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https://www.readbyqxmd.com/read/28724557/the-human-virome-implications-for-clinical-practice-in-transplantation-medicine
#1
Susanna K Tan, David A Relman, Benjamin A Pinsky
Advances in DNA sequencing technology have provided an unprecedented opportunity to study the human virome. Transplant recipients and other immunocompromised hosts are at particular risk for developing virus-related pathology; thus, the impact of the virome on health and disease may be even more relevant in this population. Here we discuss technical considerations in studying the human virome, the current literature on the virome in transplant recipients, and near future applications of sequence-based findings that can further our understanding of viruses in transplantation medicine...
July 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28724405/environmental-drivers-of-viral-community-composition-in-antarctic-soils-identified-by-viromics
#2
Evelien M Adriaenssens, Rolf Kramer, Marc W Van Goethem, Thulani P Makhalanyane, Ian Hogg, Don A Cowan
BACKGROUND: The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS: Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#3
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28713358/aquarium-viromes-viromes-of-human-managed-aquatic-systems
#4
Yiseul Kim, William Van Bonn, Tiong G Aw, Joan B Rose
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28698277/deep-sea-hydrothermal-vent-viruses-compensate-for-microbial-metabolism-in-virus-host-interactions
#5
Tianliang He, Hongyun Li, Xiaobo Zhang
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28696303/intestinal-virome-changes-precede-autoimmunity-in-type-i-diabetes-susceptible-children
#6
Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D Kostic, Tiffany W Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J Xavier, Herbert W Virgin
Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls...
July 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28677677/marine-viruses-discovered-via-metagenomics-shed-light-on-viral-strategies-throughout-the-oceans
#7
Felipe H Coutinho, Cynthia B Silveira, Gustavo B Gregoracci, Cristiane C Thompson, Robert A Edwards, Corina P D Brussaard, Bas E Dutilh, Fabiano L Thompson
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28672885/characterization-of-sinorhizobium-sp-lm21-prophages-and-virus-encoded-dna-methyltransferases-in-the-light-of-comparative-genomic-analyses-of-the-sinorhizobial-virome
#8
Przemyslaw Decewicz, Monika Radlinska, Lukasz Dziewit
The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes...
June 26, 2017: Viruses
https://www.readbyqxmd.com/read/28671295/characterization-of-the-nasopharyngeal-viral-microbiome-from-children-with-community-acquired-pneumonia-but-negative-for-luminex-xtag-respiratory-viral-panel-assay-detection
#9
Lili Xu, Yun Zhu, Lili Ren, Baoping Xu, Chunyan Liu, Zhengde Xie, Kunling Shen
In the present study, 50 nasopharyngeal swabs from children with community-acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next-generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae...
July 3, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28663745/viromes-as-genetic-reservoir-for-the-microbial-communities-in-aquatic-environments-a-focus-on-antimicrobial-resistance-genes
#10
Stefano Colombo, Stefania Arioli, Eros Neri, Giulia Della Scala, Giorgio Gargari, Diego Mora
Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28659484/case-control-comparison-of-enteric-viromes-in-captive-rhesus-macaques-with-acute-or-idiopathic-chronic-diarrhea
#11
Beatrix Kapusinszky, Amir Ardeshir, Usha Mulvaney, Xutao Deng, Eric Delwart
Diarrhea is the major cause of non-research associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, a form of human inflammatory bowel disease. To test for viral etiologies we characterized and compared the fecal virome from 32 healthy, 31 with acute diarrhea, and 29 with ICD animals. The overall fraction of eukaryotic viral reads was 0.063% for the healthy group, 0...
June 28, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28651630/maternal-inheritance-of-bifidobacterial-communities-and-bifidophages-in-infants-through-vertical-transmission
#12
Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Federica Armanini, Francesca Turroni, Kieran James, Pamela Ferretti, Valentina Gorfer, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Moreno Zolfo, Alice Viappiani, Edoardo Pasolli, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Sabina Fedi, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Massimo Soffiati, Saverio Tateo, Anna Pedrotti, Nicola Segata, Douwe van Sinderen, Marco Ventura
BACKGROUND: The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS: The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses...
June 26, 2017: Microbiome
https://www.readbyqxmd.com/read/28649326/viral-gut-metagenomics-of-sympatric-wild-and-domestic-canids-and-monitoring-of-viruses-insights-from-an-endangered-wolf-population
#13
Nádia Conceição-Neto, Raquel Godinho, Francisco Álvares, Claude K Yinda, Ward Deboutte, Mark Zeller, Lies Laenen, Elisabeth Heylen, Sara Roque, Francisco Petrucci-Fonseca, Nuno Santos, Marc Van Ranst, João R Mesquita, Jelle Matthijnssens
Animal host-microbe interactions are a relevant concern for wildlife conservation, particularly regarding generalist pathogens, where domestic host species can play a role in the transmission of infectious agents, such as viruses, to wild animals. Knowledge on viral circulation in wild host species is still scarce and can be improved by the recent advent of modern molecular approaches. We aimed to characterize the fecal virome and identify viruses of potential conservation relevance of diarrheic free-ranging wolves and sympatric domestic dogs from Central Portugal, where a small and threatened wolf population persists in a highly anthropogenically modified landscape...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28643787/single-virus-genomics-reveals-hidden-cosmopolitan-and-abundant-viruses
#14
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B Sullivan, Silvia G Acinas, Manuel Martinez-Garcia
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28637756/high-resolution-meta-transcriptomics-reveals-the-ecological-dynamics-of-mosquito-associated-rna-viruses-in-western-australia
#15
Mang Shi, Peter Neville, Jay Nicholson, John-Sebastian Eden, Allison Imrie, Edward C Holmes
Mosquitoes harbour a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a meta-transcriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28617757/looking-into-enteric-virome-in-patients-with-ibd-defining-guilty-or-innocence
#16
Susana Lopes, Patricia Andrade, Silvia Conde, Rodrigo Liberal, Cláudia C Dias, Salomão Fernandes, Jorge Pinheiro, Joana S Simões, Fátima Carneiro, Fernando Magro, Guilherme Macedo
BACKGROUND: Although there is some evidence suggesting that certain viruses may be involved in the onset of inflammatory bowel disease (IBD), data regarding viral prevalence and viral load in blood and mucosa of patients with IBD are scarce. The main aim of this study is to evaluate the prevalence and viral load of common Epstein-Barr virus (EBV), cytomegalovirus (CMV), and human herpes virus 6 in blood and mucosa of adult patients with endoscopic active IBD. METHODS: From January to December 2014, ulcerative colitis and Crohn's disease patients with active endoscopic disease were consecutively enrolled...
August 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28606917/quantitative-temporal-viromics-of-an-inducible-hiv-1-model-yields-insight-to-global-host-targets-and-phospho-dynamics-associated-with-vpr
#17
John D Lapek, Mary K Lewinski, Jacob M Wozniak, John Guatelli, David J Gonzalez
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist...
June 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28595635/the-pepper-virome-natural-co-infection-of-diverse-viruses-and-their-quasispecies
#18
Yeonhwa Jo, Hoseong Choi, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho
BACKGROUND: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. RESULTS: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host...
June 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28592325/isolation-and-characterization-of-the-first-phage-infecting-ecologically-important-marine-bacteria-erythrobacter
#19
Longfei Lu, Lanlan Cai, Nianzhi Jiao, Rui Zhang
BACKGROUND: Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter. METHODS: Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed...
June 7, 2017: Virology Journal
https://www.readbyqxmd.com/read/28586923/presence-of-human-hepegivirus-1-in-a-cohort-of-people-who-inject-drugs
#20
Abraham J Kandathil, Florian P Breitwieser, Jaiprasath Sachithanandham, Matthew Robinson, Shruti H Mehta, Winston Timp, Steven L Salzberg, David L Thomas, Ashwin Balagopal
Background: Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. Objective: To explore the plasma virome of persons who inject drugs and to characterize the sensitivity and accuracy of NGMS compared with quantitative clinical standards. Design: Longitudinal and cross-sectional studies. Setting: A clinical trial (ClinicalTrials...
July 4, 2017: Annals of Internal Medicine
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