PHAGE (New Rochelle, N.Y.)最新文献_第9页

From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs. 从树到云：PhageClouds 用于快速比较 ∼640,000 个噬菌体基因组序列，以及使用基因组网络图进行以宿主为中心的可视化。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-12-01 Epub Date: 2021-12-16 DOI: 10.1089/phage.2021.0008

Guillermo Rangel-Pineros, Andrew Millard, Slawomir Michniewski, David Scanlan, Kimmo Sirén, Alejandro Reyes, Bent Petersen, Martha R J Clokie, Thomas Sicheritz-Pontén

{"title":"From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.","authors":"Guillermo Rangel-Pineros, Andrew Millard, Slawomir Michniewski, David Scanlan, Kimmo Sirén, Alejandro Reyes, Bent Petersen, Martha R J Clokie, Thomas Sicheritz-Pontén","doi":"10.1089/phage.2021.0008","DOIUrl":"10.1089/phage.2021.0008","url":null,"abstract":"Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j® graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":" ","pages":"194-203"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7d/81/phage.2021.0008.PMC9041511.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33477955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. 噬菌体参考数据库的基础设施:鉴定当前培养噬菌体基因组收集中的大规模偏差。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-12-01 DOI: 10.1089/phage.2021.0007

Ryan Cook, Nathan Brown, Tamsin Redgwell, Branko Rihtman, Megan Barnes, Martha Clokie, Dov J Stekel, Jon Hobman, Michael A Jones, Andrew Millard

{"title":"INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes.","authors":"Ryan Cook, Nathan Brown, Tamsin Redgwell, Branko Rihtman, Megan Barnes, Martha Clokie, Dov J Stekel, Jon Hobman, Michael A Jones, Andrew Millard","doi":"10.1089/phage.2021.0007","DOIUrl":"https://doi.org/10.1089/phage.2021.0007","url":null,"abstract":"Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade. Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata. Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (∼70%) than temperate (∼30%) within our database. Collectively, this results in ∼54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host. Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 4","pages":"214-223"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041510/pdf/phage.2021.0007.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10538730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 96

Phage Genome Annotation: Where to Begin and End. 噬菌体基因组注释：从哪里开始，到哪里结束。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-12-01 Epub Date: 2021-12-16 DOI: 10.1089/phage.2021.0015

Anastasiya Shen, Andrew Millard

引用次数: 0

Lytic Bacteriophages Against Bacterial Biofilms Formed by Multidrug-Resistant Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus Isolated from Burn Wounds. 裂解噬菌体对抗烧伤创面中多重耐药铜绿假单胞菌、大肠杆菌、肺炎克雷伯菌和金黄色葡萄球菌形成的细菌生物膜。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.0004

Roja Rani Pallavali, Vijaya Lakshmi Degati, Venkata Ramireddy Narala, Kiran Kumar Velpula, Suresh Yenugu, Vijaya Raghava Prasad Durbaka

{"title":"Lytic Bacteriophages Against Bacterial Biofilms Formed by Multidrug-Resistant Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus Isolated from Burn Wounds.","authors":"Roja Rani Pallavali, Vijaya Lakshmi Degati, Venkata Ramireddy Narala, Kiran Kumar Velpula, Suresh Yenugu, Vijaya Raghava Prasad Durbaka","doi":"10.1089/phage.2021.0004","DOIUrl":"https://doi.org/10.1089/phage.2021.0004","url":null,"abstract":"Background: Use of bacteriophages as antibiofilm agents to tackle multidrug-resistant bacteria has gained importance in recent years. Materials and Methods: In this study, biofilm formation by Staphylococcus aureus, Pseudomona aeruginosa, Klebsiella pneumoniae, and Escherichia coli under different growth conditions was studied. Furthermore, the ability of bacteriophages to inhibit biofilm formation was analyzed. Results: Under dynamic growth condition, wherein the medium is renewed for every 12 h, the amount of biomass produced and log10 colony-forming unit counts of all bacterial species studied was highest when compared with other growth conditions tested. Biomass of biofilms produced was drastically reduced when incubated for 2 or 4 h with bacteriophages vB_SAnS_SADP1, vB_PAnP_PADP4, vB_KPnM_KPDP1, and vB_ECnM_ECDP3. Scanning electron microscopy and confocal laser scanning microscopy analyses indicated that the reduction in biomass was due to the lytic action of the bacteriophages. Conclusions: Results of our study reinforce the concept of developing bacteriophages as alternatives to antibiotics to treat bacterial infections.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 3","pages":"120-130"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041503/pdf/phage.2021.0004.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Solvent Extraction of Klebsiella pneumoniae Bacteriophage Lysates with 1-Dodecanol Results in Endotoxin Reduction with Low Risk of Solvent Contamination. 1-十二醇溶剂萃取肺炎克雷伯菌噬菌体裂解物可降低内毒素含量，且溶剂污染风险低。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.0005

Jordyn Michalik-Provasek, Harley Parker, Lauren Lessor, Jason J Gill

{"title":"Solvent Extraction of Klebsiella pneumoniae Bacteriophage Lysates with 1-Dodecanol Results in Endotoxin Reduction with Low Risk of Solvent Contamination.","authors":"Jordyn Michalik-Provasek, Harley Parker, Lauren Lessor, Jason J Gill","doi":"10.1089/phage.2021.0005","DOIUrl":"https://doi.org/10.1089/phage.2021.0005","url":null,"abstract":"Antimicrobial resistance in pathogenic bacteria is increasing worldwide. One solution to this crisis is bacteriophage therapy, a treatment that harnesses naturally occurring bacterial viruses to invade and lyse antimicrobial resistant bacterial hosts. In Gram-negative hosts, a by-product of bacteriophage production is bacterial endotoxin, which can cause serious immune reactions in vivo. Purification methods using organic solvent extraction can remove endotoxin in bacteriophage lysates. In this study, we investigate a method for removal of endotoxin from 16 high-titer Klebsiella pneumoniae lysates by extraction with 1-dodecanol, 1-octanol, dodecane, or decane. In these experiments, treatment with either 1-dodecanol or 1-octanol resulted in removal of 104-105 endotoxin units/mL. Recovery of bacteriophage in lysates treated with dodecanol without dialysis was >90%, and residual dodecanol was low (10-1500 ppm). Overall these results suggest that organic solvent extraction using 1-dodecanol is effective at removing bacterial endotoxin, maintaining bacteriophage titer, and reducing solvent contamination in 16 K. pneumoniae bacteriophage lysates.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 3","pages":"112-119"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8574134/pdf/phage.2021.0005.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39624974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phages and a Trip Around the World. 噬菌体和环球旅行。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.29021.mcl

Martha R J Clokie

引用次数: 0

Analysis of Four New Enterococcus faecalis Phages and Modeling of a Hyaluronidase Catalytic Domain from Saphexavirus. 四种新型粪肠球菌噬菌体的分析及透明质酸酶催化结构域的建模。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.0003

Gustavo Di Lallo, Mattia Falconi, Federico Iacovelli, Domenico Frezza, Pietro D'Addabbo

{"title":"Analysis of Four New Enterococcus faecalis Phages and Modeling of a Hyaluronidase Catalytic Domain from Saphexavirus.","authors":"Gustavo Di Lallo, Mattia Falconi, Federico Iacovelli, Domenico Frezza, Pietro D'Addabbo","doi":"10.1089/phage.2021.0003","DOIUrl":"https://doi.org/10.1089/phage.2021.0003","url":null,"abstract":"Background: Phage therapy (PT), as a method to treat bacterial infections, needs identification of bacteriophages targeting specific pathogenic host. Enterococcus faecalis, a Gram-positive coccus resident in the human gastrointestinal tract, may become pathogenic in hospitalized patients showing acquired resistance to vancomycin and thus representing a possible target for PT. Materials and Methods: We isolated four phages that infect E. faecalis and characterized them by host range screening, transmission electron microscopy, and genome sequencing. We also identified and three-dimensional modeled a new hyaluronidase enzyme. Results: The four phages belong to Siphoviridae family: three Efquatrovirus (namely vB_EfaS_TV51, vB_EfaS_TV54, and vB_EfaS_TV217) and one Saphexavirus (vB_EfaS_TV16). All of them are compatible with lytic cycle. vB_EfaS_TV16 moreover presents a gene encoding for a hyaluronidase enzyme. Conclusions: The identified phages show features suggesting their useful application in PT, particularly the Saphexavirus that may be of enhanced relevance in PT because of its potential biofilm-digestion capability.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 3","pages":"131-141"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041502/pdf/phage.2021.0003.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Isolation and Characterization of Novel Phages Targeting Xanthomonas oryzae: Culprit of Bacterial Leaf Blight Disease in Rice. 水稻白叶枯病病原菌米黄单胞菌噬菌体的分离与鉴定

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.0009

Jian Liu, Suet Lin Chia, Geok Hun Tan

{"title":"Isolation and Characterization of Novel Phages Targeting Xanthomonas oryzae: Culprit of Bacterial Leaf Blight Disease in Rice.","authors":"Jian Liu, Suet Lin Chia, Geok Hun Tan","doi":"10.1089/phage.2021.0009","DOIUrl":"https://doi.org/10.1089/phage.2021.0009","url":null,"abstract":"Background: Bacterial leaf blight (BLB) disease caused 80% of disease incidence in paddy in Kedah and Selangor states of Malaysia. The pathogenic bacterium, Xanthomonas oryzae pv. oryzae (Xoo), is one of the destructive pathogens infecting lowland irrigated and rainfed paddy in Asia's tropical and temperate environments. Bacteriophages (or phages) have been proposed to control the pathogen due to their efficacy and safety aspects. Material and Methods: In this study, a total of 70 Xoo-phages were isolated from termite which living in rice-growing area. Results: 2 lytic phages NΦ-1 and NΦ-3 were selected due to the high titer of the virus. Electron microscopic analysis showed that those phages belonged to the family Podoviridae, order Caudovirales with short noncontracted tails. Moreover, these phages have a narrow host range specifically target Xoo with a higher burst size. Whole-genome sequencing showed that the Xoo-phage NΦ-1 and NΦ-3 consists of a linear double-stranded DNA molecule of length 41,151 and 38,454 bp, respectively. Conclusion: This study successfully characterized two novel Xanthomonas phages and their potential as antimicrobial agents against BLB disease in rice.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 3","pages":"142-151"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041505/pdf/phage.2021.0009.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Investigation of Phages Infecting Escherichia coli Strains B and C, and Enterobacter cloacae in Sewage and Ebrié Lagoon, Côte d'Ivoire. Côte科特迪瓦污水和ebri<s:1>泻湖中感染大肠杆菌B、C和阴沟肠杆菌的噬菌体调查。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2020.0047

Ameyo Yayra Audrey Addablah, Solange Kakou-Ngazoa, Eric Essoh Akpa, Fred M'Bourou Ndombi, Emmanuella Adioumani, Aristide Koudou, David Coulibaly N'Golo, Mireille Kouame Sina, Stephane Kan Kouassi, Serge Aoussi, Mireille Dosso

{"title":"Investigation of Phages Infecting Escherichia coli Strains B and C, and Enterobacter cloacae in Sewage and Ebrié Lagoon, Côte d'Ivoire.","authors":"Ameyo Yayra Audrey Addablah, Solange Kakou-Ngazoa, Eric Essoh Akpa, Fred M'Bourou Ndombi, Emmanuella Adioumani, Aristide Koudou, David Coulibaly N'Golo, Mireille Kouame Sina, Stephane Kan Kouassi, Serge Aoussi, Mireille Dosso","doi":"10.1089/phage.2020.0047","DOIUrl":"https://doi.org/10.1089/phage.2020.0047","url":null,"abstract":"Background: Bacteriophages are a promising biotechnological against bacterial pathogens. Currently, phage research is garnering interest in sub-Saharan countries as bacterial resistance to antibiotics becomes widespread. They are sought in all environments as they offer the possibility of a sustainable alternative to antibiotics. Materials and Methods: Altogether 30 water samples from urban sewage and environmental water were screened for the presence of bacteriophages able to infect Escherichia coli and Enterobacter cloacae. Their genomic diversity was determined by random amplification of polymorphic DNA (RAPD)-PCR fingerprinting. Results: We isolated 35 phages including 9 polyvalent phages that infect simultaneously E. coli and E. cloacae. This study allowed first isolation of E. cloacae-specific phages in Côte d'Ivoire. All phages were distinct based on their RAPD band patterns. Conclusions: Sewage systems of Yopougon and the environmental water of Ebrié lagoon were a rich source of phages. The phage collection could be useful for phage application in Côte d'Ivoire.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"2 3","pages":"104-111"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041496/pdf/phage.2020.0047.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

inPhocus: The Diverse Landscape of Phage Studies in the Association of Southeast Asian Nations Region. inPhocus：东南亚国家联盟地区噬菌体研究的多样性景观。

PHAGE (New Rochelle, N.Y.) Pub Date : 2021-09-01 Epub Date: 2021-09-17 DOI: 10.1089/phage.2021.29020.hra

Heera Rajandas, Sivachandran Parimannan, Thomas Sicheritz-Pontén, Martha R J Clokie

引用次数: 0