Bacteriophage evolution differs by host, lifestyle and genome

Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions

Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.

Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems

Restriction-modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects of mutations. This review provides a comprehensive synthesis of current insights into RMS, emphasizing their structural and functional diversity, ecological and evolutionary roles, and expanding applications in biotechnology. By integrating recent advances with an analysis of persisting challenges, we highlight the critical contributions of RMS to both fundamental microbiology and practical applications in biomedicine and industrial biotechnology. Furthermore, we discuss emerging research directions in RMS, particularly in light of novel technologies and the increasing importance of microbial genetics in addressing global health and environmental issues.

Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.

Unveiling the role of phages in shaping the periodontal microbial ecosystem

The oral microbiome comprises various species and plays a crucial role in maintaining the oral ecosystem and host health. Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.IMPORTANCEIn the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.

New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation

Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.

Wolbachia and its pWCP plasmid show differential dynamics during the development of Culex mosquitoes

Mosquitoes are major vectors of pathogens such as arboviruses and parasites, causing significant health impacts each year. Wolbachia, an intracellular bacterium widely distributed among arthropods, represents a promising vector control solution. This bacterium can reduce the transmission of dengue, Zika, and chikungunya arboviruses and manipulate the reproduction of its host through its prophage WO. Although research on the Wolbachia mobilome primarily focuses on WO and the phenotypes it induces, the function of Wolbachia plasmid pWCP, recently discovered and reported to be strikingly conserved worldwide, remains unknown. In this study, we analyzed the presence and abundance of pWCP as well as Wolbachia in two different species of Culex mosquitoes, one of the most widespread genera in the world and a vector of numerous diseases. We compared the relative densities of the bacterium and its mobile genetic element in Culex pipiens molestus and Culex quinquefasciatus, a facultatively autogenous and an anautogenous species, respectively, throughout their development from the larval stage L1 to the adult individual specimen using quantitative Polymerase Chain Reaction (PCR). Our results suggest that 2-5 copies of pWCP occur in Wolbachia cells on average, and the plasmid co-replicates with Wolbachia cells. Moreover, Wolbachia and pWCP exhibit differential levels of abundance at specific development stages throughout the mosquito's life cycle in each species. These findings indicate important, and likely beneficial, roles for the plasmid in the bacterium's biology in different mosquito species as well as complex interaction dynamics between Wolbachia and its host during its life cycle.IMPORTANCEMosquitoes of the Culex genus are critical vectors for numerous diseases, causing significant public health concerns. The intracellular bacterium Wolbachia has emerged as a promising vector control solution due to its ability to interfere with pathogen transmission and manipulate mosquito reproduction. However, unlike the extensively studied WO phage, the biological significance and function of Wolbachia's pWCP plasmid, a recently discovered and strikingly conserved mobile genetic element in Culex species, remain unknown. This study investigates the developmental dynamics of pWCP and Wolbachia in two Culex mosquito species, Culex pipiens molestus and Culex quinquefasciatus across their life cycle. In general, the abundance levels of Wolbachia and the plasmid were found to vary across life stages and differ between the two species. However, a relatively small number of pWCP copies were observed per Wolbachia cell, together with a co-replication of the plasmid with the bacterium for most developmental stages. Altogether, these findings suggest a likely beneficial and non-parasitic role for pWCP in Wolbachia's biology, which may contribute to the intricate interactions between the bacterium and its mosquito hosts.

Pseudomonas Phage Lydia and the Evolution of the Mesyanzhinovviridae Family

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

Oral bacteriophages and their potential as adjunctive treatments for periodontitis: a narrative review

Background

There is no specific cure for periodontitis and treatment is symptomatic, primarily by physical removal of the subgingival plaque biofilm. Current non-surgical periodontal therapy becomes less effective as the periodontal pocket depth increases and as such new adjunctive treatments are required. The development of antibiotic resistance has driven a recent resurgence of interest in bacteriophage therapy.

Methods

Here we review the published literature with a focus on the subgingival phageome, key oral pathobionts and the dysbiotic nature of periodontitis leading to the emergence of synergistic, proteolytic and inflammophilic bacterial species in subgingival plaque. We discuss the opportunities available, the barriers and the steps needed to develop bacteriophage therapy as an adjunctive treatment for periodontitis.

Results

The oral phageome (or virome) is diverse, featuring abundant bacteriophage, that could target key subgingival bacteria. Yet to date few bacteriophages have been isolated and characterised from oral bacterial species, although many more have been predicted by genomic analyses. Bacteriophage therapy has yet to be tested against chronic diseases that are caused by dysbiosis of the endogenous microbial communities.

Conclusion

To be effective as an adjunctive treatment for periodontitis, bacteriophage therapy must cause the collapse of the dysbiotic bacterial community, thereby resolving inflammation and enabling the reestablishment of a health-associated mutualistic subgingival bacterial community. The isolation and characterisation of novel oral bacteriophage is an essential first step in this process.

Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism

Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC's accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at https://github.com/bioinf-mcb/MANIAC.IMPORTANCEWe introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.

Towards a unifying phylogenomic framework for tailed phages

Classifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient similarity in the genetic machinery that unifies them to reconstruct an inclusive, stable phylogeny of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability, reproducibility, and the inclusion of modes of evolution, like gene gains and losses, remain key challenges. Here, we present a novel, comprehensive, and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on the presence and absence of a fixed set of gene families which are used as binary trait data that is input into maximum likelihood models. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenome-derived phages. We also quantify the mosaicism of replication and structural genes among known families, and our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion. Taken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution.

Unravelling viral ecology and evolution over 20 years in a freshwater lake

As freshwater lakes undergo rapid anthropogenic change, long-term studies reveal key microbial dynamics, evolutionary shifts and biogeochemical interactions, yet the vital role of viruses remains overlooked. Here, leveraging a 20 year time series from Lake Mendota, WI, USA, we characterized 1.3 million viral genomes across time, seasonality and environmental factors. Double-stranded DNA phages from the class Caudoviricetes dominated the community. We identified 574 auxiliary metabolic gene families representing over 140,000 auxiliary metabolic genes, including important genes such as psbA (photosynthesis), pmoC (methane oxidation) and katG (hydrogen peroxide decomposition), which were consistently present and active across decades and seasons. Positive associations and niche differentiation between virus-host pairs, including keystone Cyanobacteria, methanotrophs and Nanopelagicales, emerged during seasonal changes. Inorganic carbon and ammonium influenced viral abundances, underscoring viral roles in both 'top-down' and 'bottom-up' interactions. Evolutionary processes favoured fitness genes, reduced genomic heterogeneity and dominant sub-populations. This study transforms understanding of viral ecology and evolution in Earth's microbiomes.

vB_EcoM-P896 coliphage isolated from duck sewage can lyse both intestinal pathogenic Escherichia coli and extraintestinal pathogenic E. coli

Pathogenic Escherichia coli strains cause diseases in both humans and animals. The limiting factors to prevent as well as control infections from pathogenic E. coli strains are their pathotypes, serotypes, and drug resistance. Herein, a bacteriophage (vB_EcoM-P896) has been isolated from duck sewage. Furthermore, aside from targeting intestinal pathogenic E. coli strains like enteropathogenic E. coli, Shiga toxin-producing E. coli, entero-invasive E. coli, and enteroaggregative E. coli, vB_EcoM-P896 can cause lysis in extraintestinal pathogenic E. coli strains such as avian pathogenic E. coli. Stability analysis revealed that vB_EcoM-P896 was stable under the following conditions: temperature, 4℃-50℃; pH, 3-11. The sequencing of the vB_EcoM-P896 genome was conducted utilizing an HiSeq system (Illumina, San Diego, CA) and subjected to de novo assembling with the aid of Spades 3.11.1. The characteristics of the DNA genome were as follows: size, 170,656 bp; GC content, 40.4%; the number of putative coding regions, 294. Transmission electron microscopy analysis of morphology and genome analysis revealed that the phage vB_EcoM-P896 belonged to the order Caudovirales and the family Myoviridae. The pan-genome analysis of vB_EcoM-P896 was divided into two levels. The first level involved the analysis of 91 strains of muscle tail phages, which were mainly divided into 5 groups. The second level involved the analysis of 24 strains of myophage with high homology. Of the 1480 gene clusters, 23 were shared core genes. Neighbor-joining phylogenetic trees were constructed using the Poisson model with MEGA6.0 based on the conserved sequences of phage proteins, the amino acid sequence of the terminase large subunit, and tail fibrin. Further analysis revealed that vB_EcoM-P896 was a typical T4-like potent phage with potential clinical applications.

Elucidation of molecular function of phage protein responsible for optimization of host cell lysis

BACKGROUND

Bacteriophages (or phages) replicate by utilizing bacterial resources and destroy their host cells at the end of the replication cycle. Phages employ multiple proteins to optimize host cell lysis, thereby maximizing the production of phage particles. However, elucidating the entire lysis process is challenging due to the abundance of uncharacterized genes in the phage genome.

RESULTS

In this study, we identified a gene orf52 from BSPM4 phage genome that showed antibacterial activity in Salmonella. Investigation of physiological role of ORF52 in the phage replication revealed that ORF52 could modulate the holin function to fine-tune a cell lysis, providing replication advantages to phages under high phage population density.

CONCLUSIONS

We concluded that ORF52 may optimize phage replication by modulating the timing of phage-mediated cell lysis. This study provides a unique example of a phage protein involved in fine-tuning lysis timing.

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.

Evolution shapes and conserves genomic signatures in viruses

The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome 1, such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse.Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors.

How to introduce a new bacteriophage on the block: a short guide to phage classification

Bacteriophage (phage) studies established the field of molecular biology and continue to propel life science research forward due to their diversity, abundance, and potential applications. In this Gem article, we orient newcomers to four common ways phages are currently classified: infection cycle, morphology, taxonomy, and supergroup. By using these classifications, researchers can determine where any novel phage fits into the scheme of the known "phage-verse".

Nine Cluster E mycobacteriophages isolated from soil

Mycobacteriophages FireRed, MISSy, MPhalcon, Murica, Sassay, Terminus, Willez, YassJohnny, and Youngblood were isolated from soil using Mycobacterium smegmatis as a host. Genome sequencing and annotation revealed that they belong to Actinobacteriophage Cluster E. Here, we describe the features of their genomes and discuss similarities within these Cluster E phages.

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

BACKGROUND

Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS

Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS

Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.

Unveiling the genomic diversity and ecological impact of phage communities in hospital wastewater

Phages are pivotal in shaping microbial communities and biogeochemical cycles, while our understanding of the diversity, functions potential, and resistance gene carriage of phages in hospital wastewater (HWW) remains limited. We collected influent and effluent samples from the 3 hospital wastewater treatment plants (HWTPs) to assess the diversity and fate of phages, the interactions between phages and hosts, and the presence of resistance genes and auxiliary metabolic genes (AMGs) encoded by phages. Compared to influent, effluent showed reduced phage abundance and altered composition, with decreases in Microviridae and Inoviridae. The gene-sharing network highlights that many phages in HWW are not classified in known viral genera, suggesting HWW as a rich source of new viruses. There was a significant association between phages and microorganisms, with approximately 32.57 % of phages expected to be capable of infecting microbial hosts, characterized primarily by lytic activity. A total of 8 unique antibiotic resistance genes, 13 unique metal resistance genes, and 5 mobile genetic elements were detected in 3 HWTPs phageomes. Phage AMGs have the potential to influence carbon, nitrogen, phosphorus, and sulfur metabolism, impacting biogeochemical cycles. This study reveals the genomic diversity and ecological role of phages in HWTPs, highlighting their environmental and ecosystem impact.

SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education

Research opportunities for undergraduate students are strongly advantageous, but implementation at a large scale presents numerous challenges. The enormous diversity of the bacteriophage population and a supportive programmatic structure provide opportunities to engage early-career undergraduates in phage discovery, genomics, and genetics. The Science Education Alliance (SEA) is an inclusive Research-Education Community (iREC) providing centralized programmatic support for students and faculty without prior experience in virology at institutions from community colleges to research-active universities to participate in two course-based projects, SEA-PHAGES (SEA Phage Hunters Advancing Genomic and Evolutionary Science) and SEA-GENES (SEA Gene-function Exploration by a Network of Emerging Scientists). Since 2008, the SEA has supported more than 50,000 undergraduate researchers who have isolated more than 23,000 bacteriophages of which more than 4,500 are fully sequenced and annotated. Students have functionally characterized hundreds of phage genes, and the phage collection has fueled the therapeutic use of phages for treatment of Mycobacterium infections. Participation in the SEA promotes student persistence in science education, and its inclusivity promotes a more equitable scientific community.

synphage: a pipeline for phage genome synteny graphics focused on gene conservation

Motivation

Visualization and comparison of genome maps of bacteriophages can be very effective, but none of the tools available on the market allow visualization of gene conservation between multiple sequences at a glance. In addition, most bioinformatic tools running locally are command line only, making them hard to setup, debug, and monitor.

Results

To address these motivations, we developed synphage, an easy-to-use and intuitive tool to generate synteny diagrams from GenBank files. This software has a user-friendly interface and uses metadata to monitor the progress and success of the data transformation process. The output plot features colour-coded genes according to their degree of conservation among the group of displayed sequences. The strength of synphage lies also in its modularity and the ability to generate multiple plots with different configurations without having to re-process all the data. In conclusion, synphage reduces the bioinformatic workload of users and allows them to focus on analysis, the most impactful area of their work.

Availability and implementation

The synphage tool is implemented in the Python language and is available from the GitHub repository at https://github.com/vestalisvirginis/synphage. This software is released under an Apache-2.0 licence. A PyPI synphage package is available at https://pypi.org/project/synphage/ and a containerized version is available at https://hub.docker.com/r/vestalisvirginis/synphage. Contributions to the software are welcome whether it is reporting a bug or proposing new features and the contribution guidelines are available at https://github.com/vestalisvirginis/synphage/blob/main/CONTRIBUTING.md.

A natural ANI gap that can define intra-species units of bacteriophages and other viruses

Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%-99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars.

IMPORTANCE

Viral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.

Genomic sequences of Mycobacterium smegmatis A cluster phages LBerry, Pembroke, and Zolita

LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect Mycobacterium smegmatis mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.

A Bioinformatic Ecosystem for Bacteriophage Genomics: PhaMMSeqs, Phamerator, pdm_utils, PhagesDB, DEPhT, and PhamClust

The last thirty years have seen a meteoric rise in the number of sequenced bacteriophage genomes, spurred on by both the rise and success of groups working to isolate and characterize phages, and the rapid and significant technological improvements and reduced costs associated with sequencing their genomes. Over the course of these decades, the tools used to glean evolutionary insights from these sequences have grown more complex and sophisticated, and we describe here the suite of computational and bioinformatic tools used extensively by the integrated research-education communities such as SEA-PHAGES and PHIRE, which are jointly responsible for 25% of all complete phage genomes in the RefSeq database. These tools are used to integrate and analyze phage genome data from different sources, for identification and precise extraction of prophages from bacterial genomes, computing "phamilies" of related genes, and displaying the complex nucleotide and amino acid level mosaicism of these genomes. While over 50,000 SEA-PHAGES students have primarily benefitted from these tools, they are freely available for the phage community at large.

Gene Transfer Among Viruses Substantially Contributes to Gene Gain of Giant Viruses

The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation, a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.

DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information

Bacteriophages are the viruses that infect bacterial cells. They are the most diverse biological entities on earth and play important roles in microbiome. According to the phage lifestyle, phages can be divided into the virulent phages and the temperate phages. Classifying virulent and temperate phages is crucial for further understanding of the phage-host interactions. Although there are several methods designed for phage lifestyle classification, they merely either consider sequence features or gene features, leading to low accuracy. A new computational method, DeePhafier, is proposed to improve classification performance on phage lifestyle. Built by several multilayer self-attention neural networks, a global self-attention neural network, and being combined by protein features of the Position Specific Scoring Matrix matrix, DeePhafier improves the classification accuracy and outperforms two benchmark methods. The accuracy of DeePhafier on five-fold cross-validation is as high as 87.54% for sequences with length >2000bp.

Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium

Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.

Phage therapy as a glimmer of hope in the fight against the recurrence or emergence of surgical site bacterial infections

PURPOSE

Over the last decade, surgery rates have risen alarmingly, and surgical-site infections are expanding these concerns. In spite of advances in infection control practices, surgical infections continue to be a significant cause of death, prolonged hospitalization, and morbidity. As well as the presence of bacterial infections and their antibiotic resistance, biofilm formation is one of the challenges in the treatment of surgical wounds.

METHODS

This review article was based on published studies on inpatients and laboratory animals receiving phage therapy for surgical wounds, phage therapy for tissue and bone infections treated with surgery to prevent recurrence, antibiotic-resistant wound infections treated with phage therapy, and biofilm-involved surgical wounds treated with phage therapy which were searched without date restrictions.

RESULTS

It has been shown in this review article that phage therapy can be used to treat surgical-site infections in patients and animals, eliminate biofilms at the surgical site, prevent infection recurrence in wounds that have been operated on, and eradicate antibiotic-resistant infections in surgical wounds, including multi-drug resistance (MDR), extensively drug resistance (XDR), and pan-drug resistance (PDR). A cocktail of phages and antibiotics can also reduce surgical-site infections more effectively than phages alone.

CONCLUSION

In light of these encouraging results, clinical trials and research with phages will continue in the near future to treat surgical-site infections, biofilm removal, and antibiotic-resistant wounds, all of which could be used to prescribe phages as an alternative to antibiotics.

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.

Phage-plasmids promote recombination and emergence of phages and plasmids

Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations

It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.

Large language models improve annotation of prokaryotic viral proteins

Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.

Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats

Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern. Proteobacteria and Actinobacteria were the main potential hosts of ARGs and viruses, and the richness of ARGs carried by the hosts was positively correlated with viral abundance, suggesting that the transmission of viruses in the hosts could disseminate ARGs. Source tracking indicated that >18 % of the ARGs and >25 % of the viruses detected in downstream habitats originated from glaciers, demonstrating that glaciers could be one of the potential sources of ARGs and viruses in downstream habitats. Increased solar radiation and emission of carbon dioxide mainly influenced the release of the ARGs and viruses from glaciers into downstream habitats. This study provides a systematic insight demonstrating the release of ARGs and viruses from the melting glaciers, potentially increasing ecological pressure.

PhageGE: an interactive web platform for exploratory analysis and visualization of bacteriophage genomes

BACKGROUND

Antimicrobial resistance is a serious threat to global health. Due to the stagnant antibiotic discovery pipeline, bacteriophages (phages) have been proposed as an alternative therapy for the treatment of infections caused by multidrug-resistant pathogens. Genomic features play an important role in phage pharmacology. However, our knowledge of phage genomics is sparse, and the use of existing bioinformatic pipelines and tools requires considerable bioinformatic expertise. These challenges have substantially limited the clinical translation of phage therapy.

FINDINGS

We have developed PhageGE (Phage Genome Explorer), a user-friendly graphical interface application for the interactive analysis of phage genomes. PhageGE enables users to perform key analyses, including phylogenetic analysis, visualization of phylogenetic trees, prediction of phage life cycle, and comparative analysis of phage genome annotations. The new R Shiny web server, PhageGE, integrates existing R packages and combines them with several newly developed functions to facilitate these analyses. Additionally, the web server provides interactive visualization capabilities and allows users to directly export publication-quality images.

CONCLUSIONS

PhageGE is a valuable tool that simplifies the analysis of phage genome data and may expedite the development and clinical translation of phage therapy. PhageGE is publicly available at https://jason-zhao.shinyapps.io/PhageGE_Update/.

Evolutionary and co-evolutionary phage training approaches enhance bacterial suppression and delay the emergence of phage resistance

The development of phage resistance by bacteria is a major barrier that impedes the therapeutic use of phages. Phage training has been proposed as a novel tool that harnesses the evolutionary potential of phages to improve phage infectivity. Both evolutionary and co-evolutionary phage training models have been previously reported to train phages. However, both of these phage training models have been reported able to effectively suppress the emergence of phage-resistant bacteria mutants, thus presenting a contradictory phenomenon. Therefore, in this study, we set out to systematically compare the effectiveness of both evolutionary and co-evolutionary phage training models with regard to phage physiology, infectivity, and genotype. To this end, a natural lytic phage capable of infecting a Klebsiella pneumonia strain was isolated from wastewater and subjected to evolutionary and co-evolutionary phage training for 30 days. After the phage training, the physiology and genomic characteristics of evolved and co-evolved phages were assessed. Our results demonstrated that both evolved and co-evolved phages exhibit improved bacterial suppression activity and are able to delay the emergence of phage resistance. Furthermore, both phages harbored unique genome mutational changes in different functionally associated phage proteins. Similarly, evolved and co-evolved phage-resistant bacteria mutants that arose post phage infection displayed varying phage resistance sensitivities, which may be correlated to the unique genome mutational change identified in cell membrane structure. In particular, co-evolved phage-resistant bacteria mutants exhibited less phage resistance compared to evolved phage-resistant bacteria mutants. These results highlighted the finding that the co-evolutionary phage training model serves as a better phage training model as it endows phage with improved infectivity, but also selects for phage-resistant bacteria with a lower phage resistance when compared to evolutionary phage training.

Bacteriophage Taxonomy: A Continually Evolving Discipline

While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.

Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates

Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.

Comparative Analyses of Bacteriophage Genomes

Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.

Benchmarking DNA isolation methods for marine metagenomics

Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrate Magallana gigas) with eight commercially available DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a "kitome", e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

Background

Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

Results

Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

Conclusions

Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.

Characterization of novel recombinant mycobacteriophages derived from homologous recombination between two temperate phages

Comparative analyses of mycobacteriophage genomes reveals extensive genetic diversity in genome organization and gene content, contributing to widespread mosaicism. We previously reported that the prophage of mycobacteriophage Butters (cluster N) provides defense against infection by Island3 (subcluster I1). To explore the anti-Island3 defense mechanism, we attempted to isolate Island3 defense escape mutants on a Butters lysogen, but only uncovered phages with recombinant genomes comprised of regions of Butters and Island3 arranged from left arm to right arm as Butters-Island3-Butters (BIBs). Recombination occurs within two distinct homologous regions that encompass lysin A, lysin B, and holin genes in one segment, and RecE and RecT genes in the other. Structural genes of mosaic BIB genomes are contributed by Butters while the immunity cassette is derived from Island3. Consequently, BIBs are morphologically identical to Butters (as shown by transmission electron microscopy) but are homoimmune with Island3. Recombinant phages overcome antiphage defense and silencing of the lytic cycle. We leverage this observation to propose a stratagem to generate novel phages for potential therapeutic use.

A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations

Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.

Genome and characteristics of Arthrobacter globiformis AZ cluster phage London

London is a predicted temperate bacteriophage with siphovirus morphology infecting Arthrobacter globiformis NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp comprising 69 predicted open-reading frames and no tRNA genes. It is categorized as a cluster AZ1 phage along with closely related actinobacteriophages Elezi, Eraser, and Niobe.

Genome sequence of Streptomyces BM cluster phage Frankenweenie

Frankenweenie is a newly isolated bacteriophage that infects Streptomyces scabiei RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.

Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy

Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities and ecosystems. They have gained attention as potential agents against antibiotic resistance. In phage therapy, lytic phages are preferred for their bacteria killing ability, while temperate phages, which can transfer antibiotic resistance or toxin genes, are avoided. Selection relies on plaque morphology and genome sequencing. This review outlines annotating genomes, identifying critical genomic features, and assigning functional labels to protein-coding sequences. These annotations prevent the transfer of unwanted genes, such as antimicrobial resistance or toxin genes, during phage therapy. Additionally, it covers International Committee on Taxonomy of Viruses (ICTV)-an established phage nomenclature system for simplified classification and communication. Accurate phage genome annotation and nomenclature provide insights into phage-host interactions, replication strategies, and evolution, accelerating our understanding of the diversity and evolution of phages and facilitating the development of phage-based therapies.

PhamClust: a phage genome clustering tool using proteomic equivalence

IMPORTANCE

Bacteriophage genomes are pervasively mosaic, presenting challenges to describing phage relatedness. Here, we describe PhamClust, a bioinformatic approach for phage genome comparisons that uses a new metric of proteomic equivalence quotient for comparative genomics. PhamClust reliably assorts genomes into groups or clusters of related phages and can subdivide clusters into subclusters. PhamClust is computationally efficient and can readily process thousands of phage genomes. It is also a useful analytic tool for exploring the different types of inter-genome relatedness characteristic of phages in different clusters.

Genome sequence of bacteriophage Aoka, a cluster FO phage isolated using Arthrobacter globiformis

We report the discovery and genome sequence of bacteriophage Aoka, an actinobacteriophage isolated from a soil sample in Pueblo, Colorado using Arthrobacter globiformis, B2880-SEA. Its genome length is 36,744 base pairs with 54 protein-coding genes. Based on gene content similarity to other actinobacteriophages, Aoka is assigned to cluster FO.

Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.

Mycobacteriophage Rita: a cluster F1 phage discovered in North Easton, Massachusetts

Mycobacteriophage Rita infects Mycobacterium smegmatis mc2155 and was isolated from a soil sample collected in North Easton, Massachusetts. Assigned to cluster F1 based on sequence similarity to other phages in the same cluster, Rita has a 58,771 bp genome and encodes 104 genes. Rita is 98% similar to phage Bipolar.

Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases

DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. The results demonstrate that 97.60% of gut phages exhibit methylation, with certain factors correlating with methylation densities. Phages with higher methylation densities appear to have potential viability advantages. Strikingly, more than one-third of the phages possess their own DNA methyltransferases (MTases). Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage-bacterium interactions. Furthermore, these MTases can be employed to accurately predict phage-host relationships. Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage-encoded MTases.