{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T06:00:41Z","timestamp":1772517641716,"version":"3.50.1"},"reference-count":61,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T00:00:00Z","timestamp":1772496000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Vet. Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>RNA viruses, a unique class of life forms, are widely distributed in nature and pose potential health risks. Monitoring the gut RNA virome in livestock is a crucial component of global health surveillance. As important companion animals, horses play a vital role in transportation and make significant contributions to various cultural and economic activities. Nevertheless, the characteristics of horse gut RNA viruses remain largely uncharted.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this study, we used metatranscriptome sequencing and bioinformatics methods to characterize viruses within the gut contents of 16 horses spanning three breeds (Thoroughbred, Akhal-Teke and Yili horse).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 497 viral genomes from 22 viral families were recovered, including both double-stranded RNA (dsRNA) and single-stranded RNA (ssRNA) viruses, and encompassed positive- and negative-sense types commonly found in mammalian hosts. Among these, Picobirnaviridae was the most abundant RNA viral family in the horse gut. Beta diversity analyses revealed variations in RNA viral abundance across the three breeds, and differential analysis identified 82 RNA viruses exhibiting significant differences (\n                      <jats:italic>p<\/jats:italic>\n                      &amp;lt; 0.05) between Akhal-Teke and Yili horses. Comparisons of coverage scores with other mammals revealed shared viral networks among intestinal RNA viruses of horses, humans, cows, and sheep.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>This study provides valuable data for future research on the horse gut RNA virome, shedding new light on the cryptic viral sharing network within the horse gut.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fvets.2026.1755551","type":"journal-article","created":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T05:23:05Z","timestamp":1772515385000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Metatranscriptomics reveals the horse gut RNA virome and a viral sharing network with human and domestic animals"],"prefix":"10.3389","volume":"13","author":[{"given":"Can","family":"Li","sequence":"first","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaiping","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ni","family":"Wei","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengwei","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyue","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cunyuan","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shihezi University","place":["Shihezi, Xinjiang, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,3,3]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"327","DOI":"10.2174\/1389202916666150707160613","article-title":"RNA viruses: RNA roles in pathogenesis, coreplication and viral load","volume":"16","author":"Poltronieri","year":"2015","journal-title":"Curr Genomics"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1038\/s41564-022-01180-2","article-title":"RNA Viromes from terrestrial sites across China expand environmental viral diversity","volume":"7","author":"Chen","year":"2022","journal-title":"Nat Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1002\/9781394179466.ch23","volume-title":"Disease of Swine","author":"Zhang","year":"2025"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1146\/annurev-virology-101416-041718","article-title":"Mechanisms and concepts in RNA virus population dynamics and evolution","volume":"5","author":"Dolan","year":"2018","journal-title":"Annu Rev Virol"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nrmicro2692","article-title":"The dependence of viral RNA replication on co-opted host factors","volume":"10","author":"Nagy","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"a006882","DOI":"10.1101\/cshperspect.a006882","article-title":"HIV-1 reverse transcription","volume":"2","author":"Hu","year":"2012","journal-title":"Cold Spring Harb Perspect Med"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"103985","DOI":"10.1016\/j.amsu.2022.103985","article-title":"Comparative overview of emerging RNA viruses: epidemiology, pathogenesis, diagnosis and current treatment","volume":"79","author":"Chakrabartty","year":"2022","journal-title":"Ann Med Surg"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/nature20167","article-title":"Redefining the invertebrate RNA virosphere","volume":"540","author":"Shi","year":"2016","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1146\/annurev-virology-092818-015851","article-title":"Expanding the RNA virosphere by unbiased metagenomics","volume":"6","author":"Zhang","year":"2019","journal-title":"Annu Rev Virol"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/s40168-024-01967-x","article-title":"A comprehensive RNA virome identified in the oyster Magallana gigas reveals the intricate network of virus sharing between seawater and mollusks","volume":"12","author":"Wu","year":"2024","journal-title":"Microbiome"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s40168-024-01782-4","article-title":"Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation","volume":"12","author":"Wang","year":"2024","journal-title":"Microbiome"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"28","DOI":"10.3390\/vetsci7010028","article-title":"Horses as a crucial part of one health","volume":"7","author":"L\u00f6nker","year":"2020","journal-title":"Vet Sci"},{"key":"ref14","volume-title":"Global horse population with respect to breeds and risk status","author":"Khadka","year":"2020"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.prot5439","article-title":"Purification of rna using trizol (tri reagent) cold spring Harb","volume":"2010","author":"Rio","year":"2010","journal-title":"PRO"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2199-7-3","article-title":"The RIN: an RNA integrity number for assigning integrity values to RNA measurements","volume":"7","author":"Schroeder","year":"2006","journal-title":"BMC Mol Biol"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1093\/clinchem\/46.11.1851","article-title":"Evaluation of DNA fragment sizing and quantification by the agilent 2100 bioanalyzer","volume":"46","author":"Panaro","year":"2000","journal-title":"Clin Chem"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1186\/s12864-018-5066-2","article-title":"A comparative analysis of library prep approaches for sequencing low input translatome samples","volume":"19","author":"Song","year":"2018","journal-title":"BMC Genomics"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"772","DOI":"10.3390\/v15030772","article-title":"Meta-transcriptomic analysis reveals novel RNA viruses in Hippocampus erectus","volume":"15","author":"Zhang","year":"2023","journal-title":"Viruses"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"4023","DOI":"10.1016\/j.cell.2022.08.023","article-title":"Expansion of the global RNA virome reveals diverse clades of bacteriophages","volume":"185","author":"Neri","year":"2022","journal-title":"Cell"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"120611","DOI":"10.1016\/j.watres.2023.120611","article-title":"Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant","volume":"245","author":"Chen","year":"2023","journal-title":"Water Res"},{"key":"ref25","author":"Seemann","year":"2025"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/s41586-021-04332-2","article-title":"Petabasescale sequence alignment catalyses viral discovery","volume":"602","author":"Edgar","year":"2022","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1126\/science.abm5847","article-title":"Cryptic and abundant marine viruses at the evolutionary origins of earth\u2019s RNA virome","volume":"376","author":"Zayed","year":"2022","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e02329-18","DOI":"10.1128\/mBio.02329-18","article-title":"Origins and evolution of the global RNA virome","volume":"9","author":"Wolf","year":"2018","journal-title":"MBio"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"2226","DOI":"10.1038\/s41467-025-57500-7","article-title":"VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data","volume":"16","author":"Zheng","year":"2025","journal-title":"Nat Commun"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"6968","DOI":"10.1038\/s41467-022-34630-w","article-title":"Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny","volume":"13","author":"Edgar","year":"2025","journal-title":"Nat Commun"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/978-1-59745-251-9_6","volume-title":"Bioinformatics for DNA sequence analysis","author":"Guindon","year":"2009"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"W587","DOI":"10.1093\/nar\/gkad359","article-title":"Tree visualization by one table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1080\/01621459.1952.10483441","article-title":"Use of ranks in one-criterion variance analysis","volume":"47","author":"Kruskal","year":"1952","journal-title":"J Am Stat Assoc"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"796025","DOI":"10.3389\/fmicb.2021.796025","article-title":"The power of microbiome studies: some considerations on which alpha and beta metrics to use and how to report results","volume":"12","author":"Kers","year":"2022","journal-title":"Front Microbiol"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern Wisconsin","volume":"27","author":"Bray","year":"1957","journal-title":"Ecol Monogr"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1093\/biomet\/53.3-4.325","article-title":"Some distance properties of latent root and vector methods used in multivariate analysis","volume":"53","author":"Gower","year":"1966","journal-title":"Biometrika"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"152477","DOI":"10.1016\/j.scitotenv.2021.152477","article-title":"PhoH-carrying virus communities responded to multiple factors and their correlation network with prokaryotes in sediments along Bohai Sea, Yellow Sea, and East China Sea in China","volume":"812","author":"Wang","year":"2022","journal-title":"Sci Total Environ"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"213","DOI":"10.2307\/1218190","article-title":"Evolution and measurement of species diversity","volume":"21","author":"Whittaker","year":"1972","journal-title":"Taxon"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.jembe.2005.12.017","article-title":"On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages","volume":"330","author":"Clarke","year":"2006","journal-title":"J Exp Mar Biol Ecol"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinform"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"btaf147","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"Coverm: read alignment statistics for metagenomics","volume":"41","author":"Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"veab022","DOI":"10.1093\/ve\/veab022","article-title":"Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis","volume":"7","author":"Yan","year":"2021","journal-title":"Virus Evol"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s40168-022-01228-9","article-title":"Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle","volume":"10","author":"Xue","year":"2022","journal-title":"Microbiome"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13068-019-1498-4","article-title":"Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases","volume":"12","author":"He","year":"2019","journal-title":"Biotechnol Biofuels"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"veae033","DOI":"10.1093\/ve\/veae033","article-title":"Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts","volume":"10","author":"Sadiq","year":"2024","journal-title":"Virus Evol"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"17022","DOI":"10.3390\/ijms242317022","article-title":"Viral diversity in samples of freshwater gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) revealed by total RNA-sequencing","volume":"24","author":"Butina","year":"2023","journal-title":"Int J Mol Sci"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.cell.2015.01.002","article-title":"Disease-specific alterations in the enteric virome in inflammatory bowel disease","volume":"160","author":"Norman","year":"2015","journal-title":"Cell"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1128\/JVI.02966-14","article-title":"Expanding the role of the virome: commensalism in the gut","volume":"89","author":"Cadwell","year":"2015","journal-title":"J Virol"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1007\/s13337-014-0207-y","article-title":"Animal picobirnavirus","volume":"25","author":"Ganesh","year":"2014","journal-title":"Virus"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/s41586-018-0012-7","article-title":"The evolutionary history of vertebrate RNA viruses","volume":"556","author":"Shi","year":"2018","journal-title":"Nature"},{"key":"ref59","volume-title":"Reference module in biomedical sciences","author":"Cho","year":"2014"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1849","DOI":"10.1099\/0022-1317-64-9-1849","article-title":"Purification and partial characterization of a new enveloped RNA virus (Berne virus)","author":"Weiss","year":"1983","journal-title":"J Gen Virol"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s40168-017-0308-0","article-title":"Virome comparisons in wild-diseased and healthy captive giant pandas","volume":"5","author":"Zhang","year":"2017","journal-title":"Microbiome"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2026.1755551\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T05:23:08Z","timestamp":1772515388000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2026.1755551\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,3]]},"references-count":61,"alternative-id":["10.3389\/fvets.2026.1755551"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2026.1755551","relation":{},"ISSN":["2297-1769"],"issn-type":[{"value":"2297-1769","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,3]]},"article-number":"1755551"}}