Isolated from a Therapeutic Phage Cocktail, Is a Broader Host Range Relative of the Phage T3

Using Escherichia coli BW25113 as a host, we isolated a novel lytic phage from the commercial poly-specific therapeutic phage cocktail Sextaphage® (Microgen, Russia). We provide genetic and phenotypic characterization of the phage and describe its host range on the ECOR collection of reference E. coli strains. The phage, hereafter named Sxt1, is a close relative of classical coliphage T3 and belongs to the Teetrevirus genus, yet its internal virion proteins, forming an ejectosome, differ from those of T3. In addition, the Sxt1 lateral tail fiber (LTF) protein clusters with those of the phages from the Berlinvirus genus. A comparison of T7, T3, and Sxt1 LTFs reveals the presence of insertions leading to the elongation of Sxt1 tail fibers, which, together with the difference in the HRDRs (host range-determining regions), might explain the expanded host specificity for the Sxt1.

High activity and specificity of bacteriophage cocktails against carbapenem-resistant Klebsiella pneumoniae belonging to the high-risk clones CG258 and ST307

Introduction

The widespread clinical and environmental dissemination of successful clones of carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a serious global public health threat. In this context, lytic bacteriophages have emerged as a promising alternative for controlling these pathogens. This study describes the biological, structural, and genomic characteristics of lytic bacteriophages against the high-risk CRKP clones CG258 and ST307 and describes their performance in combination.

Methods

An experimental study was carried out. Bacteriophages were isolated from hospital wastewater and from wastewater treatment plants (WWTP). Bacteriophages were isolated using the double layer agar technique and their characterization included host range (individual and cocktail), plating efficiency (EOP), infection or bacterial killing curve, one-step curve, bacteriophage stability at pH and temperature conditions, transmission electron microscopy (TEM) and whole genome sequencing.

Results

After purification, five active bacteriophages against CRKP were obtained, three bacteriophages (FKP3, FKP4 and FKP14) had targeted activities against CG258 CRKP and two (FKP10 and FKP12) against ST307 isolates. Seven cocktails were prepared, of which Cocktail 2, made up of the bacteriophages FKP3, FKP10, and FKP14, showed the best activity against 85.7% (n = 36/42) of CRKP isolates belonging to both clones, CG258 (80.8%; n = 21/26) and ST307 (93.8%, n = 15/16). The efficiency of the plating (EOP), infection curve, and one-step growth curve showed that the cocktail phages efficiently infected other CRKP isolates (EOP ≥ 0.5), controlled bacterial growth up to 73.5%, and had short latency periods, respectively, (5-10 min). In addition, they were stable at temperatures between 4°C and 50°C and pH between 4 and 10. All bacteriophages belonged to the Caudoviricetes class, and no genes associated with virulence factors or antibiotic resistance were detected.

Conclusion

These findings showed bacteriophages and phage cocktails with high specificity against CRKP belonging to the successful clones CG258 and ST307 with promising characteristics, making them an alternative for controlling these clones in different environmental or health settings, biocontrol agents, or disinfectants in industry and in the field of diagnosis.

Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli

Phage therapy has recently been revitalized in the West with many successful applications against multi-drug-resistant bacterial infections. However, the lack of geographically diverse bacteriophage (phage) genomes has constrained our understanding of phage diversity and its genetics underpinning host specificity, lytic capability, and phage-bacteria co-evolution. This study aims to locally isolate virulent phages against uropathogenic Escherichia coli (E. coli) and study its phenotypic and genomic features. Three obligately virulent Escherichia phages (øEc_Makalu_001, øEc_Makalu_002, and øEc_Makalu_003) that could infect uropathogenic E. coli were isolated and characterized. All three phages belonged to Krischvirus genus. One-step growth curve showed that the latent period of the phages ranged from 15 to 20 min, the outbreak period ~ 50 min, and the burst size ranged between 74 and 127 PFU/bacterium. Moreover, the phages could tolerate a pH range of 6 to 9 and a temperature range of 25-37 °C for up to 180 min without significant loss of phage viability. All phages showed a broad host spectrum and could lyse up to 30% of the 35 tested E. coli isolates. Genomes of all phages were approximately ~ 163 kb with a gene density of 1.73 gene/kbp and an average gene length of ~ 951 bp. The coding density in all phages was approximately 95%. Putative lysin, holin, endolysin, and spanin genes were found in the genomes of all three phages. All phages were strictly virulent with functional lysis modules and lacked any known virulence or toxin genes and antimicrobial resistance genes. Pre-clinical experimental and genomic analysis suggest these phages may be suitable candidates for therapeutic applications.

Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum

The archaeal superphylum DPANN (an acronym formed from the initials of the first five phyla discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota and Nanoarchaeota) is a group of ultrasmall symbionts able to survive in extreme ecosystems. The diversity and dynamics between DPANN archaea and their virome remain largely unknown. Here we use a metagenomic clustered regularly interspaced short palindromic repeats (CRISPR) screening approach to identify 97 globally distributed, non-redundant viruses and unclassified mobile genetic elements predicted to infect hosts across 8 DPANN phyla, including 7 viral groups not previously characterized. Genomic analysis suggests a diversity of viral morphologies including head-tailed, tailless icosahedral and spindle-shaped viruses with the potential to establish lytic, chronic or lysogenic infections. We also find evidence of a virally encoded Cas12f1 protein (probably originating from uncultured DPANN archaea) and a mini-CRISPR array, which could play a role in modulating host metabolism. Many metagenomes have virus-to-host ratios >10, indicating that DPANN viruses play an important role in controlling host populations. Overall, our study illuminates the underexplored diversity, functional repertoires and host interactions of the DPANN virome.

Isolation and Characterization of Lytic Bacteriophages Capable of Infecting Diverse Multidrug-Resistant Strains of Pseudomonas aeruginosa: PaCCP1 and PaCCP2

BACKGROUND/OBJECTIVES

Antimicrobial resistance (AMR) is a major public health threat, which is exacerbated by the lack of new antibiotics and the emergence of multidrug-resistant (MDR) superbugs. Comprehensive efforts and alternative strategies to combat AMR are urgently needed to prevent social, medical, and economic consequences. Pseudomonas aeruginosa is a pathogen responsible for a wide range of infections, from soft tissue infections to life-threatening conditions such as bacteremia and pneumonia. Bacteriophages have been considered as a potential therapeutic option to treat bacterial infections. Our aim was to isolate phages able to infect MDR P. aeruginosa strains.

METHODS

We isolated two lytic phages, using the conventional double layer agar technique (DLA), from samples obtained from the influent of a wastewater treatment plant in Concepción, Chile. The phages, designated as PaCCP1 and PaCCP2, were observed by electron microscopy and their host range was determined against multiple P. aeruginosa strains using DLA. Moreover, their genomes were sequenced and analyzed.

RESULTS

Phage PaCCP1 is a member of the Septimatrevirus genus and phage PaCCP2 is a member of the Pbunavirus genus. Both phages are tailed and contain dsDNA. The genome of PaCCP1 is 43,176 bp in length with a GC content of 54.4%, encoding 59 ORFs, one of them being a tRNA gene. The genome of PaCCP2 is 66,333 bp in length with a GC content of 55.6%, encoding 102 non-tRNA ORFs. PaCCP1 is capable of infecting five strains of P. aeruginosa, whereas phage PaCCP2 is capable of infecting three strains of P. aeruginosa. Both phages do not contain bacterial virulence or AMR genes and contain three and six putative Anti-CRISPR proteins.

CONCLUSIONS

Phages PaCCP1 and PaCCP2 show promise as effective treatments for MDR P. aeruginosa strains, offering a potential strategy for controlling this clinically important pathogen through phage therapy.

Isolation, Characterization, and Unlocking the Potential of Mimir124 Phage for Personalized Treatment of Difficult, Multidrug-Resistant Uropathogenic E. coli Strain

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

Multiomics analysis of Staphylococcus aureus ST239 strains resistant to virulent Herelleviridae phages

In the context of the antimicrobial therapy crisis, the significance of studying and implementing alternative treatment methods, particularly phage therapy, is increasingly evident. This study aimed to investigate the resistance of clinical Staphylococcus aureus ST239 strains to Herelleviridae phages through comparative genomics, transcriptomics, and proteomics. Analysis of resistant and sensitive S. aureus strains showed that resistant strains form a separate cluster on the phylogenetic tree, suggesting unique genetic traits underlying their phage resistance. Further in-depth analysis of the resistant SA191 strain infected with Herelleviridae phage, compared to an uninfected control, unveiled significant changes in the transcription of 462 genes (271↑ 191↓) at 5 min and 504 genes (276↑ 228↓) at 30 min post-infection. Proteomic analysis identified 184 differentially abundant proteins (41↑ 143↓) at 30 min. Functional analysis highlighted changes in the glycolysis, the tricarboxylic acid cycle, and transport systems; notable, changes were also observed in the transcription of prophage genes. Despite the observed metabolic shifts, classical resistance mechanisms related to teichoic acid synthesis, restriction-modification, and toxin-antitoxin systems were not identified, suggesting the existence of other mechanism. Our study contributes to the elucidation of S. aureus resistance mechanisms against Herelleviridae phages, highlighting the intricate nature of bacterial defense mechanisms.

GOPhage: protein function annotation for bacteriophages by integrating the genomic context

Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.

Cyanobacteria newly isolated from marine volcanic seeps display rapid sinking and robust, high-density growth

Cyanobacteria are photosynthetic organisms that play important roles in carbon cycling and are promising bioproduction chassis. Here, we isolate two novel cyanobacteria with 4.6Mbp genomes, UTEX 3221 and UTEX 3222, from a unique marine environment with naturally elevated CO₂. We describe complete genome sequences for both isolates and, focusing on UTEX 3222 due to its planktonic growth in liquid, characterize biotechnologically relevant growth and biomass characteristics. UTEX 3222 outpaces other fast-growing model strains on a solid medium. It can double every 2.35 hours in a liquid medium and grows to high density (>31 g/L biomass dry weight) in batch culture, nearly double that of Synechococcus sp. PCC 11901, whose high-density growth was recently reported. In addition, UTEX 3222 sinks readily, settling more quickly than other fast-growing strains, suggesting favorable economics of harvesting UTEX 3222 biomass. These traits may make UTEX 3222 a compelling choice for marine carbon dioxide removal (CDR) and photosynthetic bioproduction from CO₂. Overall, we find that bio-prospecting in environments with naturally elevated CO₂ may uncover novel CO₂-metabolizing organisms with unique characteristics.

IMPORTANCE

Cyanobacteria provide a potential avenue for both biomanufacturing and combatting climate change via high-efficiency photosynthetic carbon sequestration. This study identifies novel photosynthetic organisms isolated from a unique geochemical environment and describes their genomes, growth behavior in culture, and biochemical composition. These cyanobacteria appear to make a tractable research model, and cultures are made publicly available alongside information about their culture and maintenance. Application of these organisms to carbon sequestration and/or biomanufacturing is discussed, including unusual, rapid settling characteristics of the strains relevant to scaled culture.

Designing a simple and efficient phage biocontainment system using the amber suppressor initiator tRNA

Multidrug-resistant infections are becoming increasingly prevalent worldwide. One of the fastest-emerging alternative and adjuvant therapies being proposed is phage therapy. Naturally isolated phages are used in the vast majority of phage therapy treatments today. Engineered phages are being developed to enhance the effectiveness of phage therapy, but concerns over their potential escape remain a salient issue. To address this problem, we designed a biocontained phage system based on conditional replication using amber stop codon suppression. This system can be easily installed on any natural phage with a known genome sequence. To test the system, we individually mutated the start codons of three essential capsid genes in phage φX174 to the amber stop codon (UAG). These phages were able to efficiently infect host cells expressing the amber initiator tRNA, which suppresses the amber stop codon and initiates translation at TAG stop codons. The amber phage mutants were also able to successfully infect host cells and reduce their population on solid agar and liquid culture but could not produce infectious particles in the absence of the amber initiator tRNA or complementing capsid gene. We did not detect any growth-inhibiting effects on E. coli strains known to lack a receptor for φX174 and we showed that engineered phages have a limited propensity for reversion. The approach outlined here may be useful to control engineered phage replication in both the lab and clinic.