Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

Short-read and Long-read PCR-Free Sequencing of Bacteriophages Using Ultra-Low Starting DNA Input

Preparing phage DNA in sufficient quantities for sequencing is often a challenging task, especially when a sensitive bacterial host is not available for phage propagation.1 This limitation poses a significant obstacle in phage research as the availability of adequate phage DNA is often considered crucial for various analyses, including genome sequencing, functional studies, and therapeutic developments. Also, because DNA extraction from phage samples (e.g., from bacterial induction) can yield low amounts of genomic DNA, many studies utilize tagmentation for amplification-free quantitative sequencing. However, this technique has the drawback of losing phage genome ends (termini) and creating biases in genome coverage.2,3 Polymerase chain reaction (PCR)-free sequencing is often recommended or even necessary to obtain an unbiased characterization of phage genomes or communities. However, sequencing very low quantities of DNA without PCR amplification is challenging, and sequencing service providers, as well as library kit manufacturers, will only guarantee products and results with relatively high DNA inputs. In this study, we aimed to assess the feasibility of sequencing phage genomic DNA with very low DNA starting material and to determine the impact of decreasing DNA input on sequencing quality using both Illumina short-read and Nanopore long-read technologies. We analyzed the quantity and quality of output sequences (and their impact on genome assemblies) for different ranges of input DNA concentrations, starting at the recommended DNA inputs for each technology. We concluded that it is achievable to perform sequencing of high quality with DNA inputs that are lower (i.e., 1000-fold lower) than manufacturers' recommendations or requirements. In this study, we successfully sequenced phage genomic DNA (without PCR amplification) using as little as 1 ng of total input DNA (or 0.02 ng/uL in 50 uL eluted volume) for short-read sequencing with Illumina technology and 0.4 ng (or 0,036 ng/uL in 11 uL eluted volume) for long-read sequencing with Nanopore technology.

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.

Diverse phage communities are maintained stably on a clonal bacterial host

Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, we discovered that phage diversity consistently outstripped the diversity of their bacterial hosts under simple experimental conditions. We assembled and passaged dozens of diverse phage communities on a single, nonevolving strain of Escherichia coli until the phage communities reached equilibrium. In all cases, we found that two or more phage species coexisted stably, despite competition for a single, clonal host population. Phage coexistence was supported through host phenotypic heterogeneity, whereby bacterial cells adopting different growth phenotypes served as niches for different phage species. Our experiments reveal that a rich community ecology of bacteriophages can emerge on a single bacterial host.

The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Coordinated transcriptional response to environmental stress by a Synechococcus virus

Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon among cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that the production of infectious virus particles of such viruses is reduced in low P conditions. However, this reduction in progeny is not caused by impaired phage genome replication, thought to be a major sink for cellular phosphate. Instead, transcriptomic analysis showed that under low P conditions, a PstS-lacking cyanophage increased the expression of a specific gene set that included mazG, hli2, and gp43 encoding a pyrophosphatase, a high-light inducible protein and DNA polymerase, respectively. Moreover, several of the upregulated genes were controlled by the host's phoBR two-component system. We hypothesize that recycling and polymerization of nucleotides liberates free phosphate and thus allows viral morphogenesis, albeit at lower rates than when phosphate is replete or when phages encode pstS. Altogether, our data show how phage genomes, lacking obvious P-stress-related genes, have evolved to exploit their host's environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.

Genome Sequence and Characterization of Coliphage Môr Ffagbaw

Background

The quality of coastal waters around the United Kingdom is an area of increasing concern following sewer overflow, where wastewater is discharged into the environment. Coliphages, viruses that infect coliform bacteria, are associated with water quality in aquatic systems, yet remain largely uncharacterized at the genomic level.

Materials and Methods

Phage môr ffagbaw was isolated from seawater against Escherichia coli by enrichment and plaque assays. Whole genome sequencing, transmission electron microscopy, and host range analysis against the E. coli reference (ECOR) collection were used to characterize the phage.

Results

The virion had a siphovirus morphology and genomic analysis placed it within the family Drexlerviridae, subfamily Tempevirinae, and forms a new species within the genus Hanrivervirus. Spot assays revealed that phage môr ffagbaw could form plaques on 6 out of 72 ECOR strains (8%).

Conclusions

Môr ffagbaw represents a new species of phage within the genus Hanrivervirus, with a narrow host range.

Genomic analysis of Anderson typing phages of Salmonella Typhimrium: towards understanding the basis of bacteria-phage interaction

The Anderson phage typing scheme has been successfully used worldwide for epidemiological surveillance of Salmonella enterica serovar Typhimurium. Although the scheme is being replaced by whole genome sequence subtyping methods, it can provide a valuable model system for study of phage-host interaction. The phage typing scheme distinguishes more than 300 definitive types of Salmonella Typhimurium based on their patterns of lysis to a unique collection of 30 specific Salmonella phages. In this study, we sequenced the genomes of 28 Anderson typing phages of Salmonella Typhimurium to begin to characterize the genetic determinants that are responsible for the differences in these phage type profiles. Genomic analysis of typing phages reveals that Anderson phages can be classified into three different groups, the P22-like, ES18-like and SETP3-like clusters. Most Anderson phages are short tailed P22-like viruses (genus Lederbergvirus); but phages STMP8 and STMP18 are very closely related to the lambdoid long tailed phage ES18, and phages STMP12 and STMP13 are related to the long noncontractile tailed, virulent phage SETP3. Most of these typing phages have complex genome relationships, but interestingly, two phage pairs STMP5 and STMP16 as well as STMP12 and STMP13 differ by a single nucleotide. The former affects a P22-like protein involved in DNA passage through the periplasm during its injection, and the latter affects a gene whose function is unknown. Using the Anderson phage typing scheme would provide insights into phage biology and the development of phage therapy for the treatment of antibiotic resistant bacterial infections.

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

BACKGROUND

The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

RESULTS

Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

CONCLUSIONS

Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.

Isolation and characterization of Escherichia coli O157: H7 novel bacteriophage for controlling this food-borne pathogen

Escherichia coli O157: H7 is known as a high-risk food-born pathogen, and its removal is vital for maintaining food safety. The increasing trend of food-borne diseases caused by this bacterium and other pathogens indicates the low efficiency of the methods to remove pathogens from foodstuffs. One of the new and effective methods is to use of a bio-control agent called bacteriophage, which has shown good function in eliminating and reducing pathogens. In this study, a novel bacteriophage was isolated and identified from the slaughterhouse wastewater to control E. coli O157: H7. This bacteriophage belonged to the Myoviridae family. Two bacterial genera including E. coli and Salmonella, were allocated to determine the bacteriophage host range; the result showed that the anti- Salmonella effect of phage was low. The phage was stable at high temperature (80°C) and caused an acceptable reduction in the E. coli O157: H7 (4.18 log CFU / mL for 10 hours). The isolated bacteriophage was corroborated to be completely safe based on the whole genome sequencing and lack of any virulence factor from the host bacteria. Considering the characteristics of this phage and its function in vitro, this bacteriophage may be used as an effective bio-control agent in foods with the possible E. coli O157: H7 -induced contamination.

Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation

All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. This article defines 14 questions for those new to phage genomics that should be addressed before submitting a genome sequence to the International Nucleotide Sequence Database Collaboration or writing a publication.

INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes

Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade. Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata. Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (∼70%) than temperate (∼30%) within our database. Collectively, this results in ∼54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host. Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.

Phage Genome Annotation: Where to Begin and End

With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.

Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function

Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.

Fishing for phages in metagenomes: what do we catch, what do we miss?

Metagenomics and metatranscriptomics have become the principal approaches for discovery of novel bacteriophages and preliminary characterization of their ecology and biology. Metagenomic sequencing dramatically expanded the known diversity of tailed and non-tailed phages with double-stranded DNA genomes and those with single-stranded DNA genomes, whereas metatranscriptomics led to the discovery of thousands of new single-stranded RNA phages. Apart from expanding phage diversity, metagenomics studies discover major novel groups of phages with unique features of genome organization, expression strategy and virus-host interaction, such as the putative order 'crAssvirales', which includes the most abundant human-associated viruses. The continued success of metagenomics hinges on the combination of the most powerful computational methods for phage genome assembly and analysis including harnessing CRISPR spacers for the discovery of novel phages and host assignment. Together, these approaches could make a comprehensive characterization of the earth phageome a realistic goal.

A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution

Marine bacterial viruses (bacteriophages) are abundant biological entities that are vital for shaping microbial diversity, impacting marine ecosystem function, and driving host evolution.1, 2, 3 The marine roseobacter clade (MRC) is a ubiquitous group of heterotrophic bacteria^4,5 that are important in the elemental cycling of various nitrogen, sulfur, carbon, and phosphorus compounds.6, 7, 8, 9, 10 Bacteriophages infecting MRC (roseophages) have thus attracted much attention and more than 30 roseophages have been isolated,11, 12, 13 the majority of which belong to the N4-like group (Podoviridae family) or the Chi-like group (Siphoviridae family), although ssDNA-containing roseophages are also known.¹⁴ In our attempts to isolate lytic roseophages, we obtained two new phages (DSS3_VP1 and DSS3_PM1) infecting the model MRC strain Ruegeria pomeroyi DSS-3. Here, we show that not only do these phages have unusual substitution of deoxythymidine with deoxyuridine (dU) in their DNA, but they are also phylogenetically distinct from any currently known double-stranded DNA bacteriophages, supporting the establishment of a novel family (“Naomiviridae”). These dU-containing phages possess DNA that is resistant to the commonly used library preparation method for metagenome sequencing, which may have caused significant underestimation of their presence in the environment. Nevertheless, our analysis of Tara Ocean metagenome datasets suggests that these unusual bacteriophages are of global importance and more diverse than other well-known bacteriophages, e.g., the Podoviridae in the oceans, pointing to an overlooked role for these novel phages in the environment.

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Two new roseophages isolated from the marine environment

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They have an unusual deoxythymidine to deoxyuridine substitution in their genomes

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These dU genomes are resistant to a common method of metagenome library preparation

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These phages represent a new family and are globally distributed in the oceans

The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens

Although the prokaryotic communities of the rumen microbiome are being uncovered through genome sequencing, little is known about the resident viral populations. Whilst temperate phages can be predicted as integrated prophages when analyzing bacterial and archaeal genomes, the genetics underpinning lytic phages remain poorly characterized. To the five genomes of bacteriophages isolated from rumen-associated samples sequenced and analyzed previously, this study adds a further five novel genomes and predictions gleaned from them to further the understanding of the rumen phage population. Lytic bacteriophages isolated from fresh ovine and bovine fecal and rumen fluid samples were active against the predominant fibrolytic ruminal bacterium Butyrivibrio fibrisolvens. The double stranded DNA genomes were sequenced and reconstructed into single circular complete contigs. Based on sequence similarity and genome distances, the five phages represent four species from three separate genera, consisting of: (1) Butyrivibrio phages Arian and Bo-Finn; (2) Butyrivibrio phages Idris and Arawn; and (3) Butyrivibrio phage Ceridwen. They were predicted to all belong to the Siphoviridae family, based on evidence in the genomes such as size, the presence of the tail morphogenesis module, genes that share similarity to those in other siphovirus isolates and phylogenetic analysis using phage proteomes. Yet, phylogenomic analysis and sequence similarity of the entire phage genomes revealed that these five phages are unique and novel. These phages have only been observed undergoing the lytic lifecycle, but there is evidence in the genomes of phages Arawn and Idris for the potential to be temperate. However, there is no evidence in the genome of the bacterial host Butyrivibrio fibrisolvens of prophage genes or genes that share similarity with the phage genomes.

Genome Sequence and Characterization of Coliphage vB_Eco_SLUR29

Background: Bacteriophages that infect Escherichia coli are relatively easily isolated, with >600 coliphage genomes sequenced to date. Despite this there is still much to be discovered about the diversity of coliphage genomes. Materials and Methods: Within this study, we isolated a coliphage from cattle slurry collected from a farm in rural England. Results: Transmission electron microscopy identified the phage as member of the Siphoviridae family. Phylogenetic analysis and comparative genomics further placed it within the subfamily Tunavirinae and forms part of a new genus. Conclusions: Characterization of the lytic properties of vB_Eco_SLUR29 reveals that it is rapidly able to lyse its host when infected at high multiplicity of infection, but not at low multiplicity of infection.

Comparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7

With the recent rise in interest in using lytic bacteriophages as therapeutic agents, there is an urgent requirement to understand their fundamental biology to enable the engineering of their genomes. Current methods of phage engineering rely on homologous recombination, followed by a system of selection to identify recombinant phages. For bacteriophage T7, the host genes cmk or trxA have been used as a selection mechanism along with both type I and II CRISPR systems to select against wild-type phage and enrich for the desired mutant. Here, we systematically compare all three systems; we show that the use of marker-based selection is the most efficient method and we use this to generate multiple T7 tail fibre mutants. Furthermore, we found the type II CRISPR-Cas system is easier to use and generally more efficient than a type I system in the engineering of phage T7. These results provide a foundation for the future, more efficient engineering of bacteriophage T7.

Riding the wave of genomics to investigate aquatic coliphage diversity and activity

Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Comparative genomics and phylogenetic analysis of phage isolates facilitated the identification of putative new species within the genera Rb69virus and T5virus and a putative new genus within the subfamily Tunavirinae. Furthermore, genomic and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB_Eco_mar004NP2.

virMine: automated detection of viral sequences from complex metagenomic samples

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.

Metagenomics of the Viral Community in Three Cattle Slurry Samples

The diversity of viruses in slurries from dairy farming remains largely uncharacterized. Here we report viral diversity found in cattle slurry from a dairy farm in the East Midlands in the United Kingdom.

The diversity of viruses in slurries from dairy farming remains largely uncharacterized. Here we report viral diversity found in cattle slurry from a dairy farm in the East Midlands in the United Kingdom. The same slurry tank was sampled in three consecutive years, and the viral fraction was isolated and sequenced.

The future of phage clinical trials in Australia

Australia is well positioned to conduct clinical trials in phage-based technology. Despite challenges with translating phage therapy to mainstream medicine, our regulations are designed for safe and innovative development. Recent success indicates that Australia is ideal for conducting further phage clinical trials. There are also expert clinical research organisations and generous tax incentives.

Draft Genome Sequence of Escherichia Phage PGN829.1, Active against Highly Drug-Resistant Uropathogenic Escherichia coli

The Escherichia phage PGN829.1 was isolated from sewage of a tertiary care referral hospital in North India. It lyses multiple strains of highly drug-resistant uropathogenic E. coli.

The Escherichia phage PGN829.1 was isolated from sewage of a tertiary care referral hospital in North India. It lyses multiple strains of highly drug-resistant uropathogenic E. coli. It belongs to the family Podoviridae. Its genome is closest to that of Escherichia phage Vb_EcoP_PhAPEC7.

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases.

Phage Genetic Engineering Using CRISPR⁻Cas Systems

Since their discovery over a decade ago, the class of prokaryotic immune systems known as CRISPR⁻Cas have afforded a suite of genetic tools that have revolutionized research in model organisms spanning all domains of life. CRISPR-mediated tools have also emerged for the natural targets of CRISPR⁻Cas immunity, the viruses that specifically infect bacteria, or phages. Despite their status as the most abundant biological entities on the planet, the majority of phage genes have unassigned functions. This reality underscores the need for robust genetic tools to study them. Recent reports have demonstrated that CRISPR⁻Cas systems, specifically the three major types (I, II, and III), can be harnessed to genetically engineer phages that infect diverse hosts. Here, the mechanisms of each of these systems, specific strategies used, and phage editing efficacies will be reviewed. Due to the relatively wide distribution of CRISPR⁻Cas systems across bacteria and archaea, it is anticipated that these immune systems will provide generally applicable tools that will advance the mechanistic understanding of prokaryotic viruses and accelerate the development of novel technologies based on these ubiquitous organisms.

Characterizing Phage Genomes for Therapeutic Applications

Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA) for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates.

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5′cos (Lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).

Draft Genome Sequence of Bacteriophage vB_Eco_swan01

Bacteriophage vB_Eco_swan01 was isolated from an ornamental pool using Escherichia coli MG1655 as the host. Bacteriophage vB_Eco_swan01 has limited similarity with other known phages at the nucleotide level and likely represents a new bacteriophage species within the Tunavirinae.

Draft Genome Sequence of the Bacteriophage vB_Eco_slurp01

Bacteriophage vB_Eco_slurp01 was isolated from porcine feces using Escherichia coli MG1655 as a host. With a genome size of 348 kb, vB_Eco_slurp01 is one of the largest bacteriophages isolated to date.

Marine phage genomics: the tip of the iceberg

Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes.

Only a tiny fraction of marine phages have been discovered, yet are known to have important roles in the ocean.