{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T10:51:57Z","timestamp":1778755917108,"version":"3.51.4"},"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2016,3,16]],"date-time":"2016-03-16T00:00:00Z","timestamp":1458086400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0151481","type":"journal-article","created":{"date-parts":[[2016,3,16]],"date-time":"2016-03-16T20:14:46Z","timestamp":1458159286000},"page":"e0151481","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets"],"prefix":"10.1371","volume":"11","author":[{"given":"Oskar E.","family":"Karlsson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jenny","family":"Larsson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliette","family":"Hayer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikael","family":"Berg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Magdalena","family":"Jacobson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,3,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/BF03548067","article-title":"Epidemiological studies of piglet diarrhoea in intensively managed Danish sow herds. I. Pre-weaning diarrhoea","volume":"30","author":"B Svensmark","year":"1989","journal-title":"Acta Vet Scand"},{"key":"ref2","first-page":"199","article-title":"Diseases of Swine","author":"J Zimmerman","year":"2012"},{"key":"ref3","unstructured":"Sj\u00f6lund M, Zoric, M., Wallgren P. Financial impact of disease on pig production. Part III. Gastrointestinal disorders. Proceedings of the 6th European Symposium of Porcine Health Management. Sorrento, Italy; 2014. p. 111."},{"key":"ref4","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1128\/JCM.28.2.201-206.1990","article-title":"Cytopathic astrovirus isolated from porcine acute gastroenteritis in an established cell line derived from porcine embryonic kidney","volume":"28","author":"M Shimizu","year":"1990","journal-title":"J Clin Microbiol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1177\/1040638712458781","article-title":"Detection and molecular characterization of Porcine astrovirus strains associated with swine diarrhea","volume":"24","author":"SK Mor","year":"2012","journal-title":"J Vet Diagnostic Investig"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1286","DOI":"10.1128\/JVI.06589-11","article-title":"Complete Genome Sequence of a Novel Species of Porcine Bocavirus, PBoV5","volume":"86","author":"B Li","year":"2012","journal-title":"J Virol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1007\/s00705-010-0774-1","article-title":"Molecular detection of porcine kobuviruses in pigs in Korea and their association with diarrhea","volume":"155","author":"SJ Park","year":"2010","journal-title":"Arch Virol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.3201\/eid1512.090724","article-title":"Porcine Kobuvirus in Piglets, Thailand","volume":"15","author":"P Khamrin","year":"2009","journal-title":"Emerg Infect Dis"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"8239","DOI":"10.1128\/JVI.01020-08","article-title":"The first Chinese porcine sapovirus strain that contributed to an outbreak of gastroenteritis in piglets","volume":"82","author":"W Zhang","year":"2008","journal-title":"J Virol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1007\/s00705-011-1035-7","article-title":"Isolation and characterization of the first Chinese porcine sapelovirus strain","volume":"156","author":"D Lan","year":"2011","journal-title":"Arch Virol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/1746-6148-9-206","article-title":"Microbiological, pathological and histological findings in four Danish pig herds affected by a new neonatal diarrhoea syndrome","volume":"9","author":"H Kongsted","year":"2013","journal-title":"BMC Vet Res"},{"key":"ref12","unstructured":"Gin T, Le Guennec, J., Morvan, H., Martineau G-P. Clinical and laboratory investigations in 10 French pig herds dealing with enzootic neonatal diarrhoeatle. Procedings of the 21st international pig veterinary society (IPVS) congress. Vancouver, Canada; 2010. p. 758. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/orbit.dtu.dk\/fedora\/objects\/orbit:63423\/datastreams\/file_5574380\/content\" xlink:type=\"simple\">http:\/\/orbit.dtu.dk\/fedora\/objects\/orbit:63423\/datastreams\/file_5574380\/content<\/ext-link>"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1099\/jmm.0.000108","article-title":"Pathological and bacteriological characterization of neonatal porcine diarrhoea of uncertain aetiology","volume":"64","author":"J Larsson","year":"2015","journal-title":"J Med Microbiol. Microbiology Society"},{"key":"ref14","unstructured":"P. Wallgren, S.Mattsson MM. New neonatal porcine diarrhoea: aspects on etiology. Procedings of the 22nd international pig veterinary society (IPVS) congress. Jeju, Korea; 2012. p. 76. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.sva.se\/globalassets\/redesign2011\/pdf\/djurhalsa\/gris\/kongressrapporter\/6_ipvs2012_jeju_sydkorea.pdf\" xlink:type=\"simple\">http:\/\/www.sva.se\/globalassets\/redesign2011\/pdf\/djurhalsa\/gris\/kongressrapporter\/6_ipvs2012_jeju_sydkorea.pdf<\/ext-link>"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.vetmic.2013.01.022","article-title":"New viruses in veterinary medicine, detected by metagenomic approaches","volume":"165","author":"S Bel\u00e1k","year":"2013","journal-title":"Vet Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1002\/rmv.532","article-title":"Viral metagenomics","author":"EL Delwart","year":"2007","journal-title":"Reviews in Medical Virology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/455481a","article-title":"Metagenomics","volume":"455","author":"P Hugenholtz","year":"2008","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001377","article-title":"The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome","volume":"10","author":"D Gevers","year":"2012","journal-title":"PLoS Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.cell.2014.02.032","article-title":"The virome in mammalian physiology and disease","author":"HW Virgin","year":"2014","journal-title":"Cell"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/nm.3950","article-title":"Early life dynamics of the human gut virome and bacterial microbiome in infants","volume":"21","author":"ES Lim","year":"2015","journal-title":"Nat Med"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1099\/vir.0.063743-0","article-title":"Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China","volume":"95","author":"B Zhang","year":"2014","journal-title":"J Gen Virol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"11697","DOI":"10.1128\/JVI.05217-11","article-title":"The fecal virome of pigs on a high-density farm","volume":"85","author":"T Shan","year":"2011","journal-title":"J Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1177\/1040638712463212","article-title":"Diversity of viruses detected by deep sequencing in pigs from a common background","author":"KM Lager","year":"2012","journal-title":"Journal of Veterinary Diagnostic Investigation"},{"key":"ref24","article-title":"A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing","volume":"6","author":"GM Daly","year":"2011","journal-title":"PLoS One"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"4392","DOI":"10.1128\/JCM.01040-10","article-title":"Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics","volume":"48","author":"AL Blomstr\u00f6m","year":"2010","journal-title":"J Clin Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0076144","article-title":"The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing","volume":"8","author":"T Rosseel","year":"2013","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1007\/978-1-4939-2004-4_33","article-title":"Metagenomic approaches to disclose disease-associated pathogens: detection of viral pathogens in honeybees","volume":"1247","author":"F Granberg","year":"2015","journal-title":"Methods Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"R Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II. Error probabilities","volume":"8","author":"B Ewing","year":"1998","journal-title":"Genome Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nature11622","article-title":"Analyses of pig genomes provide insight into porcine demography and evolution","volume":"491","author":"MA Groenen","year":"2012","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","author":"B Langmead","year":"2012","journal-title":"Nature Methods"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"DE Wood","year":"2014","journal-title":"Genome Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"B Buchfink","year":"2014","journal-title":"Nat Methods"},{"key":"ref34","first-page":"1","article-title":"FragGeneScan: Predicting genes in short and error-prone reads","volume":"38","author":"M Rho","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e105067","DOI":"10.1371\/journal.pone.0105067","article-title":"Profile hidden Markov models for the detection of viruses within metagenomic sequence data","volume":"9","author":"P Skewes-Cox","year":"2014","journal-title":"PLoS One"},{"key":"ref36","article-title":"The NCBI handbook","author":"K Pruitt","year":"2002"},{"key":"ref37","first-page":"385","article-title":"Porcine group C rotavirus as a cause of neonatal diarrhea in a Quebec swine herd","volume":"54","author":"M Morin","year":"1990","journal-title":"Can J Vet Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1177\/104063879400600403","article-title":"Evaluation of rotavirus infection and diarrhea in Iowa commercial pigs based on an epidemiologic study of a population represented by diagnostic laboratory cases","volume":"6","author":"L a Will","year":"1994","journal-title":"J Vet Diagn Invest"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.jcpa.2014.04.003","article-title":"Neonatal Piglet Diarrhoea Associated with Enteroadherent Enterococcus hirae","volume":"151","author":"J Larsson","year":"2014","journal-title":"J Comp Pathol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e34631","DOI":"10.1371\/journal.pone.0034631","article-title":"Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing","volume":"7","author":"J Sachsenr\u00f6der","year":"2012","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"e88888","DOI":"10.1371\/journal.pone.0088888","article-title":"The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium","volume":"9","author":"J Sachsenr\u00f6der","year":"2014","journal-title":"PLoS One. Public Library of Science"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.biologicals.2014.10.004","article-title":"Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing","volume":"43","author":"M Dumarest","year":"2015","journal-title":"Biologicals"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1007\/s11262-013-0879-1","article-title":"Identification and molecular characterization of porcine kobuvirus in U. S. swine","volume":"46","author":"H Verma","year":"2013","journal-title":"Virus Genes"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1007\/s00705-015-2397-z","article-title":"Infection of farmed pigs with porcine kobuviruses in Italy","volume":"160","author":"I Di Bartolo","year":"2015","journal-title":"Arch Virol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1007\/s11262-010-0561-9","article-title":"Porcine kobuvirus from pig stool in Korea","volume":"42","author":"DJ An","year":"2011","journal-title":"Virus Genes"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1016\/j.meegid.2011.06.020","article-title":"First detection of kobuvirus in farm animals in Brazil and the Netherlands","volume":"11","author":"AF Barry","year":"2011","journal-title":"Infect Genet Evol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1007\/s00705-012-1391-y","article-title":"A field guide to eukaryotic circular single-stranded DNA viruses: Insights gained from metagenomics","volume":"157","author":"K Rosario","year":"2012","journal-title":"Arch Virol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.meegid.2015.01.001","article-title":"Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond","volume":"31","author":"S Kraberger","year":"2015","journal-title":"Infect Genet Evol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.virusres.2011.11.021","article-title":"Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes","volume":"164","author":"E Delwart","year":"2012","journal-title":"Virus Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2668","DOI":"10.1099\/vir.0.045948-0","article-title":"Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)","volume":"93","author":"K Rosario","year":"2012","journal-title":"J Gen Virol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.virol.2015.03.011","article-title":"Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage","volume":"482","author":"TG Phan","year":"2015","journal-title":"Virology"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1471-2334-14-22","article-title":"Unexplained diarrhoea in HIV-1 infected individuals","volume":"14","author":"BB Oude Munnink","year":"2014","journal-title":"BMC Infect Dis"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/s13337-012-0106-z","article-title":"Detection and Molecular Characterization of Porcine Picobirnavirus in Feces of Domestic Pigs from Kolkata, India","volume":"23","author":"B Ganesh","year":"2012","journal-title":"Indian J Virol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1016\/j.meegid.2010.06.004","article-title":"Picobirnavirus causes persistent infection in pigs","volume":"10","author":"LC Mart\u00ednez","year":"2010","journal-title":"Infect Genet Evol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nature13960","article-title":"An enteric virus can replace the beneficial function of commensal bacteria","volume":"516","author":"E Kernbauer","year":"2014","journal-title":"Nature"},{"issue":"Suppl 1","key":"ref56","doi-asserted-by":"crossref","first-page":"S227","DOI":"10.1089\/bsp.2013.0008","article-title":"The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses","volume":"11","author":"OE Karlsson","year":"2013","journal-title":"Biosecur Bioterror"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"3268","DOI":"10.1128\/JCM.00850-11","article-title":"Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples","volume":"49","author":"J Cheval","year":"2011","journal-title":"J Clin Microbiol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0151481","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,15]],"date-time":"2022-06-15T07:48:32Z","timestamp":1655279312000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0151481"}},"subtitle":[],"editor":[{"given":"Bas E.","family":"Dutilh","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,3,16]]},"references-count":57,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,3,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0151481","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,16]]}}}