{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T03:42:49Z","timestamp":1790826169058,"version":"4.1.0"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T00:00:00Z","timestamp":1585872000000},"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.0219882","type":"journal-article","created":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T13:25:17Z","timestamp":1585920317000},"page":"e0219882","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":39,"title":["A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7502-0036","authenticated-orcid":true,"given":"Melanie K.","family":"Hess","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne J.","family":"Rowe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracey C.","family":"Van Stijn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah M.","family":"Henry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon M.","family":"Hickey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rudiger","family":"Brauning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan F.","family":"McCulloch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew S.","family":"Hess","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle R.","family":"Kirk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7097-6848","authenticated-orcid":true,"given":"Sandeep","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cesar","family":"Pinares-Pati\u00f1o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Kittelmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham R.","family":"Wood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1022-3502","authenticated-orcid":true,"given":"Peter H.","family":"Janssen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4801-6207","authenticated-orcid":true,"given":"John C.","family":"McEwan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2020,4,3]]},"reference":[{"key":"pone.0219882.ref001","volume-title":"The Microbiome in Rheumatic Disease and Infection","author":"W Young","year":"2018"},{"issue":"10115","key":"pone.0219882.ref002","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/S0140-6736(17)31796-8","article-title":"Coeliac disease","volume":"391","author":"B Lebwohl","year":"2018","journal-title":"The Lancet"},{"issue":"7","key":"pone.0219882.ref003","doi-asserted-by":"crossref","first-page":"e103171","DOI":"10.1371\/journal.pone.0103171","article-title":"Two different bacterial community types are linked with the low-methane emission trait in sheep","volume":"9","author":"S Kittelmann","year":"2014","journal-title":"PLOS ONE"},{"issue":"10","key":"pone.0219882.ref004","doi-asserted-by":"crossref","first-page":"e1007580","DOI":"10.1371\/journal.pgen.1007580","article-title":"Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows","volume":"14","author":"GF Difford","year":"2018","journal-title":"PLOS Genet"},{"issue":"12","key":"pone.0219882.ref005","doi-asserted-by":"crossref","first-page":"2958","DOI":"10.1038\/ismej.2016.62","article-title":"Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants","volume":"10","author":"SKB Shabat","year":"2016","journal-title":"ISME J"},{"issue":"4","key":"pone.0219882.ref006","doi-asserted-by":"crossref","first-page":"e00703","DOI":"10.1128\/mBio.00703-17","article-title":"Heritable bovine rumen bacteria are phylogenetically related and correlated with the cow\u2019s capacity to harvest energy from its feed","volume":"8","author":"G Sasson","year":"2017","journal-title":"MBio"},{"issue":"9","key":"pone.0219882.ref007","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1101\/gr.168245.113","article-title":"Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome","volume":"24","author":"W Shi","year":"2014","journal-title":"Genome Res"},{"issue":"1","key":"pone.0219882.ref008","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/s40168-016-0201-2","article-title":"Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation","volume":"4","author":"J Kamke","year":"2016","journal-title":"Microbiome"},{"key":"pone.0219882.ref009","article-title":"BRIEF COMMUNICATION: Genetic control of the rumen microbiome in sheep","author":"SJ Rowe","year":"2015","journal-title":"Proceedings of the New Zealand Society of Animal Production"},{"issue":"7","key":"pone.0219882.ref010","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"TZ DeSantis","year":"2006","journal-title":"Appl. Environ. Microbiol"},{"key":"pone.0219882.ref011","doi-asserted-by":"crossref","first-page":"e6496","DOI":"10.7717\/peerj.6496","article-title":"Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework","volume":"7","author":"G Henderson","year":"2019","journal-title":"PeerJ"},{"issue":"1","key":"pone.0219882.ref012","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s40168-015-0105-6","article-title":"Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering","volume":"3","author":"O Franz\u00e9n","year":"2015","journal-title":"Microbiome"},{"issue":"3","key":"pone.0219882.ref013","doi-asserted-by":"crossref","first-page":"e32543","DOI":"10.1371\/journal.pone.0032543","article-title":"Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing","volume":"7","author":"K Sim","year":"2012","journal-title":"PLOS ONE"},{"issue":"4","key":"pone.0219882.ref014","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nbt.4110","article-title":"Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection","volume":"36","author":"R Seshadri","year":"2018","journal-title":"Nat. Biotechnol"},{"issue":"7","key":"pone.0219882.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0041294","article-title":"The \u201cmost wanted\u201d taxa from the human microbiome for whole genome sequencing","volume":"7","author":"AA Fodor","year":"2012","journal-title":"PLOS ONE"},{"issue":"5","key":"pone.0219882.ref016","doi-asserted-by":"crossref","first-page":"e19379","DOI":"10.1371\/journal.pone.0019379","article-title":"A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species","volume":"6","author":"RJ Elshire","year":"2011","journal-title":"PLOS ONE"},{"issue":"17","key":"pone.0219882.ref017","doi-asserted-by":"crossref","first-page":"8736","DOI":"10.1002\/ece3.4411","article-title":"Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species","volume":"8","author":"N Dussex","year":"2018","journal-title":"Ecol Evol"},{"issue":"s2","key":"pone.0219882.ref018","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1017\/S1751731113000864","article-title":"Heritability estimates of methane emissions from sheep","volume":"7","author":"C Pinares-Pati\u00f1o","year":"2013","journal-title":"Animal"},{"issue":"5","key":"pone.0219882.ref019","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nat Methods"},{"key":"pone.0219882.ref020","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"S Andrews","year":"2010"},{"issue":"5","key":"pone.0219882.ref021","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nmeth.1990","article-title":"Fast, accurate error-correction of amplicon pyrosequences using Acacia","volume":"9","author":"L Bragg","year":"2012","journal-title":"Nat Methods"},{"key":"pone.0219882.ref022","volume-title":"High-throughput rumen microbial profiling using genotyping-by-sequencing","author":"MK Hess","year":"2018"},{"issue":"1","key":"pone.0219882.ref023","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12859-015-0514-3","article-title":"GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments","volume":"16","author":"K Herten","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"pone.0219882.ref024","author":"F Krueger","year":"2015","journal-title":"Trim Galore: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files"},{"key":"pone.0219882.ref025","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"H Li","year":"2013","journal-title":"arXiv preprint arXiv:13033997"},{"issue":"1","key":"pone.0219882.ref026","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pone.0219882.ref027","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"DH Huson","year":"2007","journal-title":"Genome Res"},{"issue":"D1","key":"pone.0219882.ref028","doi-asserted-by":"crossref","first-page":"D94","DOI":"10.1093\/nar\/gky989","article-title":"GenBank","volume":"47","author":"EW Sayers","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pone.0219882.ref029","volume-title":"ASReml user guide release 4.1 structural specification","author":"A Gilmour","year":"2015"},{"issue":"9","key":"pone.0219882.ref030","doi-asserted-by":"crossref","first-page":"6030","DOI":"10.3168\/jds.2013-6766","article-title":"Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing","volume":"96","author":"E Ross","year":"2013","journal-title":"J Dairy Sci"},{"issue":"1","key":"pone.0219882.ref031","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/1471-2105-15-66","article-title":"Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest","volume":"15","author":"NJ Hudson","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"pone.0219882.ref032","unstructured":"Gailly J-l. gzip. 1.3.12 ed. http:\/\/www.gzip.org\/2007"},{"issue":"3","key":"pone.0219882.ref033","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1109\/TIT.1977.1055714","article-title":"A universal algorithm for sequential data compression","volume":"23","author":"J Ziv","year":"1977","journal-title":"IEEE Trans Inf Theory"},{"issue":"8","key":"pone.0219882.ref034","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/s12276-018-0071-8","article-title":"Single-cell RNA sequencing technologies and bioinformatics pipelines","volume":"50","author":"B Hwang","year":"2018","journal-title":"Exp Mol Med"},{"issue":"11","key":"pone.0219882.ref035","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"DH Parks","year":"2017","journal-title":"Nat Microbiol"},{"key":"pone.0219882.ref036","article-title":"Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank","author":"M Steinegger","year":"2020","journal-title":"bioRxiv"},{"issue":"suppl_1","key":"pone.0219882.ref037","doi-asserted-by":"crossref","first-page":"S101","DOI":"10.1093\/tas\/txy058","article-title":"Influence of maternal factors on the rumen microbiome and subsequent host performance","volume":"2","author":"HC Cunningham","year":"2018","journal-title":"Transl Anim Sci"},{"issue":"9","key":"pone.0219882.ref038","doi-asserted-by":"crossref","first-page":"e73056","DOI":"10.1371\/journal.pone.0073056","article-title":"Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle","volume":"8","author":"EM Ross","year":"2013","journal-title":"PLOS ONE"},{"issue":"5","key":"pone.0219882.ref039","doi-asserted-by":"crossref","first-page":"231","DOI":"10.3390\/genes9050231","article-title":"Low maternal microbiota sharing across gut, breast milk and vagina, as revealed by 16S rRNA gene and reduced metagenomic sequencing","volume":"9","author":"E Avershina","year":"2018","journal-title":"Genes"},{"key":"pone.0219882.ref040","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.mimet.2018.02.016","article-title":"Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota","volume":"149","author":"A Ravi","year":"2018","journal-title":"J Microbiol Methods"},{"key":"pone.0219882.ref041","doi-asserted-by":"crossref","first-page":"e3837","DOI":"10.7717\/peerj.3837","article-title":"Evaluation of ddRADseq for reduced representation metagenome sequencing","volume":"5","author":"MY Liu","year":"2017","journal-title":"PeerJ"},{"issue":"7402","key":"pone.0219882.ref042","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","author":"BA Meth\u00e9","year":"2012","journal-title":"Nature"},{"issue":"7285","key":"pone.0219882.ref043","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"J Qin","year":"2010","journal-title":"Nature"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0219882","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,3]],"date-time":"2020-04-03T13:25:35Z","timestamp":1585920335000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0219882"}},"subtitle":[],"editor":[{"given":"Juan J.","family":"Loor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,4,3]]},"references-count":43,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0219882","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/694133","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,3]]}}}