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62 results for “virome”
Graphic Illustration of Verity Mathis' Talk: Virome composition in fresh bat guano, frozen and fluid-preserved bat tissues
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded this invited talk by Verity Mathis at an NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Expansion of the global RNA virome reveals diverse clades of bacteriophages
<p>This deposit is intended to contain the various data generated as part of the RNA Virus in MetaTranscriptomes project ("RVMT"). This initial version is released ahead of time, near the time of submission, in hopes of providing a long lasting resource for the general scientific community. Note well - The authors listed in this initial version release are a partial list only. The RNA Virus in MetaTranscriptomes consortium is a project with over 90 researches from various institutions (see below).</p> <p>High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum <em>Lenarviricota</em>, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.</p> <p>The RNA Virus in metatranscriptomes consortium:<br> Adrienne B. Narrowe, Alexander J. Probst, Alexander Sczyrba, Annegret Kohler, Armand Séguin, Ashley Shade, Barbara J. Campbell, Björn D. Lindahl, Brandi Kiel Reese, Breanna M. Roque, Chris DeRito, Colin Averill, Daniel Cullen, David A. C. Beck, David A. Walsh, David M. Ward, Dongying Wu, Emiley Eloe-Fadrosh, Eoin L. Brodie, Erica B. Young, Erik A. Lilleskov, Federico J. Castillo, Francis M. Martin, Gary R. LeCleir, Graeme T. Attwood, Hinsby Cadillo-Quiroz, Holly M. Simon, Ian Hewson, Igor V. Grigoriev, James M. Tiedje, Janet K. Jansson, Janey Lee, Jean S. VanderGheynst, Jeff Dangl, Jeff S. Bowman, Jeffrey L. Blanchard, Jennifer L. Bowen, Jiangbing Xu, Jillian F. Banfield, Jody W Deming, Joel E. Kostka, John M. Gladden, Josephine Z Rapp, Joshua Sharpe, Katherine D. McMahon, Kathleen K. Treseder, Kay D. Bidle, Kelly C. Wrighton, Kimberlee Thamatrakoln, Klaus Nusslein, Laura K. Meredith, Lucia Ramirez, Marc Buee, Marcel Huntemann, Marina G. Kalyuzhnaya, Mark P Waldrop, Matthew B Sullivan, Matthew O. Schrenk, Matthias Hess, Michael A. Vega, Michelle A. O’Malley, Monica Medina, Naomi E. Gilbert, Nathalie Delherbe, Olivia U. Mason, Paul Dijkstra, Peter F. Chuckran, Petr Baldrian, Philippe Constant, Ramunas Stepanauskas, Rebecca A. Daly, Regina Lamendella, Robert J Gruninger, Robert M. McKay, Samuel Hylander, Sarah L. Lebeis, Sarah P Esser, Silvia G. Acinas, Steven S. Wilhelm, Steven W. Singer, Susannah S. Tringe, Tanja Woyke, TBK Reddy, Terrence H. Bell, Thomas Mock, Tim McAllister, Vera Thiel, Vincent J. Denef, Wen-Tso Liu, Willm Martens-Habbena, Xiao-Jun Allen Liu, Zachary S. Cooper, Zhong Wang. For the full list of authors and related information, please see the spreadsheet tittle "Table S9 - Consortium coauthorship" available in this collection in the folder named "Tables".</p>
Virome diversity of Hyalomma dromedarii ticks collected from camels in the United Arab Emirates
<p>Viruses are important components of the microbiome of ticks. Ticks are capable of transmitting several serious viral diseases to humans and animals. Hitherto, the composition of viral communities in <em>Hyalomma dromedarii</em> ticks associated with camels in the United Arab Emirates (UAE) remains unexplored. The purpose of this study was to characterize the RNA virome diversity in male and female <em>H. dromedarii</em> ticks collected from camels in Al Ain, UAE.<strong> </strong>We collected ticks, extracted and sequenced RNA, using Illumina (NovaSeq 6000) and Oxford Nanopore (MinION).<strong> </strong>From the total generated sequencing reads, 180,559 (~0.35 %) and 197,801 (~0.34 %) reads were identified as virus-related reads in male and female tick samples respectively. Taxonomic assignment of the viral sequencing reads was accomplished based on bioinformatic analyses. Further, viral reads were classified into 39 viral families. Poxiviridae, Phycodnaviridae, Phenuiviridae, Mimiviridae, and Polydnaviridae were the most abundant families in the tick viromes. Notably, we assembled the genomes of three RNA viruses, which were placed by phylogenetic analyses in clades that included the Bole tick virus.<strong> </strong>Overall, this study attempts to elucidate the RNA virome of ticks associated with camels in the UAE and the results obtained from this study improve the knowledge of the diversity of viruses in <em>H. dromedarii</em> ticks.</p>
Virome analysis of PRJNA361402 - reads
<p>Raw output files from virome analysis of [PRJNA361402](https://www.ncbi.nlm.nih.gov/sra?term=PRJNA361402) study using [virome-quant workflow](https://github.com/avilab/vs).</p> <p>## Files</p> <p>samples_norm.tsv -- ids and ftp links of analysed runs (see 'analyse' variable)</p> <p>treatments.csv -- treatments info</p> <p>Contents of tar archives:</p> <ol> <li><a href="/api/files/73acc472-0860-4091-b3d2-0007dfd212f1/prjna361402_phages.tar.gz?versionId=d50f3e0d-c044-4cd2-888f-c65c0f236597">prjna361402_phages.tar.gz</a> -- reads assigned to phages, csv files with blast results</li> <li><a href="/api/files/73acc472-0860-4091-b3d2-0007dfd212f1/prjna361402_phages-viruses.tar.gz?versionId=de66043e-da9c-4072-a11a-3291f859ecf1">prjna361402_phages-viruses.tar.gz</a> -- reads assigned to viruses, csv files with blast results</li> <li><a href="/api/files/73acc472-0860-4091-b3d2-0007dfd212f1/prjna361402_non-viral.tar.gz?versionId=ea1671ce-a916-4a0e-8e90-606c5af8e790">prjna361402_non-viral.tar.gz</a> -- reads assigned to other taxa, csv files with blast results</li> <li><a href="/api/files/73acc472-0860-4091-b3d2-0007dfd212f1/prjna361402_unassigned.tar.gz?versionId=b9196f22-ca96-4340-9b05-89d1dcbf8545">prjna361402_unassigned.tar.gz</a> -- fasta files with unassigned reads</li> <li><a href="/api/files/73acc472-0860-4091-b3d2-0007dfd212f1/prjna361402_stats.tar.gz?versionId=88c4b792-9dfc-47b0-b55f-b69936381c66">prjna361402_stats.tar.gz</a> -- intermediate file stats</li> </ol> <p> </p> <p> </p>
Extra tables and fastq files for "Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities."
<p>Tables:</p> <p>"mutation_analysis.xlsx" = detailed notes on variant analysis of H5N1 reads.</p> <p>"TEPHI_samples_H5N1_status1.xlsx" = Table of samples with metadata and H5N1 status</p> <p>"BioSampleObjects.txt" = Table from SRA mapping BioSample IDs to library (sample) IDs</p> <p> </p> <p>H5N1_reads_thru_p1858:</p> <p>Paired-end Illumina read files (.fastq) from all samples. Includes automated H5N1 called reads from iav_serotype tool from samples that were manually validated to have H5N1 specific reads.</p>
The rumen virome database (RVD)
<p>Given the potential role of phages in modulating microbial population, metabolism, and evolution, virome has been recognized as an indispensable yet underexplored component in microbiomes. Our understanding of the rumen virome, however, is derived from a few culture-dependent studies. To address this knowledge gap, we mined 975 published rumen metagenomes for viral sequences and created the first rumen virome database (RVD) representing 397,180 species-level viral operational taxonomic units (vOTUs). Most of the vOTUs were not classified to any existing taxa. The classified vOTUs represent viral lineages distinct from those found in the human gut microbiome. Functionally diverse auxiliary metabolic genes and antibiotic resistance genes were carried by some rumen viruses and they may affect the physiology of their hosts and the rumen fermentation process. The RVD database and the major findings of the rumen virome analyses can help and inform future studies on rumen virome. </p>
Sharing pollinators and pollen-associated viruses: understanding the diversity of the pollen virome within a co-flowering community
Open the record for dataset details and reuse information.
Data from: Protein Set Transformer: A protein-based genome language model to power high diversity viromics
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Sequence data from viral assembly graph analysis of the SERC virome
<p>Various sequence data and details that were used in publishing the manuscript describing assembly graph binning in the SERC viral metagenome. Including: assembled contigs, FASTG, predicted ORFs, two tables describing the assembled contigs and graphs.</p> <p>Also PolA and RNR sequences that were mined from the SERC assembly.</p>
Biodiversity of mudflat intertidal viromes along the Chinese coasts
<p>The study dataset contains 21,964 viral contigs (Intertidal_viruses.fa), 20,102 vOTUs (Intertidal_vOTUs.fa), 238,445 vPCs (Intertidal_vPCs.gene and Intertidal_vPCs.protein), and 2,259 mOTUs (Intertidal_mOTUs.zip) obtained from 96 intertidal sediment metagenomes spanning 12 coastal regions from southmost to northmost in China. In addition, DOM tables (DOM_scaled_int_tab.csv) used in this study can also be obtained here.</p> <p>If this study dataset is useful, please cite: Ji et al. Biodiversity of mudflat intertidal viromes along the Chinese coasts. <em>Nat Commun</em> <strong>15</strong>, 8611 (2024). https://doi.org/10.1038/s41467-024-52996-x</p> <p>For any other dataset/analysis inquiries, please contact me: jimengzhi@mail.sdu.edu.cn.</p> <p>The R code for this manuscript can be obtained from https://github.com/MengzhiJ.</p>
Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania Region of Italy.
<p>From December 2019, SARS-CoV-2 infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS-CoV-2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS-CoV-2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient’s cohort from the Campania region (Southern Italy).We found coinfections with viral species that belonged to <em>Coronaviridae, Retroviridae</em>, <em>Herpesviridae</em>, <em>Poxviridae</em>, <em>Pneumoviridae</em>, <em>Pandoraviridae,</em> and <em>Anelloviridae </em>families and only in 2% of cases (2/89) we identified respiratory viruses.</p>
Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla<span> </span><em>"Taraviricota"</em><span>, </span>a missing link in early RNA virus evolution, and<span> </span><em>"Arctiviricota"</em><span> </span>are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.</p> </div> </div> </div>
Seasonal dynamics of the wild rodent faecal virome
<p>Viral discovery studies in wild animals often rely on cross‐sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host–virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long‐term wild rodent study, we characterized viral communities of three common European rodent species (<em>Apodemus sylvaticus, A. flavicollis </em>and<em> Myodes glareolus</em>) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3‐month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.</p>
The Groundwater Virome Catalogue (GWVC)
<p>Viruses as the most abundant biological entities have drastic impacts on aquatic ecosystems, yet little was known about groundwater virome. To address this knowledge gap, we performed ultra-deep metagenomic sequencing on groundwater samples from 607 monitoring wells throughout China, and established the first <strong>Groundwater Virome Catalogue (GWVC)</strong>. The GWVC substantially expanded known aquifer virosphere, and the vast majority of the vOTUs represented previously unknown viral populations. The GWVC provided comprehensive available resources for future studies on viruses in subsurface environments.<br><em># Descriptions of files are provided in the file 'README.txt'.</em></p>
An integrated analysis of the Passifloraceae virome using public-domain data
<p>This dataset is the result of an An integrated analysis of the Passifloraceae virome using public-domain data. </p>
Cheese community and virome nucleoside mass spec from Arome
<p>These are files from LC-MS/MS analysis of nucleosides from cheese microbial communities and their viromes. For each run, we have uploaded the .mgf, .raw, and .ms1 files. We have also uploaded run descriptions, a first pass analysis from Arome, and the LC-MS/MS methods and exclusions lists. If you want to know more about the specific details of the cheeses that we sampled, please check out our pub "<a href="https://research.arcadiascience.com/pub/data-set-metagenomics-timecourse-cheese/release/1">Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points</a>". </p> <p>File list:</p> <p>Run data files: .raw, .mgf, .ms1 file types </p> <p>Run descriptions: arome_run_descriptions.csv</p> <p>First pass analysis from Arome: 20221209_Arcadia_Nucleo_HILIC_POS_quant_ALL_IDs.csv</p> <p>Exclusion lists: exclusionmasstable_1.csv, exclusionmasstable_2.csv</p> <p>Methods file: MethodSummary_POS1.txt</p>
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations
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Seasonal dynamics of the wild rodent faecal virome
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Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
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Data from: Demography, life history trade-offs, and the gastrointestinal virome of wild chimpanzees
<p>In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates—even in our closest living relatives, chimpanzees and bonobos (<i>Pan troglodytes</i> and <i>P. paniscus</i>)—are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (<i>P. t. schweinfurthii</i>), using metagenomics to characterize viromes (full viral communities) in the feces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities in Kibale National Park, Uganda. We identified 12 viruses from at least four families with genomes of both single-stranded RNA and single-stranded DNA. Although fecal viromes of both sexes varied with chimpanzee age, viral richness increased with age in males but not in females. This effect was largely due to three viruses, salivirus, porprismacovirus, and chimpanzee stool-associated RNA virus (chisavirus), which occurred more frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Fecal viromes may be useful for studying processes related to the divergent reproductive strategies of males and females, aging, and sex differences in longevity.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.