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https://www.readbyqxmd.com/read/28935725/small-circular-rep-encoding-single-stranded-dna-genomes-in-peruvian-diarrhea-virome
#1
Eda Altan, Juana Del Valle Mendoza, Xutao Deng, Tung G Phan, Mohammadreza Sadeghi, Eric L Delwart
Metagenomic analysis of diarrhea samples revealed the presence of numerous human enteric viruses and small circular Rep-encoding single-stranded DNA (CRESS-DNA) genomes. One such genome was related to smacoviruses, while eight others were related to genomes reported in the feces of different mammals. The tropism of these CRESS-DNA viruses remains unknown.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28925542/genome-characteristics-and-environmental-distribution-of-the-first-phage-that-infects-the-ld28-clade-a-freshwater-methylotrophic-bacterial-group
#2
Kira Moon, Ilnam Kang, Suhyun Kim, Sang-Jong Kim, Jang-Cheon Cho
Bacteriophages infecting major groups of freshwater heterotrophic bacteria have been rarely isolated, hampering analyses of freshwater viromes. Here we report the isolation and genomic characterization of P19250A, the first phage that infects the LD28 clade, an abundant freshwater methylotrophic bacterial group. P19250A was isolated from Lake Soyang, an oligotrophic reservoir, using an LD28 strain as a host. Morphological and genomic analyses revealed that P19250A is a lytic siphovirus with a ∼38.6-kb genome...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28919883/a-pcr-based-assay-targeting-the-major-capsid-protein-gene-of-a-dinorna-like-ssrna-virus-that-infects-coral-photosymbionts
#3
Jose Montalvo-Proaño, Patrick Buerger, Karen D Weynberg, Madeleine J H van Oppen
The coral-Symbiodinium association is a critical component of coral reefs as it is the main primary producer and builds the reef's 3-dimensional structure. A breakdown of this endosymbiosis causes a loss of the dinoflagellate photosymbiont, Symbiodinium, and/or its photosynthetic pigments from the coral tissues (i.e., coral bleaching), and can lead to coral mortality. Coral bleaching has mostly been attributed to environmental stressors, and in some cases to bacterial infection. Viral lysis of Symbiodinium has been proposed as another possible cause of some instances of coral bleaching, but this hypothesis has not yet been experimentally confirmed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28902913/identification-of-diverse-viruses-in-upper-respiratory-samples-in-dromedary-camels-from-united-arab-emirates
#4
Yan Li, Abdelmalik Ibrahim Khalafalla, Clinton R Paden, Mohammed F Yusof, Yassir M Eltahir, Zulaikha M Al Hammadi, Ying Tao, Krista Queen, Farida Al Hosani, Susan I Gerber, Aron J Hall, Salama Al Muhairi, Suxiang Tong
Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2...
2017: PloS One
https://www.readbyqxmd.com/read/28886006/the-enteric-virome-in-hematopoietic-stem-cell-transplantation-ready-for-its-close-up
#5
Shuichiro Takashima, Alan M Hanash
No abstract text is available yet for this article.
September 8, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28883464/characterizing-the-virome-of-ixodes-ricinus-ticks-from-northern-europe
#6
John H-O Pettersson, Mang Shi, Jon Bohlin, Vegard Eldholm, Ola B Brynildsrud, Katrine Mørk Paulsen, Åshild Andreassen, Edward C Holmes
RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral diversity in ticks is still poorly understood, particularly in Europe. Using a bulk RNA-sequencing approach that captures the complete transcriptome, we analysed the virome of the most common tick in Europe - Ixodes ricinus. In total, RNA sequencing was performed on six libraries consisting of 33 I...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28883450/virome-analysis-for-identification-of-novel-mammalian-viruses-in-bats-from-southeast-china
#7
Dan Hu, Changqiang Zhu, Yi Wang, Lele Ai, Lu Yang, Fuqiang Ye, Chenxi Ding, Jiafeng Chen, Biao He, Jin Zhu, Hui Qian, Wenrong Xu, Youjun Feng, Weilong Tan, Changjun Wang
Bats have been shown as important mammal resevoirs to carry a variety of zoonotic pathogens. To analyze pathogenic species in bats from southeast coastal regions of China, we performed metagenomic sequencing technology for high throughput sequencing of six sentinels from southeast coastal area of China. We obtained 5,990,261 high quality reads from intestine and lung tissue of 235 bats, including 2,975,371 assembled sequences. 631,490 reads predicted overlapping sequences for the open reading frame (ORF), which accounts for 2...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28874166/the-porcine-virome-and-xenotransplantation
#8
REVIEW
Joachim Denner
The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context...
September 6, 2017: Virology Journal
https://www.readbyqxmd.com/read/28869283/review-article-the-human-intestinal-virome-in-health-and-disease
#9
REVIEW
S R Carding, N Davis, L Hoyles
BACKGROUND: The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM: To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases...
September 4, 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28864943/two-novel-alphaflexiviridae-members-revealed-by-deep-sequencing-of-the-vanilla-orchidaceae-virome
#10
Michel Grisoni, Armelle Marais, Denis Filloux, Anne Saison, Chantal Faure, Charlotte Julian, Sébastien Theil, Sandy Contreras, Pierre-Yves Teycheney, Philippe Roumagnac, Thierry Candresse
The genomes of two novel viruses were assembled from 454 pyrosequencing data obtained from vanilla leaves from La Réunion. Based on genome organization and homologies, one agent was unambiguously classified as a member of the genus Potexvirus and named vanilla virus X (VVX). The second one, vanilla latent virus (VLV), is phylogenetically close to three unclassified members of the family Alphaflexiviridae with similarity to allexiviruses, and despite the presence of an additional 8-kDa open reading frame, we propose to include VLV as a new member of the genus Allexivirus...
September 1, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28845264/a34%C3%A2-automated-profiling-of-the-human-virome-from-raw-metagenomic-data
#11
Yumna Moosa, Michael Vilsker, Ewout Vanden Eyden, Vagner Fonseca, Sam Nooij, Koen Deforche, Tulio de Oliveira
No abstract text is available yet for this article.
March 2017: Virus Evolution
https://www.readbyqxmd.com/read/28827715/from-virus-isolation-to-metagenome-generation-for-investigating-viral-diversity-in-deep-sea-sediments
#12
Cinzia Corinaldesi, Michael Tangherlini, Antonio Dell'Anno
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790203/the-in-feed-antibiotic-carbadox-induces-phage-gene-transcription-in-the-swine-gut-microbiome
#13
Timothy A Johnson, Torey Looft, Andrew J Severin, Darrell O Bayles, Daniel J Nasko, K Eric Wommack, Adina Howe, Heather K Allen
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28780905/virome-comparisons-in-wild-diseased-and-healthy-captive-giant-pandas
#14
Wen Zhang, Shixing Yang, Tongling Shan, Rong Hou, Zhijian Liu, Wang Li, Lianghua Guo, Yan Wang, Peng Chen, Xiaochun Wang, Feifei Feng, Hua Wang, Chao Chen, Quan Shen, Chenglin Zhou, Xiuguo Hua, Li Cui, Xutao Deng, Zhihe Zhang, Dunwu Qi, Eric Delwart
BACKGROUND: The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS: Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals...
August 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28780492/known-unknowns-how-might-the-persistent-herpesvirome-shape-immunity-and-aging
#15
REVIEW
Janko Nikolich-Zugich, Felicia Goodrum, Kenneth Knox, Megan J Smithey
The microbial community that colonizes all living organisms is gaining appreciation for its contributions to both physiologic and pathogenic processes. The virome, a subset of the overall microbiome, large and diverse, including viruses that persistently inhabit host cells, endogenous viral elements genomically or epigenomically integrated into cells, and viruses that infect the other (bacterial, protozoan, fungal, and archaeal) microbiome phylla. These viruses live in the organism for its life, and therefore are to be considered part of the aging process experienced by the organism...
August 3, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28765570/characterization-and-diversity-of-phages-infecting-aeromonas-salmonicida-subsp-salmonicida
#16
Antony T Vincent, Valérie E Paquet, Alex Bernatchez, Denise M Tremblay, Sylvain Moineau, Steve J Charette
Phages infecting Aeromonas salmonicida subsp. salmonicida, the causative agent of the fish disease furunculosis, have been isolated for decades but very few of them have been characterized. Here, the host range of 12 virulent phages, including three isolated in the present study, was evaluated against a panel of 65 A. salmonicida isolates, including representatives of the psychrophilic subspecies salmonicida, smithia, masoucida, and the mesophilic subspecies pectinolytica. This bacterial set also included three isolates from India suspected of being members of a new subspecies...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28759053/the-eukaryotic-gut-virome-in-hematopoietic-stem-cell-transplantation-new-clues-in-enteric-graft-versus-host-disease
#17
Jérôme Legoff, Matthieu Resche-Rigon, Jerome Bouquet, Marie Robin, Samia N Naccache, Séverine Mercier-Delarue, Scot Federman, Erik Samayoa, Clotilde Rousseau, Prescillia Piron, Nathalie Kapel, François Simon, Gérard Socié, Charles Y Chiu
Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0...
September 2017: Nature Medicine
https://www.readbyqxmd.com/read/28755263/phage-host-associations-in-a-full-scale-activated-sludge-plant-during-sludge-bulking
#18
Ruyin Liu, Rong Qi, Juan Wang, Yu Zhang, Xinchun Liu, Simona Rossetti, Valter Tandoi, Min Yang
Sludge bulking, a notorious microbial issue in activated sludge plants, is always accompanied by dramatic changes in the bacterial community. Despite large numbers of phages in sludge systems, their responses to sludge bulking and phage-host associations during bulking are unknown. In this study, high-throughput sequencing of viral metagenomes and bacterial 16S rRNA genes were employed to characterize viral and bacterial communities in a sludge plant under different sludge conditions (sludge volume index (SVI) of 180, 132, and 73 ml/g)...
July 29, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28743462/bacteriophages-in-the-human-gut-our-fellow-travelers-throughout-life-and-potential-biomarkers-of-heath-or-disease
#19
REVIEW
Babak Bakhshinejad, Saeedeh Ghiasvand
The gastrointestinal (GI) tract is populated by a huge variety of viruses. Bacterial viruses (bacteriophages) constitute the largest and the most unrecognized part of virome. The total bacteriophage community of the human gut is called phageome. Phages colonize the gut from the earliest moments of life and become our fellow travelers throughout life. Phageome seems to be unique to each individual and shows a high degree of interpersonal variation. In the healthy gut, a vast majority of phages have a lysogenic lifestyle...
July 22, 2017: Virus Research
https://www.readbyqxmd.com/read/28732571/examining-the-gut-bacteriome-virome-and-mycobiome-in-glucose-metabolism-disorders-are-we-on-the-right-track
#20
REVIEW
Charikleia Stefanaki, Melpomeni Peppa, George Mastorakos, George P Chrousos
Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism...
August 2017: Metabolism: Clinical and Experimental
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