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1.
Nat Commun ; 12(1): 3503, 2021 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-34108477

RESUMO

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.


Assuntos
Bacteriófagos/metabolismo , Ecossistema , Enxofre/metabolismo , Motivos de Aminoácidos , Bacteriófagos/classificação , Bacteriófagos/genética , Caudovirales/classificação , Caudovirales/genética , Caudovirales/metabolismo , Metabolismo Energético , Microbiologia Ambiental , Genes Virais/genética , Variação Genética , Genoma Viral/genética , Metagenômica , Oxirredução , Filogenia , Domínios Proteicos , Tiossulfatos/metabolismo , Proteínas Virais/química , Proteínas Virais/genética
2.
Virus Genes ; 57(5): 434-442, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34156584

RESUMO

The increasing prevalence of Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a serious threat to global health. Phages and phage-derived enzymes gained increasing attention for controling CRKP infections. In this study, a lytic phage P510 infecting KL64 type K. pneumoniae was isolated and characterized. Whole genome analysis and electron microscopy analysis showed that phage P510 belonged to genus Przondovirus, family Autographiviridae, the order Caudovirales. The tail fiber protein of the phage was predicted to encode capsule depolymerase. Further analysis demonstrated that recombinant depolymerase P510dep had polysaccharide-degrading activity against KL64-types capsule of K. pneumoniae, and its lysis spectrum matched to host range of phage P510. We also demonstrated that the recombinant depolymerase was able to significantly inhibit biofilm formation. The discovery of the phage-derived depolymerase lays the foundation for controlling the spread of CRKPs.


Assuntos
Bacteriófagos/genética , Genoma Viral/genética , Glicosídeo Hidrolases/genética , Klebsiella pneumoniae/genética , Bacteriófagos/enzimologia , Bacteriófagos/patogenicidade , Biofilmes/crescimento & desenvolvimento , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/virologia , Caudovirales/enzimologia , Caudovirales/genética , Caudovirales/patogenicidade , Humanos , Klebsiella pneumoniae/patogenicidade , Klebsiella pneumoniae/virologia , Proteínas Virais/genética
3.
Microbiologyopen ; 10(2): e1186, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33970533

RESUMO

Aging is a critical factor affecting physical health and disease in mammals. Emerging evidence indicates that aging may affect the gut bacteriome in cynomolgus macaques, but little is known about whether or how the gut virome changes with age. Here, we compared the DNA gut viral composition of 16 female cynomolgus monkeys (Macaca fascicularis) at three life stages (young, adult, and old) using the shotgun metagenome sequencing method. We found that the DNA gut virome from these monkeys differed substantially among the three groups. The gut viruses were dominated by bacteriophages, the most abundant of which was the Caudovirales order (i.e., Siphoviridae, Myoviridae, and Podoviridae families). Additionally, the co-occurrence analysis revealed that the age-related bacteriophages were correlated in an extensive and complex manner with the main intestinal bacteria (i.e., Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria phyla). Furthermore, the age-related DNA gut viral functions were enriched for genetic information processing, nucleotide, and folate metabolism. Our gut virome analysis provides new insight into how aging influences the gut virome of non-human primates.


Assuntos
Fezes/virologia , Microbioma Gastrointestinal , Macaca fascicularis/virologia , Metagenoma , Viroma , Envelhecimento , Animais , Bacteriófagos/classificação , Bacteriófagos/genética , Caudovirales/efeitos dos fármacos , Caudovirales/genética , DNA Viral , Feminino , Metagenômica/métodos , Análise de Sequência de DNA
4.
Arch Virol ; 166(4): 1171-1175, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33559747

RESUMO

Seven novel tailed lytic viruses (Ds3CZ, Ds5CZ, Ds9CZ, Ds16CZ, Ds20CZ, Ds23CZ, Ds25CZ) infecting the bacterium Dickeya solani were isolated in the Czech Republic. Genomes of these viruses are dsDNA, 149,364 to 155,285 bp in length, and the genome arrangement is very similar to that of the type virus Dickeya virus LIMEstone 1. All but the Ds25CZ virus should be regarded as strains of a single species. Most of the sequence differences are due to the presence or absence of homing endonuclease (HE) genes, with 23 HEs found in Ds3CZ, Ds5CZ, and Ds20CZ, 22 in Ds9CZ, 19 in Ds16CZ, 18 in Ds25CZ, and 15 in Ds23CZ.


Assuntos
Caudovirales/genética , Caudovirales/isolamento & purificação , Dickeya/virologia , Caudovirales/classificação , República Tcheca , DNA Viral/genética , Endonucleases/genética , Variação Genética , Genoma Viral/genética , Filogenia , Doenças das Plantas/microbiologia , Doenças das Plantas/virologia , Solanum tuberosum/microbiologia , Solanum tuberosum/virologia , Proteínas Virais/genética
5.
Virol J ; 18(1): 9, 2021 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-33407669

RESUMO

BACKGROUND: Nowadays, hundreds of thousands of deaths per year are caused by antibiotic resistant nosocomial infections and the prognosis for future years is much worse, as evidenced by modern research. Bacteria of the Klebsiella genus are one of the main pathogens that cause nosocomial infections. Among the many antimicrobials offered to replace or supplement traditional antibiotics, bacteriophages are promising candidates. METHODS: This article presents microbiological, physicochemical and genomic characterization of 4 virulent bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. Phages were studied by electron microscopy; their host range, lytic activity, adsorption rate, burst size, latent period, frequency of phage-resistant forms generation, lysis dynamics and sensitivity of phage particles to temperature and pH were identified; genomes of all 4 bacteriophages were studied by restriction digestion and complete genome sequence. RESULTS: Studied phages showed wide host range and high stability at different temperature and pH values. In contrast with single phages, a cocktail of bacteriophages lysed all studied bacterial strains, moreover, no cases of the emergence of phage-resistant bacterial colonies were detected. Genomic data proved that isolated viruses do not carry antibiotic resistance, virulence or lysogenic genes. Three out of four bacteriophages encode polysaccharide depolymerases, which are involved in the degradation of biofilms and capsules. CONCLUSIONS: The bacteriophages studied in this work are promising for further in vivo studies and might be used in phage therapy as part of a complex therapeutic and prophylactic phage preparation. The conducted studies showed that the complex preparation is more effective than individual phages. The use of the complex phage cocktail allows to extend the lytic spectrum, and significantly reduces the possibility of phage-resistant forms generation.


Assuntos
Bacteriófagos/fisiologia , Caudovirales/fisiologia , Klebsiella pneumoniae/virologia , Terapia por Fagos/métodos , Bacteriólise , Bacteriófagos/classificação , Bacteriófagos/genética , Caudovirales/classificação , Caudovirales/genética , Caudovirales/isolamento & purificação , DNA Viral/genética , Genoma Viral/genética , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Especificidade de Hospedeiro , Concentração de Íons de Hidrogênio , Infecções por Klebsiella/terapia , Temperatura , Proteínas Virais/genética , Proteínas Virais/metabolismo , Ligação Viral , Latência Viral
6.
Virus Res ; 292: 198219, 2021 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-33137401

RESUMO

crAssphages are a broad group of diverse bacteriophages in the order Caudovirales that have been found to be highly abundant in the human gastrointestinal tract. Despite their high prevalence, we have an incomplete understanding of how crAssphages shape and respond to ecological and evolutionary dynamics in the gut. Here, we report genomes of crAssphages from feces of one South African woman and three infants. Across the complete genome sequences of the South African crAssphages described here, we identify particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, contrasted against purifying selection, genome-wide. We further validate these findings against a crAssphage genome from previous studies. Together, our results suggest hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.


Assuntos
Bacteriófagos/isolamento & purificação , Caudovirales/isolamento & purificação , Fezes/virologia , Genoma Viral , Proteínas da Cauda Viral/genética , Adulto , Bacteriófagos/classificação , Bacteriófagos/genética , Caudovirales/classificação , Caudovirales/genética , Feminino , Microbioma Gastrointestinal , Genômica , Humanos , Lactente , Recém-Nascido , Masculino , Filogenia , Adulto Jovem
7.
Environ Microbiol ; 23(2): 728-743, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32627268

RESUMO

Our current knowledge of the virosphere in deep-sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep-sea sediments of Southwest Indian Ocean. Analysis of 19 676 106 non-redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1106 high-confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to ~120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the order Caudovirales, including primarily members of the families Myoviridae, Podoviridae and Siphoviridae. Most of these viruses infect Proteobacteria and, less frequently, Planctomycetes, Firmicutes, Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients.


Assuntos
Genes Virais/genética , Genoma Viral/genética , Sedimentos Geológicos/virologia , Vírus/classificação , Vírus/genética , Bactérias/virologia , Caudovirales/genética , Caudovirales/isolamento & purificação , Genômica , Oceano Índico , Metagenoma , Metagenômica , Myoviridae/genética , Myoviridae/isolamento & purificação , Filogenia , Podoviridae/genética , Podoviridae/isolamento & purificação , Siphoviridae/genética , Siphoviridae/isolamento & purificação , Vírion , Vírus/isolamento & purificação
8.
Viruses ; 12(12)2020 11 27.
Artigo em Inglês | MEDLINE | ID: mdl-33261037

RESUMO

Many filamentous vibriophages encode virulence genes that lead to the emergence of pathogenic bacteria. Most genomes of filamentous vibriophages characterized up until today were isolated from human pathogens. Despite genome-based predictions that environmental Vibrios also contain filamentous phages that contribute to bacterial virulence, empirical evidence is scarce. This study aimed to characterize the bacteriophages of a marine pathogen, Vibrio alginolyticus (Kiel-alginolyticus ecotype) and to determine their role in bacterial virulence. To do so, we sequenced the phage-containing supernatant of eight different V. alginolyticus strains, characterized the phages therein and performed infection experiments on juvenile pipefish to assess their contribution to bacterial virulence. We were able to identify two actively replicating filamentous phages. Unique to this study was that all eight bacteria of the Kiel-alginolyticus ecotype have identical bacteriophages, supporting our previously established theory of a clonal expansion of the Kiel-alginolyticus ecotype. We further found that in one of the two filamentous phages, two phage-morphogenesis proteins (Zot and Ace) share high sequence similarity with putative toxins encoded on the Vibrio cholerae phage CTXΦ. The coverage of this filamentous phage correlated positively with virulence (measured in controlled infection experiments on the eukaryotic host), suggesting that this phage contributes to bacterial virulence.


Assuntos
Caudovirales/genética , Genoma Bacteriano , Inovirus/genética , Vibrio alginolyticus/genética , Vibrio alginolyticus/virologia , Animais , Carga Bacteriana , Caudovirales/classificação , Caudovirales/isolamento & purificação , DNA Viral , Doenças dos Peixes/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Inovirus/classificação , Inovirus/isolamento & purificação , Vibrioses/veterinária , Vibrio alginolyticus/classificação , Vibrio alginolyticus/patogenicidade , Virulência
9.
Nat Commun ; 11(1): 4506, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908149

RESUMO

Bacteriophages play critical roles in the biosphere, but their vast genomic diversity has obscured their evolutionary origins, and phylogenetic analyses have traditionally been hindered by their lack of universal phylogenetic marker genes. In this study we mine metagenomic data and identify a clade of Caudovirales that encodes the ß and ß' subunits of multi-subunit RNA polymerase (RNAP), a high-resolution phylogenetic marker which enables detailed evolutionary analyses. Our RNAP phylogeny revealed that the Caudovirales RNAP forms a clade distinct from cellular homologs, suggesting an ancient acquisition of this enzyme. Within these multimeric RNAP-encoding Caudovirales (mReC), we find that the similarity of major capsid proteins and terminase large subunits further suggests they form a distinct clade with common evolutionary origin. Our study characterizes a clade of RNAP-encoding Caudovirales and suggests the ancient origin of this enzyme in this group, underscoring the important role of viruses in the early evolution of life on Earth.


Assuntos
Evolução Biológica , Caudovirales/genética , RNA Polimerases Dirigidas por DNA/genética , Subunidades Proteicas/genética , Proteínas Virais/genética , DNA Viral/genética , Conjuntos de Dados como Assunto , Transferência Genética Horizontal , Metagenômica , Filogenia , Análise de Sequência de DNA
10.
Viruses ; 12(10)2020 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-32992766

RESUMO

Staphylococcus epidermidis is a major causative agent of nosocomial infections, mainly associated with the use of indwelling devices, on which this bacterium forms structures known as biofilms. Due to biofilms' high tolerance to antibiotics, virulent bacteriophages were previously tested as novel therapeutic agents. However, several staphylococcal bacteriophages were shown to be inefficient against biofilms. In this study, the previously characterized S. epidermidis-specific Sepunavirus phiIBB-SEP1 (SEP1), which has a broad spectrum and high activity against planktonic cells, was evaluated concerning its efficacy against S. epidermidis biofilms. The in vitro biofilm killing assays demonstrated a reduced activity of the phage. To understand the underlying factors impairing SEP1 inefficacy against biofilms, this phage was tested against distinct planktonic and biofilm-derived bacterial populations. Interestingly, SEP1 was able to lyse planktonic cells in different physiological states, suggesting that the inefficacy for biofilm control resulted from the biofilm 3D structure and the protective effect of the matrix. To assess the impact of the biofilm architecture on phage predation, SEP1 was tested in disrupted biofilms resulting in a 2 orders-of-magnitude reduction in the number of viable cells after 6 h of infection. The interaction between SEP1 and the biofilm matrix was further assessed by the addition of matrix to phage particles. Results showed that the matrix did not inactivate phages nor affected phage adsorption. Moreover, confocal laser scanning microscopy data demonstrated that phage infected cells were less predominant in the biofilm regions where the matrix was more abundant. Our results provide compelling evidence indicating that the biofilm matrix can work as a barrier, allowing the bacteria to be hindered from phage infection.


Assuntos
Biofilmes/crescimento & desenvolvimento , Fagos de Staphylococcus/fisiologia , Staphylococcus epidermidis/virologia , Biomassa , Caudovirales/fisiologia , Contagem de Colônia Microbiana , Matriz Extracelular de Substâncias Poliméricas/ultraestrutura , Matriz Extracelular de Substâncias Poliméricas/virologia , Interações Hospedeiro-Patógeno , Staphylococcus epidermidis/fisiologia
11.
Molecules ; 25(19)2020 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-32987777

RESUMO

For the first time, we are introducing TTPBgp12 and TFPgp17 as new members of the tail tubular proteins B (TTPB) and tail fiber proteins (TFP) family, respectively. These proteins originate from Yersinia enterocolitica phage φYeO3-12. It was originally thought that these were structural proteins. However, our results show that they also inhibit bacterial growth and biofilm formation. According to the bioinformatic analysis, TTPBgp12 is functionally and structurally similar to the TTP of Enterobacteria phage T7 and adopts a ß-structure. TFPgp17 contains an intramolecular chaperone domain at its C-terminal end. The N-terminus of TFPgp17 is similar to other representatives of the TFP family. Interestingly, the predicted 3D structure of TFPgp17 is similar to other bacterial S-layer proteins. Based on the thermal unfolding experiment, TTPBgp12 seems to be a two-domain protein that aggregates in the presence of sugars such as maltose and N-acetylglucosamine (GlcNAc). These sugars cause two unfolding events to transition into one global event. TFPgp17 is a one-domain protein. Maltose and GlcNAc decrease the aggregation temperature of TFPgp17, while the presence of N-acetylgalactosamine (GalNAc) increases the temperature of its aggregation. The thermal unfolding analysis of the concentration gradient of TTPBgp12 and TFPgp17 indicates that with decreasing concentrations, both proteins increase in stability. However, a decrease in the protein concentration also causes an increase in its aggregation, for both TTPBgp12 and TFPgp17.


Assuntos
Caudovirales , Proteínas Estruturais Virais , Yersinia enterocolitica/virologia , Caudovirales/química , Caudovirales/genética , Caudovirales/metabolismo , Domínios Proteicos , Proteínas Estruturais Virais/química , Proteínas Estruturais Virais/genética , Proteínas Estruturais Virais/metabolismo
12.
Arch Virol ; 165(10): 2355-2359, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32748178

RESUMO

Two Staphylococcus aureus bacteriophages, KSAP7 and KSAP11, were isolated from sewage and characterized. Based on morphology and DNA sequences, they were assigned to the genus Silviavirus, subfamily Twortvirinae, family Herelleviridae, whose members are hypothesized to be suitable for bacteriophage therapy. The KSAP7 and KSAP11 genomes were 137,950 and 138,307 bp in size, respectively. Although their DNA sequences were almost identical, evidence of site-specific DNA rearrangements was found in two regions. Changes in the number of PIEPEK amino acid sequence repeats encoded by orf10 and the insertion/deletion of a 541-bp sequence that includes a possible tail-related gene were identified.


Assuntos
Caudovirales/genética , DNA Viral/genética , Genoma Viral , Filogenia , Fagos de Staphylococcus/genética , Staphylococcus aureus/virologia , Sequência de Aminoácidos , Caudovirales/classificação , Caudovirales/isolamento & purificação , Rearranjo Gênico , Tamanho do Genoma , Mutação INDEL , Japão , Fases de Leitura Aberta , Terapia por Fagos , Alinhamento de Sequência , Fagos de Staphylococcus/classificação , Fagos de Staphylococcus/isolamento & purificação
13.
Viruses ; 12(5)2020 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-32443723

RESUMO

Bacteriophage 80α is a representative of a class of temperate phages that infect Staphylococcus aureus and other Gram-positive bacteria. Many of these phages carry genes encoding toxins and other virulence factors. This phage, 80α, is also involved in high-frequency mobilization of S. aureus pathogenicity islands (SaPIs), mobile genetic elements that carry virulence factor genes. Bacteriophage 80α encodes a minor capsid protein, gp44, between the genes for the portal protein and major capsid protein. Gp44 is essential for a productive infection by 80α but not for transduction of SaPIs or plasmids. We previously demonstrated that gp44 is an ejection protein that acts to promote progression to the lytic cycle upon infection and suggested that the protein might act as an anti-repressor of CI in the lytic-lysogenic switch. However, an 80α Δ44 mutant also exhibited a reduced rate of lysogeny. Here, we show that gp44 is a non-specific DNA binding protein with affinity for the blunt ends of linear DNA. Our data suggest a model in which gp44 promotes circularization of the genome after injection into the host cell, a key initial step both for lytic growth and for the establishment of lysogeny.


Assuntos
Fagos de Staphylococcus/metabolismo , Staphylococcus aureus/genética , Staphylococcus aureus/virologia , Proteínas Virais/metabolismo , Capsídeo/metabolismo , Proteínas do Capsídeo/genética , Caudovirales/genética , DNA/genética , Proteínas de Ligação a DNA/metabolismo , Ilhas Genômicas/genética , Sequências Repetitivas Dispersas , Lisogenia , Fagos de Staphylococcus/genética , Proteínas Virais/química , Proteínas Virais/genética , Fatores de Virulência/genética
14.
PLoS Comput Biol ; 16(5): e1007894, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32453718

RESUMO

The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus on nucleotide features, ignoring other representations of genomic information. Here we investigate the predictive potential of features generated from four different 'levels' of viral genome representation: nucleotide, amino acid, amino acid properties and protein domains. This more fully exploits the biological information present in the virus genomes. Over a hundred and eighty binary datasets for infecting versus non-infecting viruses at all taxonomic ranks of both eukaryote and prokaryote hosts were compiled. The viral genomes were converted into the four different levels of genome representation and twenty feature sets were generated by extracting k-mer compositions and predicted protein domains. We trained and tested Support Vector Machine, SVM, classifiers to compare the predictive capacity of each of these feature sets for each dataset. Our results show that all levels of genome representation are consistently predictive of host taxonomy and that prediction k-mer composition improves with increasing k-mer length for all k-mer based features. Using a phylogenetically aware holdout method, we demonstrate that the predictive feature sets contain signals reflecting both the evolutionary relationship between the viruses infecting related hosts, and host-mimicry. Our results demonstrate that incorporating a range of complementary features, generated purely from virus genome sequences, leads to improved accuracy for a range of virus host prediction tasks enabling computational assignment of host taxonomic information.


Assuntos
Biologia Computacional/métodos , Genoma Viral , Nucleotídeos/análise , Máquina de Vetores de Suporte , Algoritmos , Área Sob a Curva , Bactérias/virologia , Caudovirales/genética , Bases de Dados Factuais , Modelos Lineares , Metagenômica/métodos , Filogenia , Análise de Sequência de DNA , Vírus/genética
15.
Syst Biol ; 69(1): 110-123, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31127947

RESUMO

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.


Assuntos
Caudovirales/classificação , Filogenia , Caudovirales/genética , Classificação , Genoma Viral/genética
16.
Meat Sci ; 162: 108023, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31812064

RESUMO

After High Event Periods, beef subprimals are usually removed from vacuum and treated with antimicrobials. After re-packaging, subprimals are tested to verify the presence of STEC. In this study, bacteriophage and organic acids were applied on beef contaminated with STEC O157:H7 to evaluate the efficiency of industry practices. Beef samples inoculated with STEC were treated with bacteriophage, lactic acid, and peroxyacetic acid and kept under vacuum or aerobic conditions. STEC loads were evaluated 30 min and 6 h after antimicrobial applications. Under aerobic conditions for 30 min and 6 h, phage reduced STEC in beef by approximately 1.4 log whereas organic acids led to a 0.5 log reduction. Under vacuum for 30 min, bacteriophage significantly reduced STEC by 1 log. No effects were observed when samples were treated with organic acids. Under vacuum after 6 h, bacteriophage reduced STEC loads by 1.4 log, lactic acid reduced by 0.6 log, and no effects were observed when peroxyacetic acid was applied.


Assuntos
Anti-Infecciosos/farmacologia , Caudovirales/fisiologia , Escherichia coli O157/efeitos dos fármacos , Escherichia coli O157/virologia , Carne Vermelha/microbiologia , Animais , Bovinos , Manipulação de Alimentos/métodos , Microbiologia de Alimentos , Ácido Láctico/farmacologia , Ácido Peracético/farmacologia , Vácuo
17.
J Glob Antimicrob Resist ; 21: 68-75, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-31678321

RESUMO

OBJECTIVES: The aim of this study is to characterize a new bacteriophage able to infect Enterococcus faecalis, and to evaluate its ability to disrupt biofilm. METHODS: The vB_EfaH_EF1TV (EF1TV) host-range was determined by spot test and efficiency of plating using a collection of 15E. faecalis clinical strains. The phage genome was sequenced with a next generation sequencing approach. Anti-biofilm activity was tested by crystal violet method and confocal laser scanning microscopy. Phage-resistant mutants were selected and sequenced to investigate receptors exploited by phage for infection. RESULTS: EF1TV is a newly discoveredE. faecalis phage which belongs to the Herelleviridae family. EF1TV, whose genome is 98% identical to φEF24C, is characterized by a linear dsDNA genome of 143,507 bp with direct terminal repeats of 1,911 bp. The phage is able to infect E. faecalis and shows also the ability to degrade biofilm produced by strains of this species. The results were confirmed by confocal laser scanning microscopy analyzing the biofilm reduction in the same optical field before and after phage infection. CONCLUSIONS: The EF1TV phage shows promising features such as an obligatory lytic nature, an anti-biofilm activity and the absence of integration-related proteins, antibiotic resistance determinants and virulence factors, and therefore could be a promising tool for therapeutic applications.


Assuntos
Biofilmes/crescimento & desenvolvimento , Caudovirales/fisiologia , Enterococcus faecalis/fisiologia , Sequenciamento Completo do Genoma/métodos , Bacteriólise , Enterococcus faecalis/ultraestrutura , Enterococcus faecalis/virologia , Tamanho do Genoma , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Microscopia Confocal
18.
Microbiol Res ; 228: 126300, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31422230

RESUMO

Two morphologically different bacteriophages were isolated from the river and soil samples from various locations of Maharashtra, India against the phytopathogen Pseudomonas sp. that was recently reported to cause a new bacterial blight of pomegranate. Both the phages belonged to the order Caudovirales representing the families Siphoviridae (vB_Psp.S_PRɸL2) and Myoviridae (vB_Psp.M_SSɸL8). The multiplicity of infection ranged from 0.01 to 0.1, phage adsorption rate from 39% to 66%, latent period from 10 to 20 min with a burst size of 24-85 phage particles per infected host cell. The genome size of phages PRɸL2 and SSɸL8 was approximately 25.403 kb and 29.877 kb respectively. Restriction digestion pattern of phage genomic DNA was carried out for phage PRɸL2, Eco RI resulted in two bands and Hind III resulted in three bands while for phage SSɸL8, both Eco RI and Hind III each resulted in three bands. SDS-PAGE protein profile showed six bands for PRɸL2 and nine bands for SSɸL8 of different proteins. Phages showed high pH stability over a range of 4-9, temperature stability over a range of 4-50 °C and UV radiation showed a reduction up to 89.36% for PRɸL2 and 96% for SSɸL8. In short, the present research work discusses for the first time in-detailed characterization of phages of a phytopathogen Pseudomonas sp. from Maharashtra, India, which can be further efficiently used for biological control of the causative agent of a new bacterial blight disease of pomegranate.


Assuntos
Lythraceae/microbiologia , Doenças das Plantas/microbiologia , Fagos de Pseudomonas/classificação , Fagos de Pseudomonas/isolamento & purificação , Pseudomonas/virologia , Caudovirales/classificação , Caudovirales/genética , Caudovirales/isolamento & purificação , Caudovirales/ultraestrutura , DNA Viral/análise , Especificidade de Hospedeiro , Concentração de Íons de Hidrogênio , Índia , Viabilidade Microbiana , Myoviridae/classificação , Myoviridae/genética , Myoviridae/isolamento & purificação , Myoviridae/ultraestrutura , Fagos de Pseudomonas/genética , Fagos de Pseudomonas/ultraestrutura , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/isolamento & purificação , Siphoviridae/ultraestrutura , Temperatura , Raios Ultravioleta/efeitos adversos , Proteínas Virais/análise
19.
Viruses ; 11(9)2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31443379

RESUMO

Impetigo is a contagious skin infection predominantly caused by Staphylococcus aureus. Decontamination of S. aureus from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against S. aureus. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly S. aureus, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of S. aureus while improving the cutaneous bacterial microflora.


Assuntos
Caudovirales/metabolismo , Endopeptidases/farmacologia , Impetigo/tratamento farmacológico , Staphylococcus aureus , Administração Cutânea , Animais , Antibacterianos/administração & dosagem , Antibacterianos/farmacologia , Bacteriólise , Caudovirales/patogenicidade , Endopeptidases/administração & dosagem , Endopeptidases/genética , Genes Bacterianos , Genes Virais , Impetigo/microbiologia , Metagenômica , Camundongos , Microbiota/genética , Pseudomonas aeruginosa/virologia , RNA Ribossômico 16S , Proteínas Recombinantes/administração & dosagem , Proteínas Recombinantes/farmacologia , Pele/microbiologia , Pele/patologia , Infecções Estafilocócicas/tratamento farmacológico , Fagos de Staphylococcus/metabolismo , Fagos de Staphylococcus/patogenicidade , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/virologia , Staphylococcus epidermidis/virologia , Streptococcus mitis/virologia
20.
Sci Rep ; 9(1): 11342, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31383901

RESUMO

The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.


Assuntos
Caudovirales/genética , Genoma Viral , Herpesviridae/genética , Evolução Molecular , Infecções por Herpesviridae/virologia , Humanos , Filogenia , Proteínas Virais/genética
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