{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:49:36Z","timestamp":1792788576638,"version":"4.5.0"},"reference-count":52,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Results Driven Agriculture Research","id":[{"id":"https:\/\/ror.org\/0537mjm80","id-type":"ROR","asserted-by":"crossref"}]},{"name":"NSERC Discovery grant"},{"name":"NSERC NFRF grant"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["anim microbiome"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Viruses play a key role in cattle respiratory tract (RT) health, yet, profiling the upper respiratory tract (URT) virome (DNA and RNA viruses) from deep nasopharyngeal swabs (DNS) remains challenging due to their low biomass, lack of well-defined enrichment approaches, and a high proportion of unclassified viral sequences. This study aimed to optimize DNS preservation, nucleic acid extraction, and bioinformatics pipelines to enhance URT virome characterization in beef calves.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Three DNS preservation methods were tested (RNAlater, brain heart infusion (BHI) medium\/glycerol at -80\u00a0\u00b0C, and BHI medium\/glycerol followed by RNAlater). Three nucleic acid extraction kits (QIAamp Fast DNA Stool Mini Kit, GeneJET Genomic DNA Purification Kit, and mirVana\u2122 miRNA Isolation Kit) were evaluated to compare total nucleic acid yields. Viral DNA and RNA were extracted separately using the NucleoSpin Virus Kit, which was optimized for viral nucleic acid recovery. The DNS samples that preserved in RNAlater and extracted using the NucleoSpin Virus kit generated highest viral DNA (1.35\u2009\u00b1\u20090.12\u00a0\u00b5g) and RNA (1.57\u2009\u00b1\u20090.09\u00a0\u00b5g) (mean\u2009\u00b1\u2009SEM) yields for metagenomics sequencing. Metagenomic sequencing and viral taxonomic assignment using Kraken2 and Kaiju, respectively showed that Kaiju allowed maximum exact matches for viral taxonomy assignment and provided high-resolution outputs for the profiling of cattle URT viromes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The use of an optimized nucleic acid extraction method and Kaiju-based classification enhanced viral nucleic acid recovery and taxonomic classification from low-biomass DNS samples. The findings highlighted the importance of effective storage conditions and extraction methods in maximizing viral nucleic acid yield, while demonstrating that Kaiju provided more reliable viral taxonomic assignments than Kraken2. These advancements provide a framework for more accurate assessment of the URT virome in cattle and other farm animals, enabling deeper investigation into the roles of viruses in RT health.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s42523-026-00567-4","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T19:40:34Z","timestamp":1791920434000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Optimized approaches to profile low biomass DNA and RNA virome in the upper respiratory tract of beef cattle"],"prefix":"10.1186","volume":"8","author":[{"given":"Yue","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mi","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilusha","family":"Malmuthuge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trevor W.","family":"Alexander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard","family":"Timsit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le Luo","family":"Guan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,13]]},"reference":[{"issue":"9","key":"567_CR1","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1016\/j.tim.2019.04.005","volume":"27","author":"M Zeineldin","year":"2019","unstructured":"Zeineldin M, Lowe J, Aldridge B. Contribution of the mucosal microbiota to bovine respiratory health. Trends Microbiol. 2019;27(9):753\u201370. https:\/\/doi.org\/10.1016\/j.tim.2019.04.005.","journal-title":"Trends Microbiol"},{"issue":"1","key":"567_CR2","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s40168-020-00869-y","volume":"8","author":"C McMullen","year":"2020","unstructured":"McMullen C, Alexander TW, L\u00e9guillette R, Workentine M, Timsit E. Topography of the respiratory tract bacterial microbiota in cattle. Microbiome. 2020;8(1):91. 10.1186\/ s40168-020-00869-y.","journal-title":"Microbiome"},{"issue":"5","key":"567_CR3","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","volume":"15","author":"WH Man","year":"2017","unstructured":"Man WH, de Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259\u201370. 10. 1038\/ nrmicro.2017.14.","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"567_CR4","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/bs.pmbts.2022.07.002","volume":"192","author":"L Narendrakumar","year":"2022","unstructured":"Narendrakumar L, Ray A. Respiratory tract microbiome and pneumonia. Prog Mol Biol Transl Sci. 2022;192(1):97\u2013124. https:\/\/doi.org\/10.1016\/bs.pmbts.2022.07.002.","journal-title":"Prog Mol Biol Transl Sci"},{"key":"567_CR5","doi-asserted-by":"publisher","unstructured":"Clinton NA, Hameed SA, Agyei EK, Jacob JC, Oyebanji VO, Jabea CE. Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res. 2022; 2022:7883945. https:\/\/doi.org\/10.1155\/2022\/ 7883945.","DOI":"10.1155\/2022\/"},{"issue":"2","key":"567_CR6","doi-asserted-by":"publisher","first-page":"455","DOI":"10.3390\/v15020455","volume":"15","author":"RK Ambrose","year":"2023","unstructured":"Ambrose RK, Blakebrough-Hall C, Gravel JL, Gonzalez LA, Mahony TJ. Characterisation of the upper respiratory tract virome of feedlot cattle and its association with bovine respiratory disease. Viruses. 2023;15(2):455. 10.339 0\/v150 20455.","journal-title":"Viruses"},{"issue":"1","key":"567_CR7","doi-asserted-by":"publisher","first-page":"8319","DOI":"10.1038\/s41598-023-34730-7","volume":"13","author":"S Megremis","year":"2023","unstructured":"Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep. 2023;13(1):8319. 10.103 8\/s41598-023-34730-7.","journal-title":"Sci Rep"},{"key":"567_CR8","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/s12866-015-0494-5","volume":"15","author":"YD Niu","year":"2015","unstructured":"Niu YD, Cook SR, Wang J, Klima CL, Hsu YH, Kropinski AM, Turner D, McAllister TA. Comparative analysis of multiple inducible phages from Mannheimia haemolytica. BMC Microbiol. 2015;15:175. https:\/\/doi.org\/10.1186\/s12866-015-0494-5.","journal-title":"BMC Microbiol"},{"key":"567_CR9","doi-asserted-by":"publisher","first-page":"622049","DOI":"10.3389\/fvets.2021.622049","volume":"8","author":"Z Luo","year":"2021","unstructured":"Luo Z, Geng S, Lu B, Han G, Wang Y, Luo Y, Yang Z, Cao S, Yao X, Isolation. Genomic Analysis, and Preliminary Application of a Bovine Klebsiella pneumoniae Bacteriophage vB_Kpn_B01. Front Vet Sci. 2021;8:622049. https:\/\/doi.org\/10.3389\/fvets.2021.622049.","journal-title":"Front Vet Sci"},{"issue":"1","key":"567_CR10","doi-asserted-by":"publisher","first-page":"9392","DOI":"10.1038\/s41598-021-88878-1","volume":"11","author":"D Johnston","year":"2021","unstructured":"Johnston D, Earley B, McCabe MS, Kim J, Taylor JF, Lemon K, Duffy C, McMenamy M, Cosby SL, Waters SM. Messenger RNA biomarkers of Bovine Respiratory Syncytial Virus infection in the whole blood of dairy calves. Sci Rep. 2021;11(1):9392. https:\/\/doi.org\/10.1038\/s41598-021-88878-1.","journal-title":"Sci Rep"},{"key":"567_CR11","doi-asserted-by":"crossref","unstructured":"Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond). 2022; 79:103985. doi: 10.1016\/ j. amsu.2022.103985","DOI":"10.1016\/j.amsu.2022.103985"},{"issue":"1","key":"567_CR12","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s13567-022-01086-1","volume":"53","author":"M Gaudino","year":"2022","unstructured":"Gaudino M, Nagamine B, Ducatez MF, Meyer G. Understanding the mechanisms of viral and bacterial coinfections in bovine respiratory disease: a comprehensive literature review of experimental evidence. Vet Res. 2022;53(1):70. https:\/\/doi.org\/10.1186\/s13567-022-01086-1.","journal-title":"Vet Res"},{"key":"567_CR13","doi-asserted-by":"publisher","first-page":"745076","DOI":"10.3389\/fmicb.2021.745076","volume":"12","author":"H Jurasz","year":"2021","unstructured":"Jurasz H, Paw\u0142owski T, Perlejewski K. Contamination issue in viral metagenomics: problems, solutions, and clinical perspectives. Front Microbiol. 2021;12:745076. https:\/\/doi.org\/10.3389\/fmicb.2021.745076.","journal-title":"Front Microbiol"},{"issue":"1","key":"567_CR14","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s42523-022-00197-6","volume":"4","author":"WB Crosby","year":"2022","unstructured":"Crosby WB, Pinnell LJ, Richeson JT, Wolfe C, Castle J, Loy JD, Gow SP, Seo KS, Capik SF, Woolums AR, Morley PS. Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle. Anim Microbiome. 2022;4(1):49. 10.1186 \/s42523-022-00197-6.","journal-title":"Anim Microbiome"},{"issue":"1","key":"567_CR15","doi-asserted-by":"publisher","first-page":"19","DOI":"10.3390\/vetsci5010019","volume":"5","author":"D Relova","year":"2018","unstructured":"Relova D, Rios L, Acevedo AM, Coronado L, Perera CL, P\u00e9rez LJ. Impact of RNA degradation on viral diagnosis: an understated but essential step for the successful establishment of a diagnosis network. Vet Sci. 2018;5(1):19. 10.3390\/ vetsci5010019.","journal-title":"Vet Sci"},{"key":"567_CR16","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.vetmic.2019.02.030","volume":"231","author":"C McMullen","year":"2019","unstructured":"McMullen C, Orsel K, Alexander TW, van der Meer F, Plastow G, Timsit E. Comparison of the nasopharyngeal bacterial microbiota of beef calves raised without the use of antimicrobials between healthy calves and those diagnosed with bovine respiratory disease. Vet Microbiol. 2019;231:56\u201362. https:\/\/doi.org\/10.1016\/j.vetmic.2019.02.030.","journal-title":"Vet Microbiol"},{"key":"567_CR17","unstructured":"Simon A. FastQC: a quality control tool for high throughput sequence data. 2010. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc"},{"issue":"4","key":"567_CR18","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357\u20139. https:\/\/doi.org\/10.1038\/nmeth.1923.","journal-title":"Nat Methods"},{"key":"567_CR19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033","author":"D Li","year":"2015","unstructured":"Li D, Liu CM, Luo R, Sadakane K, Lam TW. Bioinformatics. 2015;31(10):1674\u20136. https:\/\/doi.org\/10.1093\/bioinformatics\/btv033. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph."},{"issue":"4","key":"567_CR20","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1590\/S1517-838220100004000023","volume":"41","author":"DD Oskouei","year":"2010","unstructured":"Oskouei DD, Bekmen N, Ellidokuz H, Y\u0131lmaz O. Evaluation of different cryoprotective agents in maintenance of viability of Helicobacter pylori in stock culture media. Braz J Microbiol. 2010;41(4):1038\u201346. https:\/\/doi.org\/10.1590\/S1517-838220100004000023.","journal-title":"Braz J Microbiol"},{"key":"567_CR21","doi-asserted-by":"crossref","unstructured":"Bulavin IV, Brailko VA, Grebennikova OA, Mitrofanova IV, Zhdanova IV, Khokhlov YS. The quality of the DNA isolated from Lavandula angustifolia leaves. In I International Symposium on Botanical Gardens and Landscapes 1298. 2019; 563\u2013568.","DOI":"10.17660\/ActaHortic.2020.1298.77"},{"key":"567_CR22","unstructured":"American Type Culture Collection. Bacteriology culture guide. https:\/\/www.atcc.org\/resources\/culture-guides\/bacteriology-culture-guide"},{"issue":"1\u20132","key":"567_CR23","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.jviromet.2005.05.002","volume":"128","author":"C Uhlenhaut","year":"2005","unstructured":"Uhlenhaut C, Kracht M. Viral infectivity is maintained by an RNA protection buffer. J Virol Methods. 2005;128(1\u20132):189\u201391. https:\/\/doi.org\/10.1016\/j.jviromet.2005.05.002.","journal-title":"J Virol Methods"},{"issue":"3","key":"567_CR24","doi-asserted-by":"publisher","first-page":"e0187721","DOI":"10.1128\/Spectrum.01877-21","volume":"9","author":"A Mordant","year":"2021","unstructured":"Mordant A, Kleiner M. Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes. Microbiol Spectr. 2021;9(3):e0187721. https:\/\/doi.org\/10.1128\/Spectrum.01877-21.","journal-title":"Microbiol Spectr"},{"key":"567_CR25","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.mimet.2015.03.021","volume":"113","author":"VL Hale","year":"2015","unstructured":"Hale VL, Tan CL, Knight R, Amato KR. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods. 2015;113:16\u201326. 10.10 16\/j.mimet.2015.03.021.","journal-title":"J Microbiol Methods"},{"issue":"3","key":"567_CR26","doi-asserted-by":"publisher","first-page":"e00021","DOI":"10.1128\/mSystems.00021-16","volume":"1","author":"SJ Song","year":"2016","unstructured":"Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems. 2016;1(3):e00021\u201316. 10.1128\/mSystems. 000 21 \u2013 16.","journal-title":"mSystems"},{"key":"567_CR27","doi-asserted-by":"publisher","first-page":"e4827","DOI":"10.7717\/peerj.4827","volume":"6","author":"KR Horng","year":"2018","unstructured":"Horng KR, Ganz HH, Eisen JA, Marks SL. Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ. 2018;6:e4827. 10.77 17\/ peerj.4827.","journal-title":"PeerJ"},{"key":"567_CR28","doi-asserted-by":"crossref","unstructured":"Flint SJ, Racaniello VR, Rall GF, Skalka AM, Enquist LW. Principles of virology. 4th ed. Washington (DC): ASM Press; 2015; (2).","DOI":"10.1128\/9781555819521"},{"issue":"3","key":"567_CR29","doi-asserted-by":"publisher","first-page":"51","DOI":"10.3892\/br.2024.1739","volume":"20","author":"K Yamamoto","year":"2024","unstructured":"Yamamoto K, Chiba M. Examination and comparison of the RNA extraction methods using mouse serum. Biomed Rep. 2024;20(3):51. https:\/\/doi.org\/10.3892\/br.2024.1739.","journal-title":"Biomed Rep"},{"issue":"1","key":"567_CR30","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/s12866-020-01894-5","volume":"20","author":"MY Lim","year":"2020","unstructured":"Lim MY, Park YS, Kim JH, Nam YD. Evaluation of fecal DNA extraction protocols for human gut microbiome studies. BMC Microbiol. 2020;20(1):212. https:\/\/doi.org\/10.1186\/s12866-020-01894-5.","journal-title":"BMC Microbiol"},{"issue":"1","key":"567_CR31","doi-asserted-by":"publisher","first-page":"16321","DOI":"10.1038\/s41598-018-34294-x","volume":"8","author":"F Teng","year":"2018","unstructured":"Teng F, Darveekaran Nair SS, Zhu P, Li S, Huang S, Li X, Xu J, Yang F. Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling. Sci Rep. 2018;8(1):16321. https:\/\/doi.org\/10.1038\/s41598-018-34294-x.","journal-title":"Sci Rep"},{"key":"567_CR32","doi-asserted-by":"publisher","first-page":"114017","DOI":"10.1016\/j.ijheh.2022.114017","volume":"245","author":"M Ruskov\u00e1","year":"2022","unstructured":"Ruskov\u00e1 M, Bu\u010dkov\u00e1 M, Achs A, Pu\u0161k\u00e1rov\u00e1 A, Wu JH, Kuchta T, \u0160ubr Z, Pangallo D. Useful molecular tools for facing next pandemic events: Effective sample preparation and improved RT-PCR for highly sensitive detection of SARS-CoV-2 in wastewater environment. Int J Hyg Environ Health. 2022;245:114017. 10.1016\/j. ijheh.2022.114017.","journal-title":"Int J Hyg Environ Health"},{"key":"567_CR33","doi-asserted-by":"publisher","first-page":"122827","DOI":"10.1016\/j.watres.2024.122827","volume":"270","author":"E Cuevas-Ferrando","year":"2025","unstructured":"Cuevas-Ferrando E, S\u00e1nchez G, P\u00e9rez-Catalu\u00f1a A. Exploring plant virus diversity in wastewater and reclaimed water through metagenomic analysis. Water Res. 2025;270:122827. https:\/\/doi.org\/10.1016\/j.watres.2024.122827.","journal-title":"Water Res"},{"issue":"4","key":"567_CR34","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1590\/s0074-02762001000400022","volume":"96","author":"OC de Aulet","year":"2001","unstructured":"de Aulet OC, de Castillo MC, de Ruiz Holgado AP, de Nader OM. A comparative study of preservation and storage of Haemophilus influenzae. Mem Inst Oswaldo Cruz. 2001;96(4):583\u20136. https:\/\/doi.org\/10.1590\/s0074-02762001000400022.","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"567_CR35","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s13127-010-0012-4","volume":"10","author":"ZT Nagy","year":"2010","unstructured":"Nagy ZT. A hands-on overview of tissue preservation methods for molecular genetic analyses. Organisms Divers Evol. 2010;10:91\u2013105.","journal-title":"Organisms Divers Evol"},{"issue":"2","key":"567_CR36","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1016\/j.jneumeth.2013.08.010","volume":"219","author":"Q Cai","year":"2013","unstructured":"Cai Q, Wang B, Patel M, Yang SM, Hu BH. RNAlater facilitates microdissection of sensory cell-enriched samples from the mouse cochlea for transcriptional analyses. J Neurosci Methods. 2013;219(2):240\u201351. 10.1016\/j. jneu meth.2013.08.010.","journal-title":"J Neurosci Methods"},{"key":"567_CR37","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.petrol.2012.09.003","volume":"98","author":"K Takamura","year":"2012","unstructured":"Takamura K, Fischer H, Morrow NR. Physical properties of aqueous glycerol solutions. J Petrol Sci Eng. 2012;98:50\u201360. https:\/\/doi.org\/10.1016\/j.petrol.2012.09.003.","journal-title":"J Petrol Sci Eng"},{"issue":"7","key":"567_CR38","doi-asserted-by":"publisher","first-page":"1940","DOI":"10.3390\/ani11071940","volume":"11","author":"E Studer","year":"2021","unstructured":"Studer E, Sch\u00f6necker L, Meylan M, Stucki D, Dijkman R, Holwerda M, Glaus A, Becker J. Prevalence of BRD-related viral pathogens in the upper respiratory tract of Swiss veal calves. Anim (Basel). 2021;11(7):1940. 10.3390\/ ani11071940.","journal-title":"Anim (Basel)"},{"issue":"1","key":"567_CR39","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-023-015","volume":"11","author":"BP Brito","year":"2023","unstructured":"Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. Microbiome. 2023;11(1):158. https:\/\/doi.org\/10.1186\/s40168-023-015. 91 \u2013 1.","journal-title":"Microbiome"},{"key":"567_CR40","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/978-1-4939-2990-0_2","volume":"1347","author":"J Sabina","year":"2015","unstructured":"Sabina J, Leamon JH. Bias in Whole genome amplification: causes and considerations. Methods Mol Biol. 2015;1347:15\u201341. https:\/\/doi.org\/10.1007\/978-1-4939-2990-0_2.","journal-title":"Methods Mol Biol"},{"issue":"21","key":"567_CR41","doi-asserted-by":"publisher","first-page":"7663","DOI":"10.1128\/AEM.00289-11","volume":"77","author":"KH Kim","year":"2011","unstructured":"Kim KH, Bae JW. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol. 2011;77(21):7663\u20138. https:\/\/doi.org\/10.1128\/AEM.00289-11.","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"567_CR42","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20(1):257. https:\/\/doi.org\/10.1186\/s13059-019-1891-0.","journal-title":"Genome Biol"},{"issue":"12","key":"567_CR43","doi-asserted-by":"publisher","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","volume":"17","author":"J Lu","year":"2022","unstructured":"Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Metagenome analysis using the Kraken software suite. Nat Protoc. 2022;17(12):2815\u201339. https:\/\/doi.org\/10.1038\/s41596-022-00738-y.","journal-title":"Nat Protoc"},{"key":"567_CR44","doi-asserted-by":"publisher","first-page":"11257","DOI":"10.1038\/ncomms11257","volume":"7","author":"P Menzel","year":"2016","unstructured":"Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:11257. https:\/\/doi.org\/10.1038\/ncomms11257.","journal-title":"Nat Commun"},{"issue":"16","key":"567_CR45","doi-asserted-by":"publisher","first-page":"e93","DOI":"10.1093\/nar\/gkaa568","volume":"48","author":"A Tovo","year":"2020","unstructured":"Tovo A, Menzel P, Krogh A, Cosentino Lagomarsino M, Suweis S. Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju. Nucleic Acids Res. 2020;48(16):e93. https:\/\/doi.org\/10.1093\/nar\/gkaa568.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"567_CR46","doi-asserted-by":"publisher","first-page":"340","DOI":"10.3390\/pathogens11030340","volume":"11","author":"EC Carbo","year":"2022","unstructured":"Carbo EC, Sidorov IA, van Rijn-Klink AL, Pappas N, van Boheemen S, Mei H, Hiemstra PS, Eagan TM, Claas ECJ, Kroes ACM, de Vries JJC. Performance of five metagenomic classifiers for virus pathogen detection using respiratory samples from a clinical cohort. Pathogens. 2022;11(3):340. 10.3390\/ pathogens11030340.","journal-title":"Pathogens"},{"issue":"10","key":"567_CR47","doi-asserted-by":"publisher","first-page":"5340","DOI":"10.1128\/JVI.00064-15","volume":"89","author":"TF Ng","year":"2015","unstructured":"Ng TF, Kondov NO, Deng X, Van Eenennaam A, Neibergs HL, Delwart E. A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol. 2015;89(10):5340\u20139. https:\/\/doi.org\/10.1128\/JVI.00064-15.","journal-title":"J Virol"},{"issue":"5","key":"567_CR48","doi-asserted-by":"publisher","first-page":"e0267036","DOI":"10.1371\/journal.pone.0267036","volume":"17","author":"A Nagy","year":"2022","unstructured":"Nagy A, Abdallah F, El Damaty HM, Tariq A, Merwad AMA, Alhatlani BY, Elsohaby I. Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations. PLoS ONE. 2022;17(5):e0267036. https:\/\/doi.org\/10.1371\/journal.pone.0267036.","journal-title":"PLoS ONE"},{"issue":"4","key":"567_CR49","doi-asserted-by":"publisher","first-page":"2209","DOI":"10.1111\/tbed.13873","volume":"68","author":"M Zhang","year":"2021","unstructured":"Zhang M, Hill JE, Alexander TW, Huang Y. The nasal viromes of cattle on arrival at western Canadian feedlots and their relationship to development of bovine respiratory disease. Transbound Emerg Dis. 2021;68(4):2209\u201318. https:\/\/doi.org\/10.1111\/tbed.13873.","journal-title":"Transbound Emerg Dis"},{"issue":"4","key":"567_CR50","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1046\/j.1439-0450.2003.00658.x","volume":"50","author":"C G\u00e5nheim","year":"2003","unstructured":"G\u00e5nheim C, Hult\u00e9n C, Carlsson U, Kindahl H, Niskanen R, Waller KP. The acute phase response in calves experimentally infected with bovine viral diarrhoea virus and\/or Mannheimia haemolytica. J Vet Med B Infect Dis Vet Public Health. 2003;50(4):183\u201390. 10.1046\/ j.1439-0450.2003.00658. x.","journal-title":"J Vet Med B Infect Dis Vet Public Health"},{"key":"567_CR51","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.vetmic.2019.03.027","volume":"231","author":"X Zhang","year":"2019","unstructured":"Zhang X, Outlaw C, Olivier AK, Woolums A, Epperson W, Wan XF. Pathogenesis of co-infections of influenza D virus and Mannheimia haemolytica in cattle. Vet Microbiol. 2019;231:246\u201353. https:\/\/doi.org\/10.1016\/j.vetmic.2019.03.027.","journal-title":"Vet Microbiol"},{"issue":"3","key":"567_CR52","doi-asserted-by":"publisher","first-page":"e0169021","DOI":"10.1128\/spectrum.01690-21","volume":"9","author":"A Lion","year":"2021","unstructured":"Lion A, Secula A, Ran\u00e7on C, Boulesteix O, Pinard A, Deslis A, H\u00e4gglund S, Salem E, Cassard H, N\u00e4slund K, Gaudino M, Moreno A, Brocchi E, Delverdier M, Zohari S, Baranowski E, Valarcher JF, Ducatez MF, Meyer G. Enhanced pathogenesis caused by Influenza D virus and mycoplasma bovis coinfection in calves: a disease severity linked with overexpression of IFN-\u03b3 as a key player of the enhanced innate immune response in lungs. Microbiol Spectr. 2021;9(3):e0169021. https:\/\/doi.org\/10.1128\/spectrum.01690-21.","journal-title":"Microbiol Spectr"}],"container-title":["Animal Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s42523-026-00567-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s42523-026-00567-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s42523-026-00567-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T23:17:54Z","timestamp":1791933474000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s42523-026-00567-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,13]]},"references-count":52,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["567"],"URL":"https:\/\/doi.org\/10.1186\/s42523-026-00567-4","relation":{"references":[{"id-type":"doi","id":"10.1093\/bioinformatics\/btv033","asserted-by":"subject"}]},"ISSN":["2524-4671"],"issn-type":[{"value":"2524-4671","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,13]]},"assertion":[{"value":"22 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The experiment received approval by the animal ethics committee at University of Calgary. (Project number: AC18-0145).","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"101"}}