Bacteriophage最新文献

{"title":"Testing a proposed paradigm shift in analysis of phage DNA packaging","authors":"P. Serwer, E. Wright","doi":"10.1080/21597081.2016.1268664","DOIUrl":"https://doi.org/10.1080/21597081.2016.1268664","url":null,"abstract":"ABSTRACT We argue that a paradigm shift is needed in the analysis of phage DNA packaging. We then test a prediction of the following paradigm shift-engendering hypothesis. The motor of phage DNA packaging has two cycles: (1) the well-known packaging ATPase-driven (type 1) cycle and (2) a proposed back-up, shell expansion/contraction-driven (type 2) cycle that reverses type 1 cycle stalls by expelling accidentally packaged non-DNA molecules. We test the prediction that increasing the cellular concentration of all macromolecules will cause packaging-active capsids to divert to states of hyper-expansion and contraction. We use a directed evolution-derived, 3-site phage T3 mutant, adapted to propagation in concentrated bacterial cytoplasm. We find this prediction correct while discovering novel T3 capsids previously obscure.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72674028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural proteins of Enterococcus faecalis bacteriophage ϕEf11","authors":"R. Stevens, Hongming Zhang, Chaiwing Hsiao, S. Kachlany, Eduardo M. B. Tinoco, Jessica DePew, D. Fouts","doi":"10.1080/21597081.2016.1251381","DOIUrl":"https://doi.org/10.1080/21597081.2016.1251381","url":null,"abstract":"ABSTRACT φEf11, a temperate Siphoviridae bacteriophage, was isolated by induction from a root canal isolate of Enterococcus faecalis. Sequence analysis suggested that the φEf11 genome included a contiguous 8 gene module whose function was related to head structure assembly and another module of 10 contiguous genes whose products were responsible for tail structure assembly. SDS-PAGE analysis of virions of a φEf11 derivative revealed 11 well-resolved protein bands. To unify the deduced functional gene assignments emanating from the DNA sequence data, with the structural protein analysis of the purified virus, 6 of the SDS-PAGE bands were subjected to mass spectrometry analysis. 5 of the 6 protein bands analyzed by mass spectrometry displayed identical amino acid sequences to those predicted to be specified by 4 of the ORFs identified in the φEf11 genome. These included: ORF8 (predicted scaffold protein), ORF10 (predicted major head protein), ORF15 (predicted major tail protein), and ORF23 (presumptive antireceptor).","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90045027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"My scientific life","authors":"M. Salas","doi":"10.1080/21597081.2016.1271250","DOIUrl":"https://doi.org/10.1080/21597081.2016.1271250","url":null,"abstract":"I was born in Canero, Spain, a very small village in the north coast of Asturias. When I was one year old, my parents moved to Gij on, also in Asturias, where I spent my childhood and early youth. There, I attended the school and obtained the baccalaureate title in 1954. Since I wanted to pursue a university career, I had to spend one year doing the so-called pre-university studies and to decide whether I wanted to follow a scientific or a humanistic career. I choose to go into science. At the end of the year I had to decide which specific career I wanted to follow. I doubted between medicine and chemistry. Since medicine was not available at Oviedo University, close to Gij on, I decided to go to Madrid University to follow a course common for both careers. Finally, I decided to study chemistry. In the third year we studied organic chemistry, and I enjoyed very much the long hours we spent in the laboratory. I thought that, in the future, I would like to do research in organic chemistry. But that was not the case. In the summer of 1958, when I had finished my third year of chemistry, I went to Gij on to spend the holidays, and I was very lucky to meet Severo Ochoa, which had a decisive influence on my future. I attended a conference he gave about his work and I was fascinated by his talk. Since my father was a good friend of Ochoa, besides being cousins in law, I had the chance to talk to him about my future. I had not yet studied biochemistry and he promised to send me a biochemistry book. I was very excited when I received the book General Biochemistry by Fruton and Simmonds, dedicated by Severo Ochoa. When I finished my chemistry studies I had decided to dedicate myself to biochemistry. Ochoa advised me to do the Ph.D. Thesis in Madrid with Alberto Sols, an excellent biochemist, who had been trained with Carl and Gerty Cori at the Washington University School of Medicine in St. Louis. Then, I could go to Ochoa’s laboratory at New York University (NYU) School of Medicine for a postdoctoral training. Ochoa wrote me a reference letter for Alberto Sols who accepted me, even if I was a woman, since he could not refuse a request made by Severo Ochoa who had already obtained the Nobel Prize. Thus, in January 1961, I started my Ph.D. Thesis working on carbohydrate metabolism, mainly on glucose-phosphate isomerase from yeast. I found that the enzyme has an anomerase-like activity producing the open form of glucose6-phosphate. This was the first finding in my scientific career, something that was very exciting for me. The work was published in the Journal of Biological Chemistry. At the end of my studies in chemistry, I","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89610643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases","authors":"K. Moelling, F. Broecker","doi":"10.1080/21597081.2016.1251380","DOIUrl":"https://doi.org/10.1080/21597081.2016.1251380","url":null,"abstract":"ABSTRACT We have analyzed fecal bacterial and viral communities of a patient with recurrent C. difficile infection (rCDI) who was cured by fecal microbiota transplantation (FMT). The “Zürich Patient” experienced immediate cure and has remained free of symptoms for now over 5 y. Donor-similar bacterial compositions after 4.5 y post-FMT demonstrated sustainable engraftment of donor microbiota predominated by Bacteroidetes and Firmicutes bacteria. Appearance of beneficial species Faecalibacterium prausnitzii and Akkermansia municiphila was detected while disease-related Proteobacteria decreased. Stabilization of the microbiota took longer than expected from the rapidly improving clinical symptoms, suggesting the need for longer-lasting patient observation. The virome was mainly composed of Caudovirales bacteriophages but surprisingly also contained sequences related to a Chlorella giant virus that normally infects green algae not known to inhabitate the human intestine. FMT is highly effective against rCDI and is presently broadening its application to other conditions including inflammatory bowel disease (IBD). Here, we discuss the prospects and challenges of FMT against rCDI and other indications including a focus on bacteriophages.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73409555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Félix Hubert d'Herelle (1873–1949): History of a scientific mind","authors":"W. Summers","doi":"10.1080/21597081.2016.1270090","DOIUrl":"https://doi.org/10.1080/21597081.2016.1270090","url":null,"abstract":"ABSTRACT The discovery of bacteriophage one century ago by the French-Canadian Félix d'Herelle set off controversies as to the nature of bacteriophage as well as over the priority and credit for this discovery. The background and life of d'Herelle reveals a complex, self-taught outsider in science who was strongly influenced by his admiration of Louis Pasteur, but also his attachment to the philosophical positions of early 17th century philosophers, especially Francis Bacon. D'Herelle left substantial unpublished writings on his philosophical musings toward the end of his life.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74654879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage therapy dosing: The problem(s) with multiplicity of infection (MOI)","authors":"S. Abedon","doi":"10.1080/21597081.2016.1220348","DOIUrl":"https://doi.org/10.1080/21597081.2016.1220348","url":null,"abstract":"ABSTRACT The concept of bacteriophage multiplicity of infection (MOI) – ratios of phages to bacteria – historically has been less easily applied than many phage workers would prefer or, perhaps, may be aware. Here, toward clarification of the concept, I discuss multiplicity of infection in terms of semantics, history, mathematics, pharmacology, and actual practice. For phage therapy and other biocontrol purposes it is desirable, especially, not to solely employ MOI to describe what phage quantities have been applied during dosing. Why? Bacterial densities can change between bacterial challenge and phage application, may not be easily determined immediately prior to phage dosing, and/or target bacterial populations may not be homogeneous with regard to phage access and thereby inconsistent in terms of what MOI individual bacteria experience. Toward experiment reproducibility and as practiced generally for antibacterial application, phage dosing instead should be described in terms of concentrations of formulations (phage titers) as well as volumes applied and, in many cases, absolute numbers of phages delivered. Such an approach typically will be far more desirable from a pharmacological perspective than solely indicating ratios of agents to bacteria. This essay was adapted, with permission, from an appendix of the 2011 monograph, Bacteriophages and Biofilms, Nova Science Publishers.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81678234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriophages safely reduce Salmonella contamination in pet food and raw pet food ingredients","authors":"N. Soffer, T. Abuladze, Joelle E. Woolston, Manrong Li, L. F. Hanna, Serena Heyse, D. Charbonneau, A. Sulakvelidze","doi":"10.1080/21597081.2016.1220347","DOIUrl":"https://doi.org/10.1080/21597081.2016.1220347","url":null,"abstract":"ABSTRACT Contamination of pet food with Salmonella is a serious public health concern, and several disease outbreaks have recently occurred due to human exposure to Salmonella tainted pet food. The problem is especially challenging for raw pet foods (which include raw meats, seafood, fruits, and vegetables). These foods are becoming increasingly popular because of their nutritional qualities, but they are also more difficult to maintain Salmonella-free because they lack heat-treatment. Among various methods examined to improve the safety of pet foods (including raw pet food), one intriguing approach is to use bacteriophages to specifically kill Salmonella serotypes. At least 2 phage preparations (SalmoFresh® and Salmonelex™) targeting Salmonella are already FDA cleared for commercial applications to improve the safety of human foods. However, similar preparations are not yet available for pet food applications. Here, we report the results of evaluating one such preparation (SalmoLyse®) in reducing Salmonella levels in various raw pet food ingredients (chicken, tuna, turkey, cantaloupe, and lettuce). Application of SalmoLyse® in low (ca. 2–4×106 PFU/g) and standard (ca. 9×106 PFU/g) concentrations significantly (P < 0.01) reduced (by 60–92%) Salmonella contamination in all raw foods examined compared to control treatments. When SalmoLyse®-treated (ca. 2×107 PFU/g) dry pet food was fed to cats and dogs, it did not trigger any deleterious side effects in the pets. Our data suggest that the bacteriophage cocktail lytic for Salmonella can significantly and safely reduce Salmonella contamination in various raw pet food ingredients.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"279 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86736057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of 9 novel Paenibacillus larvae bacteriophages","authors":"Casey Stamereilers, L. Leblanc, Diane G. Yost, P. Amy, Philippos K. Tsourkas","doi":"10.1080/21597081.2016.1220349","DOIUrl":"https://doi.org/10.1080/21597081.2016.1220349","url":null,"abstract":"ABSTRACT American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 3′ overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84103864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes","authors":"V. Delesalle, Natalie T Tanke, Albert C. Vill, G. Krukonis","doi":"10.1080/21597081.2016.1219441","DOIUrl":"https://doi.org/10.1080/21597081.2016.1219441","url":null,"abstract":"ABSTRACT The presence of tRNA genes in bacteriophages has been explained on the basis of codon usage (tRNA genes are retained in the phage genome if they correspond to codons more common in the phage than in its host) or amino acid usage (independent of codon, the amino acid corresponding to the retained tRNA gene is more common in the phage genome than in the bacterial host). The existence of a large database of sequenced mycobacteriophages, isolated on the common host Mycobacterium smegmatis, allows us to test the above hypotheses as well as explore other hypotheses for the presence of tRNA genes. Our analyses suggest that amino acid rather than codon usage better explains the presence of tRNA genes in mycobacteriophages. However, closely related phages that differ in the presence of tRNA genes in their genomes are capable of lysing the common bacterial host and do not differ in codon or amino acid usage. This suggests that the benefits of having tRNA genes may be associated with either growth in the host or the ability to infect more hosts (i.e., host range) rather than simply infecting a particular host.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90554848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of novel Staphylococcus aureus lytic phage and defining their combinatorial virulence using the OmniLog® system","authors":"Luis A. Estrella, Javier Quiñones, M. Henry, R. M. Hannah, R. Pope, Theron Hamilton, Nimfa Teneza-mora, E. Hall, Biswas Biswajit","doi":"10.1080/21597081.2016.1219440","DOIUrl":"https://doi.org/10.1080/21597081.2016.1219440","url":null,"abstract":"ABSTRACT Skin and soft tissue infections (SSTI) caused by methicillin resistant Staphylococcus aureus (MRSA) are difficult to treat. Bacteriophage (phage) represent a potential alternate treatment for antibiotic resistant bacterial infections. In this study, 7 novel phage with broad lytic activity for S. aureus were isolated and identified. Screening of a diverse collection of 170 clinical isolates by efficiency of plating (EOP) assays shows that the novel phage are virulent and effectively prevent growth of 70–91% of MRSA and methicillin sensitive S. aureus (MSSA) isolates. Phage K, which was previously identified as having lytic activity on S. aureus was tested on the S. aureus collection and shown to prevent growth of 82% of the isolates. These novel phage group were examined by electron microscopy, the results of which indicate that the phage belong to the Myoviridae family of viruses. The novel phage group requires β-N-acetyl glucosamine (GlcNac) moieties on cell wall teichoic acids for infection. The phage were distinct from, but closely related to, phage K as characterized by restriction endonuclease analysis. Furthermore, growth rate analysis via OmniLog® microplate assay indicates that a combination of phage K, with phage SA0420ᶲ1, SA0456ᶲ1 or SA0482ᶲ1 have a synergistic phage-mediated lytic effect on MRSA and suppress formation of phage resistance. These results indicate that a broad spectrum lytic phage mixture can suppress the emergence of resistant bacterial populations and hence have great potential for combating S. aureus wound infections.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88767722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}