{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:10:44Z","timestamp":1785888644536,"version":"3.56.0"},"reference-count":111,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T00:00:00Z","timestamp":1651017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T00:00:00Z","timestamp":1651017600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001054","name":"Meat and Livestock Australia","doi-asserted-by":"publisher","award":["P.PSH.0799"],"award-info":[{"award-number":["P.PSH.0799"]}],"id":[{"id":"10.13039\/501100001054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2022,4,27]]},"abstract":"<jats:p>In addition to the host tissue collected during the sampling process, bovine vaginal samples are saturated with large amounts of extracellular DNA and secreted proteins that are essential for physiological purposes, including the reproductive cycle and immune defense. Due to the high host-to-microbe genome ratio, which hampers the sequencing efficacy for metagenome samples and the recovery of the actual metagenomic profiles, bovine vaginal samples cannot benefit from the full potential of shotgun sequencing.<\/jats:p>","DOI":"10.1128\/spectrum.00412-21","type":"journal-article","created":{"date-parts":[[2022,4,11]],"date-time":"2022-04-11T13:01:14Z","timestamp":1649682074000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":11,"title":["Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2432-2509","authenticated-orcid":true,"given":"Chian Teng","family":"Ong","sequence":"first","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gry","family":"Boe-Hansen","sequence":"additional","affiliation":[{"name":"School of Veterinary Science, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth M.","family":"Ross","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick J.","family":"Blackall","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Conny","family":"Turni","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben J.","family":"Hayes","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ala E.","family":"Tabor","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia"},{"name":"School of Chemistry and Molecular Bioscience, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-015-0094-5"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-39576-6"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0965-1"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01069"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00484"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1097\/MOU.0000000000000396"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0427-1"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-74677-7"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy107"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3003605"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2017-12592"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.4137\/BBI.S15389"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.2527\/af.2016-0030"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.4238\/2015.June.12.4"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.theriogenology.2017.12.028"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1586\/eri.10.14"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13467-w"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01753-15"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.68.4.669-685.2004"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-06665-3"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3935"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2020.00371"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.4014\/jmb.2002.02010"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5797-8"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2010-3668"},{"key":"e_1_3_3_27_2","first-page":"383","volume-title":"Arthur's Veterinary Reproduction and Obstetrics","author":"Noakes DE","year":"2001","unstructured":"Noakes DE, Parkinson TJ, England GCW, Arthur GH. 2001. Chapter 22 - Infertility in the cow: structural and functional abnormalities, management deficiencies and non-specific infections, p 383\u2013472. In Noakes DE, Parkinson TJ, England GCW, Arthur GH (ed), Arthur's Veterinary Reproduction and Obstetrics (Eighth Edition). W.B. Saunders, Philadelphia, PA, USA."},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1530\/rep.0.1230837"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.2527\/1999.77suppl_2101x"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-69317-z"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.theriogenology.2016.02.016"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0234-1"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2016-12058"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2016-12061"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0532-4"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.2527\/jas1973.3761362x"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1111\/rda.13496"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0076096"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0426-3"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa021"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00019-17"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/s42523-021-00106-3"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.anaerobe.2009.04.009"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-12-164"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.3791\/52117"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03050-15"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.01.091"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01277"},{"key":"e_1_3_3_49_2","doi-asserted-by":"crossref","unstructured":"Ganda E Beck KL Haiminen N Kawas B Cronk B Anderson RR Goodman LB Wiedmann M. 2020. DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid. bioRxiv. https:\/\/www.doi.org\/10.1101\/2020.08.21.262337.","DOI":"10.1101\/2020.08.21.262337"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1085\/jgp.201411296"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2019.11.305"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9074-0_20"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/jas\/skz212"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1093\/jas\/skz210"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-13-19"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.3390\/ani9121007"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0143294"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01047"},{"key":"e_1_3_3_59_2","first-page":"25","article-title":"The smart solution for DNA removal in biopharmaceutical production by benzonase endonuclease","volume":"2","author":"Zhu Y","year":"2013","unstructured":"Zhu Y, Li M, Chen W, Peters A. 2013. The smart solution for DNA removal in biopharmaceutical production by benzonase endonuclease. J Appl Virol 2:25\u201333.","journal-title":"J Appl Virol"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1016\/0304-5102(91)80120-R"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a000414"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2007.00091.x"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2009.11.009"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2018.00255"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2020.105856"},{"key":"e_1_3_3_66_2","first-page":"1412","article-title":"The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data","volume":"8","author":"Wen Y","year":"2016","unstructured":"Wen Y, Xiao F, Wang C, Wang Z. 2016. The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data. Am J Transl Res 8:1412\u20131425.","journal-title":"Am J Transl Res"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1111\/jam.13239"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/jas\/skaa178"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200974"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tvjl.2014.08.023"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.5808\/GI.2018.16.4.e21"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3451"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0542-0"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12917-019-2009-3"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-23-2-122"},{"key":"e_1_3_3_76_2","doi-asserted-by":"publisher","DOI":"10.1017\/s0022172400046271"},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.S0022-0302(94)77277-5"},{"key":"e_1_3_3_78_2","doi-asserted-by":"publisher","DOI":"10.4315\/0362-028x-66.6.931"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2016.03.005"},{"key":"e_1_3_3_80_2","doi-asserted-by":"publisher","DOI":"10.3168\/jds.2015-9673"},{"key":"e_1_3_3_81_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.4.2765-2774.2006"},{"key":"e_1_3_3_82_2","unstructured":"Andrew S. 2010. FastQC: a quality control tool for high throughput sequence data. Available online at: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"e_1_3_3_83_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_3_84_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_3_85_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_3_86_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_3_3_87_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"e_1_3_3_88_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.104"},{"key":"e_1_3_3_89_2","unstructured":"RStudio Team. 2020. RStudio: Integrated development environment for R. RStudio PBC Boston MA. http:\/\/www.rstudio.com\/."},{"key":"e_1_3_3_90_2","unstructured":"Oksanen J Blanchet FG Friendly M Kindt R Legendre P McGlinn D Minchin PR O'Hara RB Simpson GL Solymos P Stevens HH Szoecs E Wagner H. 2020. vegan: community ecology package. R package version 2.5\u20137. https:\/\/CRAN.R-project.org\/package=vegan."},{"key":"e_1_3_3_91_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217"},{"key":"e_1_3_3_92_2","unstructured":"Hadley WR L Henry K.M\u00fcller 2020. dplyr: A grammar of data manipulation. https:\/\/CRAN.R-project.org\/package=dplyr."},{"key":"e_1_3_3_93_2","doi-asserted-by":"crossref","unstructured":"Wickham H. 2016. ggplot2: Elegant graphics for data analysis. Springer-Verlag New York USA. https:\/\/ggplot2.tidyverse.org.","DOI":"10.1007\/978-3-319-24277-4"},{"key":"e_1_3_3_94_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"e_1_3_3_95_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2016.02.020"},{"key":"e_1_3_3_96_2","unstructured":"Bushnell B. 2020. BBMap short-read aligner and other bioinformatics tools v38.84."},{"key":"e_1_3_3_97_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv697"},{"key":"e_1_3_3_98_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"e_1_3_3_99_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki025"},{"key":"e_1_3_3_100_2","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00999"},{"key":"e_1_3_3_101_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1344"},{"key":"e_1_3_3_102_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1234"},{"key":"e_1_3_3_103_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku702"},{"key":"e_1_3_3_104_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms13219"},{"key":"e_1_3_3_105_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature21059"},{"key":"e_1_3_3_106_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.45"},{"key":"e_1_3_3_107_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000465"},{"key":"e_1_3_3_108_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.27"},{"key":"e_1_3_3_109_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.59"},{"key":"e_1_3_3_110_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359"},{"key":"e_1_3_3_111_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2007.00434.x"},{"key":"e_1_3_3_112_2","first-page":"115","volume-title":"Nucleic acid techniques in bacterial systematics.","author":"Lane D","year":"1991","unstructured":"Lane D. 1991. 16S\/23S rRNA sequencing, p 115\u2013175. In Stackebrandt E, Goodfellow M. (ed), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, USA."}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00412-21","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00412-21","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T11:46:40Z","timestamp":1675252000000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00412-21"}},"subtitle":[],"editor":[{"given":"Kang","family":"Ning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,4,27]]},"references-count":111,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,4,27]]}},"alternative-id":["10.1128\/spectrum.00412-21"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00412-21","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,27]]},"assertion":[{"value":"2021-05-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-03-21","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-04-11","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00412-21"}}