Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity

Isolation of Bacteriophages from Soil Samples in a Poorly Equipped Field Laboratory in Kruger National Park

Bacteriophages are viruses that infect bacteria. Bacteriophages are ubiquitous and are the most abundant organisms on the planet. Despite this, very little is known about the influence and effect of bacteriophages within terrestrial environments. Additionally, the natural soil microbiome profiles remain largely unexplored. Here we describe protocols that can be used, in field or rural laboratories containing only basic equipment, to make bacteriophage isolation more accessible and to facilitate such research.

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.

Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity

Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were explored through comparative genomics approaches to reveal shared and unique characteristics. These bacteriophages are in the Salasmaviridae family with small (18,548-27,206 bp) double-stranded DNA genomes encoding 25-46 predicted open reading frames. We observe extensive nucleotide and amino acid sequence divergence among a set of core-function genes that present clear synteny. We identify two examples of sequence directed recombination within essential genes, as well as explore the expansion of gene content in these genomes through the introduction of novel open reading frames. Together, these findings highlight the complex evolutionary relationships of phage genomes that include old, common origins as well as new components introduced through mosaicism.

Characteristics and complete genome analysis of the novel virulent phage Bfsp1 infecting Cytobacillus firmus

We isolated, identified, and characterised Bfsp1, a novel virulent phage of Cytobacillus firmus. Morphologically, Bfsp1 is similar to phi29-like phages. The linear, double-stranded DNA genome of Bfsp1 is 22,320 bp in length, has a GC content of 36.06%, and has 10-bp inverted terminal repeats. The genome contains 33 open reading frames, and functions of 15 of them were predicted. Comparative genome analysis showed that Bfsp1 is distinct from other known phages, and this was confirmed by phylogenetic analysis. Morphological, genomic, and phylogenetic data indicated that Bfsp1 is a novel member of the family Salasmaviridae.

Bacillus subtilis phage phi18: genomic analysis and receptor identification

Bacillus subtilis strains play a pivotal role in the fermentation industry. B. subtilis phages can cause severe damage by infecting bacterial cells used in industrial fermentation processes. In this work, we isolated and characterized a Bacillus subtilis-infecting phage, termed phi18. Transmission electron microscopy revealed that phage phi18 particles have typical myovirus morphology, with an icosahedral head connected to a contractile tail. Genomic analysis revealed that the phage genome is a linear double-stranded DNA molecule of 147,298 bp with terminal redundancy of 14,434 bp, and 226 protein coding genes and four tRNA genes were predicted in the genome. Phage-resistant mutants were selected from a mariner transposon-insertion library of B. subtilis 168 in which two bacterial genes, tagE and pgcA, which are required for the glycosylation of wall teichoic acid (WTA), were found to be disrupted, suggesting that WTA is the receptor for phage phi18. Comparative genomic analysis showed that phage phi18 is a new member of the genus Okubovirus of the family Herelleviridae. Finally, general characteristics of the phage-resistant mutants, including biofilm formation, growth, and sporulation, were examined. The results showed that the phage-resistant mutants grew as rapidly as the parental strain B. subtilis 168 at 42 °C, suggesting that these phage-resistant mutants may be used as starters in fermentation processes.

Tyroviruses are a new group of temperate phages that infect Bacillus species in soil environments worldwide

BACKGROUND

Bacteriophages are widely considered to be highly abundant and genetically diverse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus, despite the potential for some of its members, such as Bacillus anthracis, to cause serious human disease.

RESULTS

We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis. Using modern phylogenetic approaches we place these five new Bacillus phages, as well as 21 similar phage genomes retrieved from publicly available databases and metagenomic datasets into the Tyrovirus group, a newly proposed group named so due to the conservation of three distinct tyrosine recombinases. Genomic analysis of these large phages (~ 160-170 kb) reveals their DNA packaging mechanism and genomic features contributing to virion morphogenesis, host cell lysis and phage DNA replication processes. Analysis of the three tyrosine recombinases suggest Tyroviruses undergo a prophage lifecycle that may involve both host integration and plasmid stages. Further we show that Tyroviruses rely on divergent invasion mechanisms, with a subset requiring host S-layer for infection.

CONCLUSIONS

Ultimately, we expand upon our understanding on the classification, phylogeny, and genomic organisation of a new and substantial phage group that prey on critically relevant Bacillus species. In an era characterised by a rapidly evolving landscape of phage genomics the deposition of future Tyroviruses will allow the further unravelling of the global spread and evolutionary history of these Bacillus phages.

Whole Genome Sequence Analysis of Lactiplantibacillus plantarum Bacteriophage P2

Phage P2 was isolated from failed fermentation broth carried out by Lactiplantibacillus plantarum IMAU10120. A previous study in our laboratory showed that this phage belonged to the Siphoviridae family. In this study, this phage’s genomic characteristics were analyzed using whole-genome sequencing. It was revealed that phage P2 was 77.9 kb in length and had 39.28% G + C content. Its genome included 96 coding sequences (CDS) and two tRNA genes involved in the function of the structure, DNA replication, packaging, and regulation. Phage P2 had higher host specificity; many tested strains were not infected. Cell wall adsorption experiments showed that the adsorption receptor component of phage P2 might be a part of the cell wall peptidoglycan. This research might enrich the knowledge about genomic information of lactobacillus phages and provide some primary data to establish phage control measures.

Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage-host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more genes than SPP1. We identified a new putative gene in SPP1 based on a conserved sequence found in all phages. Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. Patterns of divergence point to genes or gene domains likely involved in adaptation to diverse hosts or different environments. Ultimately, comparative genomics of related phages provides insight into the long-term selective pressures that affect phage-bacteria interactions and alter phage genome content.

Screening of Potential Vibrio cholerae Bacteriophages for Cholera Therapy: A Comparative Genomic Approach

Cholera continues to be a major burden for developing nations, especially where sanitation, quality of water supply, and hospitalization have remained an issue. Recently, growing antimicrobial-resistant strains of Vibrio cholerae underscores alternative therapeutic strategies for cholera. Bacteriophage therapy is considered one of the best alternatives for antibiotic treatment. For the identification of potential therapeutic phages for cholera, we have introduced a comprehensive comparative analysis of whole-genome sequences of 86 Vibrio cholerae phages. We have witnessed extensive variation in genome size (ranging from 33 to 148 kbp), GC (G + C) content (varies from 34.5 to 50.8%), and the number of proteins (ranging from 15 to 232). We have identified nine clusters and three singletons using BLASTn, confirmed by nucleotide dot plot and sequence identity. A high degree of sequence and functional similarities in both the genomic and proteomic levels have been observed within the clusters. Evolutionary analysis confirms that phages are conserved within the clusters but diverse between the clusters. For each therapeutic phage, the top 2 closest phages have been identified using a system biology approach and proposed as potential therapeutic phages for cholera. This method can be applied for the classification of the newly isolated Vibrio cholerae phage. Furthermore, this systematic approach might be useful as a model for screening potential therapeutic phages for other bacterial diseases.

Three Novel Bacteriophages, J5a, F16Ba, and z1a, Specific for Bacillus anthracis, Define a New Clade of Historical Wbeta Phage Relatives

Bacillus anthracis is a potent biowarfare agent, able to be highly lethal. The bacteria dwell in the soil of certain regions, as natural flora. Bacteriophages or their lytic enzymes, endolysins, may be an alternative for antibiotics and other antibacterials to fight this pathogen in infections and to minimize environmental contamination with anthrax endospores. Upon screening environmental samples from various regions in Poland, we isolated three new siphophages, J5a, F16Ba, and z1a, specific for B. anthracis. They represent new species related to historical anthrax phages Gamma, Cherry, and Fah, and to phage Wbeta of Wbetavirus genus. We show that the new phages and their closest relatives, phages Tavor_SA, Negev_SA, and Carmel_SA, form a separate clade of the Wbetavirus genus, designated as J5a clade. The most distinctive feature of J5a clade phages is their cell lysis module. While in the historical phages it encodes a canonical endolysin and a class III holin, in J5a clade phages it encodes an endolysin with a signal peptide and two putative holins. We present the basic characteristic of the isolated phages. Their comparative genomic analysis indicates that they encode two receptor-binding proteins, of which one may bind a sugar moiety of B. anthracis cell surface.

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.

Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats

Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community.

IMPORTANCE Hot springs harbor microbial communities dominated by a limited variety of microorganisms and, as such, have become a model for studying community ecology and understanding how biotic and abiotic interactions shape their structure. Viruses in hot springs are shown to be ubiquitous, numerous, and active components of these communities. However, lytic and lysogenic viral communities of thermophilic phototrophic microbial mats (PMMs) remain largely unexplored. In this work, we use the power of viral metagenomics to reveal changes in the viral community following a mitomycin C induction experiment in PMMs. The importance of our research is that it will improve our understanding of viral lifestyles in PMMs via exploring the differences in the composition of natural and induced viral communities at the genome and gene levels. This novel information will contribute to deciphering which biotic and abiotic factors may control the transitions between lytic and lysogenic cycles in these extreme environments.

Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity

Obesity has increased at an alarming rate over the past two decades in the United States. In addition to increased body mass, obesity is often accompanied by comorbidities such as Type II Diabetes Mellitus and metabolic dysfunction-associated fatty liver disease, with serious impacts on public health. Our understanding of the role the intestinal microbiota in obesity has rapidly advanced in recent years, especially with respect to the bacterial constituents. However, we know little of when changes in these microbial populations occur as obesity develops. Further, we know little about how other domains of the microbiota, namely bacteriophage populations, are affected during the progression of obesity. Our goal in this study was to monitor changes in the intestinal microbiome and metabolic phenotype following western diet feeding. We accomplished this by collecting metabolic data and fecal samples for shotgun metagenomic sequencing in a mouse model of diet-induced obesity. We found that after two weeks of consuming a western diet (WD), the animals weighed significantly more and were less metabolically stable than their chow fed counterparts. The western diet induced rapid changes in the intestinal microbiome with the most pronounced dissimilarity at 12 weeks. Our study highlights the dynamic nature of microbiota composition following WD feeding and puts these events in the context of the metabolic status of the mammalian host.

Genome Annotations of Two Bacillus Phages, Tomato and BaseballField

Tomato and Baseball Field are Bacillus bacteriophages that were isolated and annotated by students in the Howard Hughes Medical Institute Phage Hunters program. Tomato has a unique truncation of the tape measure gene that is not found in other closely related C1 Bacillus phages. Baseball Field is a strictly lytic phage with a compact genome of 26 kb.

Tomato and BaseballField are Bacillus bacteriophages that were isolated and annotated by students in the Howard Hughes Medical Institute Phage Hunters program. Tomato has a unique truncation of the tape measure gene that is not found in other closely related C1 Bacillus phages. BaseballField is a strictly lytic phage with a compact genome of 26 kb.

Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity

In the present study, we sequenced the complete genome of Bradyrhizobium diazoefficiens 113-2. The genomic characteristics of six selected rhizobial strains (two fast-growing rhizobia, two medium-slow-growing rhizobia and two slow-growing rhizobia) with four different legume hosts were analyzed by comparative genomic analysis. Genomes of B. diazoefficiens 113-2 and B. diazoefficiens USDA110 were found to share a large synteny blocks and a high ANI value, supporting 113-2 as a strain of B. diazoefficiens. 5,455 singletons and 11,656 clusters were identified among the six rhizobia genomes, and most of the pair-wise comparisons clusters were shared by the two genomes of strains in the same genus. Similar genus-specific gene numbers in the assigned COG functional terms were present in the two strains of the same genus, while the numbers were decreased with the increase of growth rate in most of the COG terms. KEGG pathway analysis of B. diazoefficiens 113-2 suggested that the rhizobial genes in ABC transporters and Two-Component system were mainly species-specific. Besides, the candidate genes related to secretion system and surface polysaccharides biosynthesis in the genomes of the six strains were explored and compared. 39 nodulation gene families, 12 nif gene families and 10 fix gene families in the genomes of these six strains were identified, and gene classes in most of gene families and the types and total gene numbers of gene families were substantially different among these six genomes. We also performed synteny analyses for above-mentioned nod, nif, and fix gene groupings, and selected NodW, NolK, NoeJ, NifB, FixK, and FixJ gene families to perform phylogeny analyses. Our results provided valuable molecular insights into species specificity and host specificity. The genetic information responsible for host specificity will play important roles in expanding the host range of rhizobia among legumes, which might provide new clues for the understanding of the genetic determinants of non-legume-rhizobium symbiosis.

Phages in Anaerobic Systems

Since the discovery of phages in 1915, these viruses have been studied mostly in aerobic systems, or without considering the availability of oxygen as a variable that may affect the interaction between the virus and its host. However, with such great abundance of anaerobic environments on the planet, the effect that a lack of oxygen can have on the phage-bacteria relationship is an important consideration. There are few studies on obligate anaerobes that investigate the role of anoxia in causing infection. In the case of facultative anaerobes, it is a well-known fact that their shifting from an aerobic environment to an anaerobic one involves metabolic changes in the bacteria. As the phage infection process depends on the metabolic state of the host bacteria, these changes are also expected to affect the phage infection cycle. This review summarizes the available information on phages active on facultative and obligate anaerobes and discusses how anaerobiosis can be an important parameter in phage infection, especially among facultative anaerobes.

Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

BACKGROUND

Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica. A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents.

RESULTS

Here we provide a comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica which is the full complement of the prophages that could be retrieved from public databases. We discovered extensive variation in genome sizes (ranging from 6.4 to 358.7 kb) and guanine plus cytosine (GC) content (ranging from 35.5 to 65.4%) and observed a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages.

CONCLUSIONS

Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.

Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae

Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella and, as a result of the continuous emergence of multi-drug resistant (MDR) strains, the cause of severe nosocomial infections. The decline in the effectiveness of antibiotic treatments for infections caused by MDR bacteria has generated particular interest in the study of bacteriophages. In this study, we characterized a total of 40 temperate bacteriophages (prophages) with a genome range of 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains of K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). Genomic comparison of the 40 prophage genomes led to the identification of four prophages isolated from different strains and of genome sizes of around 33.3, 36.1, 39.6 and 42.6 kb. These prophages showed sequence similarities (query cover >90 %, identity >99.9 %) with international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 and 4280, respectively. Phylogenetic analysis revealed the evolutionary proximity among the members of the four groups of the most frequently identified prophages in the bacterial genomes studied (33.3, 36.1, 39.6 and 42.6 kb), with bootstrap values of 100 %. This allowed the prophages to be classified into three clusters: A, B and C. Interestingly, these temperate bacteriophages did not infect the highest number of strains as indicated by a host-range assay, these results could be explained by the development of superinfection exclusion mechanisms. In addition, bioinformatic analysis of the 40 identified prophages revealed the presence of 2363 proteins. In total, 59.7 % of the proteins identified had a predicted function, mainly involving viral structure, transcription, replication and regulation (lysogenic/lysis). Interestingly, some proteins had putative functions associated with bacterial virulence (toxin expression and efflux pump regulators), phage defence profiles such as toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) and methyltransferase proteins.

Discovery of several thousand highly diverse circular DNA viruses

Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.

When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized.

This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison.

Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses.

Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.

Characterization of a new podovirus infecting Paenibacillus larvae

The Paenibacillus larvae infecting phage API480 (vB_PlaP_API480) is the first reported podovirus for this bacterial species, with an 58 nm icosahedral capsid and a 12 × 8 nm short, non-contractile tail. API480 encodes 77 coding sequences (CDSs) on its 45,026 bp dsDNA genome, of which 47 were confirmed using mass spectrometry. This phage has got very limited genomic and proteomic similarity to any other known ones registered in public databases, including P. larvae phages. Comparative genomics indicates API480 is a new species as it's a singleton with 28 unique proteins. Interestingly, the lysis module is highly conserved among P. larvae phages, containing a predicted endolysin and two putative holins. The well kept overall genomic organisation (from the structural and morphogenetic modules to the host lysis, DNA replication and metabolism related proteins) confirms a common evolutionary ancestor among P. larvae infecting phages. API480 is able to infect 69% of the 61 field strains with an ERIC I genotype, as well as ERIC II strains. Furthermore, this phage is very stable when exposed to high glucose concentrations and to larval gastrointestinal conditions. This highly-specific phage, with its broad lytic activity and stability in hive conditions, might potentially be used in the biocontrol of American Foulbrood (AFB).

Staphylococci phages display vast genomic diversity and evolutionary relationships

Background

Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp.

Results

These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain.

Conclusions

This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5647-8) contains supplementary material, which is available to authorized users.

Complete Genome Sequence of Cluster C2 Bacillus Phage Maceta

Bacillus phage Maceta was isolated from the soil of commercially purchased annual flowers using the host Bacillus thuringiensis serovar kurstaki. Isolated DNA was then sequenced and annotated. Maceta has a relatively small genome, containing 45,023 bp, and shares an average nucleotide identity of 96% with other cluster C2 Bacillus phage.

Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis

Background

In the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Georgia. We report here major trends in the molecular evolution of these phages, which we designate as “Basilisk-Like-Phages” (BLPs), and illustrate patterns in their evolution, genomic plasticity and core genome architecture.

Results

Comparative whole genome sequence analysis revealed a close evolutionary relationship between our phages and two unclassified Bacillus cereus group phages, phage Basilisk, a broad host range phage (Grose JH et al., J Vir. 2014;88(20):11846-11860) and phage PBC4, a highly host-restricted phage and close relative of Basilisk (Na H. et al. FEMS Microbiol. letters. 2016;363(12)). Genome comparisons of phages v_B-Bak1, v_B-Bak6, and v_B-Bak10 revealed significant similarity in sequence, gene content, and synteny with both Basilisk and PBC4. Transmission electron microscopy (TEM) confirmed the three phages belong to the Siphoviridae family. In contrast to the broad host range of phage Basilisk and the single-strain specificity of PBC4, our three phages displayed host specificity for Bacillus anthracis. Bacillus species including Bacillus cereus, Bacillus subtilis, Bacillus anthracoides, and Bacillus megaterium were refractory to infection.

Conclusions

Data reported here provide further insight into the shared genomic architecture, host range specificity, and molecular evolution of these rare B. cereus group phages. To date, the three phages represent the only known close relatives of the Basilisk and PBC4 phages and their shared genetic attributes and unique host specificity for B. anthracis provides additional insight into candidate host range determinants.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5056-4) contains supplementary material, which is available to authorized users.

Genome Sequence of Bacillus Phage Saddex

The complete genome of Bacillus phage Saddex was determined and annotated in this study. Saddex has distinct sections with similarities to other Bacillus phages, such as Kida, even though these phages were isolated more than 800 km apart by separate laboratories.

Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages

Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.

Comparative Genomic Analysis of 130 Bacteriophages Infecting Bacteria in the Genus Pseudomonas

Bacteria of the genus Pseudomonas are genetically diverse and ubiquitous in the environment. Like other bacteria, those of the genus Pseudomonas are susceptible to bacteriophages which can significantly affect their host in many ways, ranging from cell lysis to major changes in morphology and virulence. Insights into phage genomes, evolution, and functional relationships with their hosts have the potential to contribute to a broader understanding of Pseudomonas biology, and the development of novel phage therapy strategies. Here we provide a broad-based comparative and evolutionary analysis of 130 complete Pseudomonas phage genome sequences available in online databases. We discovered extensive variation in genome size (ranging from 3 to 316 kb), G + C percentage (ranging from 37 to 66%), and overall gene content (ranging from 81–96% of genome space). Based on overall nucleotide similarity and the numbers of shared gene products, 100 out of 130 genome sequences were grouped into 12 different clusters; 30 were characterized as singletons, which do not have close relationships with other phage genomes. For 5/12 clusters, constituent phage members originated from two or more different Pseudomonas host species, suggesting that phage in these clusters can traverse bacterial species boundaries. An analysis of CRISPR spacers in Pseudomonas bacterial genome sequences supported this finding. Substantial diversity was revealed in analyses of phage gene families; out of 4,462 total families, the largest had only 39 members and there were 2,992 families with only one member. An evolutionary analysis of 72 phage gene families, based on patterns of nucleotide diversity at non-synonymous and synonymous sites, revealed strong and consistent signals for purifying selection. Our study revealed highly diverse and dynamic Pseudomonas phage genomes, and evidence for a dominant role of purifying selection in shaping the evolution of genes encoded in them.

Comparative Analysis of 37 Acinetobacter Bacteriophages

Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.

The Efficacy of Isolated Bacteriophages from Pig Farms against ESBL/AmpC-Producing Escherichia coli from Pig and Turkey Farms

Extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases are plasmid (but also chromosomally) encoded enzymes found in Enterobacteriaceae, determining resistance to a variety of important antibiotics including penicillins, cephalosporins, and monobactams. In recent decades, the prevalence of ESBL/AmpC-producing bacteria has increased rapidly across the world. Here, we evaluate the potential use of bacteriophages in terms of a reduction of antibiotic-resistant bacteria in healthy animals. The aim of our studies was to isolate bacteriophages capable of destroying ESBL/AmpC-producing Escherichia coli isolated from livestock habitats. The efficacy of isolated phages against ESBL/AmpC E. coli strains varies, but creation of a phage cocktail with broad activity spectrum is possible. This may indicate that the role of phages may not be limited to phage therapy, but bacterial viruses may also be applied against spread of bacteria with antibiotic resistance genes in the environment. We also addressed the hypothesis, that phages, effective for therapeutic purposes may be isolated from distant places and even from different environments other than the actual location of the targeted bacteria. This may be beneficial for practical purposes, as the construction of effective phage preparations does not require access to disease outbreaks.

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

Background

Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes.

Results

The original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome.

Conclusions

Using available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.

Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages

Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.

Aligning the unalignable: bacteriophage whole genome alignments

Background

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences.

Results

In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressiveMauve aligner – which implements a partial order strategy, but whose alignments are linearized – shows a greatly improved interactive graphic display, while avoiding misalignments.

Conclusions

Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains.

A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0869-5) contains supplementary material, which is available to authorized users.

Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae

Background

Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype.

Results

In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents.

Conclusions

We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.

Phage on the stage

The resurgence of interest in bacteriophages for use in combating antibiotic resistant bacteria is coincident with an urgent call for more effective science education practices, including hands-on learning opportunities. To address this issue, a number of solutions have been proposed, including a large educational experiment, begun in 2007 by the Howard Hughes Medical Institute and currently involving over 85 colleges and universities, which has students discovering unique phages, obtaining images, and purifying phage DNA. A subset of these phage genomes is sequenced and analyzed using bioinformatics tools. Papers describing individual phage discoveries and comparative genomic studies are being published regularly. The vast majority of students in the program are in their first year of college, a critical time in capturing their interest and retaining them as science majors. This viral discovery model is being adopted and modified by a wide variety of educational institutions using a number of different bacterial hosts. In the opinion of the authors, this program and others like it represent a model accessible to virtually any undergraduate setting. And because of these programs, bacteriophage enthusiasts (academics, health professionals, biotechnology companies) can look forward to more well prepared students entering their ranks and should anticipate many more potentially useful phages discovered and characterized.

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

DOI:http://dx.doi.org/10.7554/eLife.06416.001

Viruses are unable to replicate independently. To generate copies of itself, a virus must instead invade a target cell and commandeer that cell's replication machinery. Different viruses are able to invade different types of cell, and a group of viruses known as bacteriophages (or phages for short) replicate within bacteria. The enormous number and diversity of phages in the world means that they play an important role in virtually every ecosystem.

Despite their importance, relatively little is known about how different phage populations are related to each other and how they evolved. Many phages contain their genetic information in the form of strands of DNA. Using genetic sequencing to find out where and how different genes are encoded in the DNA can reveal information about how different viruses are related to each other. These relationships are particularly complicated in phages, as they can exchange genes with other viruses and microbes.

Previous studies comparing the genomes—the complete DNA sequence—of reasonably small numbers of phages that infect the Mycobacterium group of bacteria have found that the phages can be sorted into ‘clusters’ based on similarities in their genes and where these are encoded in their DNA. However, the number of phages investigated so far has been too small to conclude how different clusters are related. Are the clusters separate, or do they form a ‘continuum’ with different genes and DNA sequences shared between different clusters?

Here, Pope, Bowman, Russell et al. compare the individual genomes of 627 bacteriophages that infect the bacterial species Mycobacterium smegmatis. This is by far the largest number of phage genomes analyzed from a single host species. The large number of genomes analyzed allowed a much clearer understanding of the complexity and diversity of these phages to be obtained. The isolation, sequencing and analysis of the hundreds of M. smegmatis bacteriophage genomes was performed by an integrated research and education program, called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This enabled thousands of undergraduate students from different institutions to contribute to the phage discovery and sequencing project, and co-author the report. SEA-PHAGES therefore shows that it is possible to successfully incorporate genuine scientific research into an undergraduate course, and that doing so can benefit both the students and researchers involved.

The results show that while the genomes could be categorized into 28 clusters, the genomes are not completely unrelated. Instead, a spread of diversity is seen, as genes and groups of genes are shared between different clusters. Pope, Bowman, Russell et al. further reveal that the phage population is in a constant state of change, and continuously acquires genes from other microorganisms and viruses.

DOI:http://dx.doi.org/10.7554/eLife.06416.002