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https://www.readbyqxmd.com/read/28304358/a-pelagic-microbiome-viruses-to-protists-from-a-small-cup-of-seawater
#1
Flavia Flaviani, Declan C Schroeder, Cecilia Balestreri, Joanna L Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C Pfaff, Edward P Rybicki
The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment...
March 17, 2017: Viruses
https://www.readbyqxmd.com/read/28270584/viruses-in-the-oceanic-basement
#2
Olivia D Nigro, Sean P Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn A Miranda, Christopher R Schvarcz, Michael S Rappé, Grieg F Steward
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge...
March 7, 2017: MBio
https://www.readbyqxmd.com/read/28261669/environmental-viral-genomes-shed-new-light-on-virus-host-interactions-in-the-ocean
#3
Yosuke Nishimura, Hiroyasu Watai, Takashi Honda, Tomoko Mihara, Kimiho Omae, Simon Roux, Romain Blanc-Mathieu, Keigo Yamamoto, Pascal Hingamp, Yoshihiko Sako, Matthew B Sullivan, Susumu Goto, Hiroyuki Ogata, Takashi Yoshida
Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral "dark matter." However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs)...
March 2017: MSphere
https://www.readbyqxmd.com/read/28261185/metagenomic-sequencing-for-surveillance-of-food-and-waterborne-viral-diseases
#4
David F Nieuwenhuijse, Marion P G Koopmans
A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28259747/exosome-based-immunomodulation-during-aging-a-nano-perspective-on-inflamm-aging
#5
REVIEW
Francesco Prattichizzo, Luigina Micolucci, Monica Cricca, Sabrina De Carolis, Emanuela Mensà, Antonio Ceriello, Antonio Domenico Procopio, Massimiliano Bonafè, Fabiola Olivieri
Exosomes are nanovesicles formed by inward budding of endosomal membranes. They exert complex immunomodulatory effects on target cells, acting both as antigen-presenting vesicles and as shuttles for packets of information like proteins, coding and non-coding RNA, and nuclear and mitochondrial DNA fragments. Albeit different, all such functions seem to be encompassed in the adaptive mechanism mediating the complex interactions of the organism with a variety of stressors, providing both for defense and for the evolution of symbiotic relationships with others organisms (gut microbiota, bacteria, and viruses)...
March 1, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#6
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217745/the-baltic-sea-virome-diversity-and-transcriptional-activity-of-dna-and-rna-viruses
#7
Lisa Zeigler Allen, John P McCrow, Karolina Ininbergs, Christopher L Dupont, Jonathan H Badger, Jeffery M Hoffman, Martin Ekman, Andrew E Allen, Birgitta Bergman, J Craig Venter
Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae...
January 2017: MSystems
https://www.readbyqxmd.com/read/28194314/evolutionary-and-functional-implications-of-hypervariable-loci-within-the-skin-virome
#8
Geoffrey D Hannigan, Qi Zheng, Jacquelyn S Meisel, Samuel S Minot, Frederick D Bushman, Elizabeth A Grice
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers...
2017: PeerJ
https://www.readbyqxmd.com/read/28192164/origins-and-challenges-of-viral-dark-matter
#9
REVIEW
Siddharth R Krishnamurthy, David Wang
The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40 and 90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases...
February 9, 2017: Virus Research
https://www.readbyqxmd.com/read/28192039/endemic-infection-of-stranded-southern-sea-otters-enhydra-lutris-nereis-with-novel-parvovirus-polyomavirus-and-adenovirus
#10
Juliana D Siqueira, Terry Ng, Melissa Miller, Linlin Li, Xutao Deng, Erin Dodd, Francesca Batac, Eric Delwart
Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened species under federal law and a fully protected species under California law. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities...
February 13, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28179422/viruses-comprise-an-extensive-pool-of-mobile-genetic-elements-in-eukaryote-cell-cultures-and-human-clinical-samples
#11
Jakob Thannesberger, Hans-Joerg Hellinger, Ingeborg Klymiuk, Marie-Theres Kastner, Franz J J Rieder, Martina Schneider, Susanne Fister, Thomas Lion, Karin Kosulin, Johannes Laengle, Michael Bergmann, Thomas Rattei, Christoph Steininger
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter)...
February 8, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28167933/virome-assembly-and-annotation-a-surprise-in-the-namib-desert
#12
Uljana Hesse, Peter van Heusden, Bronwyn M Kirby, Israel Olonade, Leonardo J van Zyl, Marla Trindade
Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28159153/the-virome-of-the-human-respiratory-tract
#13
REVIEW
Kristine M Wylie
The human respiratory tract virome is defined here as the viruses present in the human respiratory tract that can infect human cells. Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens...
March 2017: Clinics in Chest Medicine
https://www.readbyqxmd.com/read/28152382/statoviruses-a-novel-taxon-of-rna-viruses-present-in-the-gastrointestinal-tracts-of-diverse-mammals
#14
Andrew B Janowski, Siddharth R Krishnamurthy, Efrem S Lim, Guoyan Zhao, Jason M Brenchley, Dan H Barouch, Chrissie Thakwalakwa, Mark J Manary, Lori R Holtz, David Wang
Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts...
April 2017: Virology
https://www.readbyqxmd.com/read/28134265/consensus-statement-virus-taxonomy-in-the-age-of-metagenomics
#15
REVIEW
Peter Simmonds, Mike J Adams, Mária Benkő, Mya Breitbart, J Rodney Brister, Eric B Carstens, Andrew J Davison, Eric Delwart, Alexander E Gorbalenya, Balázs Harrach, Roger Hull, Andrew M Q King, Eugene V Koonin, Mart Krupovic, Jens H Kuhn, Elliot J Lefkowitz, Max L Nibert, Richard Orton, Marilyn J Roossinck, Sead Sabanadzovic, Matthew B Sullivan, Curtis A Suttle, Robert B Tesh, René A van der Vlugt, Arvind Varsani, F Murilo Zerbini
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome...
January 3, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28122648/microbiota-transfer-therapy-alters-gut-ecosystem-and-improves-gastrointestinal-and-autism-symptoms-an-open-label-study
#16
Dae-Wook Kang, James B Adams, Ann C Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L Pollard, Simon Roux, Michael J Sadowsky, Karen Schwarzberg Lipson, Matthew B Sullivan, J Gregory Caporaso, Rosa Krajmalnik-Brown
BACKGROUND: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 10(13) bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD...
January 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28114361/studies-on-the-virome-of-the-entomopathogenic-fungus-beauveria-bassiana-reveal-novel-dsrna-elements-and-mild-hypervirulence
#17
Ioly Kotta-Loizou, Robert H A Coutts
The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests. Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely. Here we show that 21.3% of a collection of B. bassiana isolates sourced from worldwide locations, harbor dsRNA elements. Molecular characterization of these elements revealed the prevalence of mycoviruses belonging to the Partitiviridae and Totiviridae families, the smallest reported virus to date, belonging to the family Narnaviridae, and viruses unassigned to a family or genus...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28110145/virusseeker-a-computational-pipeline-for-virus-discovery-and-virome-composition-analysis
#18
Guoyan Zhao, Guang Wu, Efrem S Lim, Lindsay Droit, Siddharth Krishnamurthy, Dan H Barouch, Herbert W Virgin, David Wang
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences...
March 2017: Virology
https://www.readbyqxmd.com/read/28100412/virome-of-us-bovine-calf-serum
#19
Mohammadreza Sadeghi, Beatrix Kapusinszky, Danielle M Yugo, Tung Gia Phan, Xutao Deng, Isis Kanevsky, Tanja Opriessnig, Amelia R Woolums, David J Hurley, Xiang-Jin Meng, Eric Delwart
Using viral metagenomics we analyzed four bovine serum pools assembled from 715 calves in the United States. Two parvoviruses, bovine parvovirus 2 (BPV2) and a previously uncharacterized parvovirus designated as bosavirus (BosaV), were detected in 3 and 4 pools respectively and their complete coding sequences generated. Based on NS1 protein identity, bosavirus qualifies as a member of a new species in the copiparvovirus genus. Also detected were low number of reads matching ungulate tetraparvovirus 2, bovine hepacivirus, and several papillomaviruses...
January 15, 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28100302/fecal-virome-of-healthy-chickens-reveals-a-large-diversity-of-the-eukaryote-viral-community-including-novel-circular-single-stranded-dna-viruses
#20
Diane Lima, Samuel Paulo Cibulski, Fabrine Finkler, Thais Teixeira, Ana Paula Varela, Cristine Cerva, Márcia Loiko, Camila Scheffer, Helton Dos Santos, Fabiana Mayer, Paulo Roehe
This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes...
January 18, 2017: Journal of General Virology
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