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https://www.readbyqxmd.com/read/29155033/the-gut-virome-of-the-protochordate-model-organism-ciona-intestinalis-subtype-a
#1
Brittany A Leigh, Anni Djurhuus, Mya Breitbart, Larry J Dishaw
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members...
November 15, 2017: Virus Research
https://www.readbyqxmd.com/read/29154906/increase-in-taxonomic-assignment-efficiency-of-viral-reads-in-metagenomic-studies
#2
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
November 14, 2017: Virus Research
https://www.readbyqxmd.com/read/29140453/faecal-transplantation-for-ibd-management-pitfalls-and-promises
#3
M N Quraishi, T Critchlow, N Bhala, N Sharma, T Iqbal
Background: Faecal microbiota transplantation (FMT) as a potential treatment for inflammatory bowel disease (IBD) is an area of active current research, having been stimulated by the remarkable efficacy of FMT in treatment of Clostridium difficile-associated colitis. Sources of data: This review is based on data from numerous case series on FMT in IBD since 1989 and results of four RCTs in ulcerative colitis (UC); three fully published. Areas of agreement: Early signals of short to medium-term efficacy of FMT for UC are promising...
November 13, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/29138044/new-insight-into-the-rna-aquatic-virosphere-via-viromics
#4
REVIEW
Alexander Culley
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research...
November 11, 2017: Virus Research
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#5
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery (1-3) . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome (4) . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29118750/an-rna-virome-associated-to-the-golden-orb-weaver-spider-nephila-clavipes
#6
Humberto J Debat
The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29117243/virome-analysis-of-two-sympatric-bat-species-desmodus-rotundus-and-molossus-molossus-in-french-guiana
#7
Arielle Salmier, Sourakhata Tirera, Benoit de Thoisy, Alain Franc, Edith Darcissac, Damien Donato, Christiane Bouchier, Vincent Lacoste, Anne Lavergne
Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats...
2017: PloS One
https://www.readbyqxmd.com/read/29114244/phage-and-nucleocytoplasmic-large-viral-sequences-dominate-coral-viromes-from-the-arabian-gulf
#8
Huda Mahmoud, Liny Jose
Corals that naturally thrive under extreme conditions are gaining increasing attention due to their importance as living models to understand the impact of global warming on world corals. Here, we present the first metagenomic study of viral communities in corals thriving in a thermally variable water body in which the temperature fluctuates between 11 and 39°C in different seasons. The viral assemblages of two of the most abundant massive (Porites harrisoni) and branching (Acropora downingi) corals in offshore and inshore reef systems in the northern Arabian Gulf were investigated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29108696/metagenomics-for-the-study-of-viruses-in-urban-sewage-as-a-tool-for-public-health-surveillance
#9
X Fernandez-Cassi, N Timoneda, S Martínez-Puchol, M Rusiñol, J Rodriguez-Manzano, N Figuerola, S Bofill-Mas, J F Abril, R Girones
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10L of sewage collected in different seasons enabled the detection of many viruses...
November 3, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29103997/metagenomics-reshapes-the-concepts-of-rna-virus-evolution-by-revealing-extensive-horizontal-virus-transfer
#10
REVIEW
Valerian V Dolja, Eugene V Koonin
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp)...
November 8, 2017: Virus Research
https://www.readbyqxmd.com/read/29053145/geometagenomics-illuminates-the-impact-of-agriculture-on-the-distribution-and-prevalence-of-plant-viruses-at-the-ecosystem-scale
#11
Pauline Bernardo, Tristan Charles-Dominique, Mohamed Barakat, Philippe Ortet, Emmanuel Fernandez, Denis Filloux, Penelope Hartnady, Tony A Rebelo, Stephen R Cousins, François Mesleard, Damien Cohez, Nicole Yavercovski, Arvind Varsani, Gordon W Harkins, Michel Peterschmitt, Carolyn M Malmstrom, Darren P Martin, Philippe Roumagnac
Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France)...
October 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/29052506/the-proposed-new-species-cacao-red-vein-virus-and-three-previously-recognized-badnavirus-species-are-associated-with-cacao-swollen-shoot-disease
#12
Nomatter Chingandu, Koffie Kouakou, Romain Aka, George Ameyaw, Osman A Gutierrez, Hans-Werner Herrmann, Judith K Brown
BACKGROUND: Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only ~50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. METHODS: The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing...
October 19, 2017: Virology Journal
https://www.readbyqxmd.com/read/29026445/viral-communities-of-the-human-gut-metagenomic-analysis-of-composition-and-dynamics
#13
REVIEW
Varun Aggarwala, Guanxiang Liang, Frederic D Bushman
BACKGROUND: The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. MAIN BODY: Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29018436/use-of-rnalater-%C3%A2-preservation-for-virome-sequencing-in-outbreak-settings
#14
Claudia Kohl, Merle Wegener, Andreas Nitsche, Andreas Kurth
Outbreaks of infectious diseases may occur in animal and human populations; this underlines the need for suitable One Health approaches. During outbreak situations, straightforward identification of etiological agents is indispensable for taking countermeasures. A recently published protocol for metagenomic virus detection in clinical specimens (TUViD-VM) was developed for snap-frozen tissues which can be challenging to obtain. Here, we describe the use of RNALater(®) -treated tissue at ambient temperatures for virome sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28989970/virioplankton-assemblage-structure-in-the-lower-river-and-ocean-continuum-of-the-amazon
#15
Bruno S de O Silva, Felipe H Coutinho, Gustavo B Gregoracci, Luciana Leomil, Louisi S de Oliveira, Adriana Fróes, Diogo Tschoeke, Ana Carolina Soares, Anderson S Cabral, Nicholas D Ward, Jeffrey E Richey, Alex V Krusche, Patricia L Yager, Carlos Eduardo de Rezende, Cristiane C Thompson, Fabiano L Thompson
The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river's lower reach (n = 5) and plume (n = 7)...
September 2017: MSphere
https://www.readbyqxmd.com/read/28983731/viral-metagenomics-of-six-bat-species-in-close-contact-with-humans-in-southern-china
#16
Xue-Yan Zheng, Min Qiu, Wei-Jie Guan, Jin-Ming Li, Shao-Wei Chen, Ming-Ji Cheng, Shu-Ting Huo, Zhong Chen, Yi Wu, Li-Na Jiang, Qing Chen
Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions...
October 5, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28982318/virome-and-inflammasomes-a-finely-tuned-balance-with-important-consequences-for-the-host-health
#17
Giulia Freer, Fabrizio Maggi, Mauro Pistello
The virome is a multifaceted network of viruses inhabiting humans in health and disease. The virome forms a conspicuous portion of the so-called microbiome. Massive amount of data recently emerging demonstrates that the microbiome, once generically referred to as human (or animal) flora, is not a static entity but closely reflects what we eat, how and where we live, what we do, and many other unexpected variables. Composition, location, and amount of the microbiome have a direct impact on innate and adaptive host immune defences...
October 5, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28982120/identification-of-sapovirus-gv-2-astrovirus-va3-and-novel-anelloviruses-in-serum-from-patients-with-acute-hepatitis-of-unknown-aetiology
#18
Eloy Gonzales-Gustavson, N Timoneda, X Fernandez-Cassi, A Caballero, J F Abril, M Buti, F Rodriguez-Frias, R Girones
Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients with hepatitis without identified aetiological agents were evaluated. Additionally, one pool of patients with hepatitis E (HEV) and pools of healthy volunteers were included as controls...
2017: PloS One
https://www.readbyqxmd.com/read/28967228/characterization-of-the-human-dna-gut-virome-across-populations-with-different-subsistence-strategies-and-geographical-origin
#19
Simone Rampelli, Silvia Turroni, Stephanie L Schnorr, Matteo Soverini, Sara Quercia, Monica Barone, Andrea Castagnetti, Elena Biagi, Giorgio Gallinella, Patrizia Brigidi, Marco Candela
It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru)...
October 2, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28964254/fangorn-forest-f2-a-machine-learning-approach-to-classify-genes-and-genera-in-the-family-geminiviridae
#20
José Cleydson F Silva, Thales F M Carvalho, Elizabeth P B Fontes, Fabio R Cerqueira
BACKGROUND: Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species...
September 30, 2017: BMC Bioinformatics
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