{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T01:54:43Z","timestamp":1772762083184,"version":"3.50.1"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2016,8,10]],"date-time":"2016-08-10T00:00:00Z","timestamp":1470787200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Copenhagen research centre for Control of antibiotic resistance (UC-Care)"},{"DOI":"10.13039\/100008393","name":"Teknologi og Produktion, Det Frie Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["060202775"],"award-info":[{"award-number":["060202775"]}],"id":[{"id":"10.13039\/100008393","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0160331","type":"journal-article","created":{"date-parts":[[2016,8,10]],"date-time":"2016-08-10T14:05:32Z","timestamp":1470837932000},"page":"e0160331","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Differential Analysis of the Nasal Microbiome of Pig Carriers or Non-Carriers of Staphylococcus aureus"],"prefix":"10.1371","volume":"11","author":[{"given":"Carmen","family":"Espinosa-Gongora","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niels","family":"Larsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristian","family":"Sch\u00f8nning","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Merete","family":"Fredholm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luca","family":"Guardabassi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,8,10]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.chom.2015.04.008","article-title":"An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases","volume":"17","author":"M Wlodarska","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/978-1-4939-0897-4_14","article-title":"Microbiota, inflammation and obesity","volume":"817","author":"Y Sanz","year":"2014","journal-title":"Adv Exp Med Biol"},{"key":"ref3","article-title":"The gut microbiota and Type 1 Diabetes","author":"E Gulden","year":"2015","journal-title":"Clin Immunol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"e61959","DOI":"10.1371\/journal.pone.0061959","article-title":"Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis","volume":"8","author":"JS Kuehn","year":"2013","journal-title":"PLoS One"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1111\/1758-2229.12285","article-title":"Early-life establishment of the swine gut microbiome and impact on host phenotypes","volume":"7","author":"N Mach","year":"2015","journal-title":"Environ Microbiol Rep"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1080\/00071668.2014.931930","article-title":"Probiotics and broiler growth performance: a meta-analysis of randomised controlled trials","volume":"55","author":"JE Blajman","year":"2014","journal-title":"Br Poult Sci"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s40104-015-0014-3","article-title":"Study and use of the probiotic <italic>Lactobacillus reuteri<\/italic> in pigs: a review","volume":"6","author":"C Hou","year":"2015","journal-title":"J Anim Sci Biotechnol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.3382\/ps.2012-02168","article-title":"Evaluating the efficacy of an avian-specific probiotic to reduce the colonization of <italic>Campylobacter jejuni<\/italic> in broiler chickens","volume":"91","author":"K Ghareeb","year":"2012","journal-title":"Poult Sci"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.jgar.2013.03.011","article-title":"Public health impact and antimicrobial selection of meticillin-resistant staphylococci in animals","volume":"1","author":"L Guardabassi","year":"2013","journal-title":"Journal of Global Antimicrobial Resistance"},{"key":"ref10","unstructured":"DANMAP 2014\u2014Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark. 2015."},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e0135826","DOI":"10.1371\/journal.pone.0135826","article-title":"Effects of Reducing Antimicrobial Use and Applying a Cleaning and Disinfection Program in Veal Calf Farming: Experiences from an Intervention Study to Control Livestock-Associated MRSA","volume":"10","author":"A Dorado-Garcia","year":"2015","journal-title":"PLoS One"},{"key":"ref12","first-page":"35","article-title":"Development of pig accommodation suitable for testing the effects of hygiene and disinfection on MRSA carrier pigs","volume":"65","author":"ES Giotis","year":"2011","journal-title":"Pig Journal"},{"key":"ref13","first-page":"13","article-title":"Effect of a disinfectant powder on methicillin-resistant <italic>Staphylococcus aureus<\/italic> in pigs, bedding and air samples under simulated farm conditions","volume":"68","author":"C Espinosa-Gongora","year":"2013","journal-title":"The Pig Journal"},{"key":"ref14","unstructured":"Gr\u00f8ntvedt C, Sunde M, Angen \u00d8, Steihaug Barstad A, \u00c5mdal S, L\u00f8tvedt S, et al., editors. Control of LA-MRSA in Swine\u2014is it Possible? Lessons Learned from Outbreaks and Eradication in Norway. 4th ASM-ESCMID Conference on Methicillin-resistant Staphylococci in Animals: Veterinary and Public Health Implications; 2015 November 2\u20135; Chicago, Illinois."},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1128\/AEM.03392-14","article-title":"Individual predisposition to <italic>Staphylococcus aureus<\/italic> colonization in pigs on the basis of quantification, carriage dynamics, and serological profiles","volume":"81","author":"C Espinosa-Gongora","year":"2015","journal-title":"Appl Environ Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/s12917-015-0599-y","article-title":"Genome-wide association study reveals a locus for nasal carriage of <italic>Staphylococcus aureus<\/italic> in Danish crossbred pigs","volume":"11","author":"P Skallerup","year":"2015","journal-title":"BMC Vet Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e71108","DOI":"10.1371\/journal.pone.0071108","article-title":"Human gut microbiota changes reveal the progression of glucose intolerance","volume":"8","author":"X Zhang","year":"2013","journal-title":"PLoS One"},{"key":"ref18","unstructured":"Larsen N, Ingerslev H-C, Molbak L, Ahrens P, Boye M. BION-meta, a 16S\/23S sequence classification pipeline. In preparation. 2016."},{"key":"ref19","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal Database Project: data and tools for high throughput rRNA analysis","volume":"42","author":"JR Cole","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Q Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref21","year":"2015"},{"key":"ref22","doi-asserted-by":"crossref","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":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"3220","DOI":"10.1093\/bioinformatics\/btt551","article-title":"ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses","volume":"29","author":"MA Huntley","year":"2013","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"PJ McMurdie","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref25","unstructured":"Kolde R. pheatmap: Pretty Heatmaps. R package version 1.0.8. 2015."},{"key":"ref26","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/1746-6148-10-69","article-title":"Evaluation of the nasal microbiota in slaughter-age pigs and the impact on nasal methicillin-resistant <italic>Staphylococcus aureus<\/italic> (MRSA) carriage","volume":"10","author":"JS Weese","year":"2014","journal-title":"BMC Vet Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1086\/423376","article-title":"Predicting the <italic>Staphylococcus aureus<\/italic> nasal carrier state: derivation and validation of a &quot;culture rule&quot;","volume":"39","author":"JL Nouwen","year":"2004","journal-title":"Clin Infect Dis"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2180-12-20","article-title":"Defining the &quot;core microbiome&quot; of the microbial communities in the tonsils of healthy pigs","volume":"12","author":"BA Lowe","year":"2012","journal-title":"BMC Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/2049-2618-2-44","article-title":"The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition","volume":"2","author":"AJ Cremers","year":"2014","journal-title":"Microbiome"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e0123216","DOI":"10.1371\/journal.pone.0123216","article-title":"Sinonasal microbiome sampling: a comparison of techniques","volume":"10","author":"A Bassiouni","year":"2015","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.chom.2013.11.005","article-title":"Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and <italic>S<\/italic>. <italic>aureus<\/italic> carriage","volume":"14","author":"M Yan","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e34242","DOI":"10.1371\/journal.pone.0034242","article-title":"A core human microbiome as viewed through 16S rRNA sequence clusters","volume":"7","author":"SM Huse","year":"2012","journal-title":"PLoS One"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"151ra124","DOI":"10.1126\/scitranslmed.3003783","article-title":"Sinus microbiome diversity depletion and <italic>Corynebacterium tuberculostearicum<\/italic> enrichment mediates rhinosinusitis","volume":"4","author":"NA Abreu","year":"2012","journal-title":"Sci Transl Med"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/j.jaci.2015.02.008","article-title":"Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome","volume":"136","author":"VR Ramakrishnan","year":"2015","journal-title":"J Allergy Clin Immunol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1400216","DOI":"10.1126\/sciadv.1400216","article-title":"<italic>Staphylococcus aureus<\/italic> and the ecology of the nasal microbiome","volume":"1","author":"CM Liu","year":"2015","journal-title":"Science advances"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e0152493","DOI":"10.1371\/journal.pone.0152493","article-title":"A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker","volume":"11","author":"SW Peterson","year":"2016","journal-title":"PLoS One"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1111\/all.12374","article-title":"Decreased diversity of nasal microbiota and their secreted extracellular vesicles in patients with chronic rhinosinusitis based on a metagenomic analysis","volume":"69","author":"EB Choi","year":"2014","journal-title":"Allergy"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.clim.2015.05.022","article-title":"The bacterial microbiota in inflammatory lung diseases","volume":"159","author":"GB Huffnagle","year":"2015","journal-title":"Clin Immunol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"16731","DOI":"10.1073\/pnas.0804812105","article-title":"<italic>Faecalibacterium prausnitzii<\/italic> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients","volume":"105","author":"H Sokol","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/s12866-015-0512-7","article-title":"Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig","volume":"15","author":"MJ Slifierz","year":"2015","journal-title":"BMC Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"418132","DOI":"10.1155\/2013\/418132","article-title":"Technological aptitude and applications of <italic>Leuconostoc mesenteroides<\/italic> bioactive strains isolated from Algerian raw camel milk","volume":"2013","author":"Z Benmechernene","year":"2013","journal-title":"Biomed Res Int"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1139\/cjm-2015-0481","article-title":"In vitro probiotic profiling of novel <italic>Enterococcus faecium<\/italic> and <italic>Leuconostoc mesenteroides<\/italic> from Tunisian freshwater fishes","volume":"62","author":"R El-Jeni","year":"2016","journal-title":"Can J Microbiol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1128\/AAC.44.8.2130-2132.2000","article-title":"Antimicrobial susceptibilities and clinical sources of <italic>Facklamia<\/italic> species","volume":"44","author":"L LaClaire","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"key":"ref44","first-page":"91","article-title":"Lactic Acid Bacteria","author":"L Hoyles","year":"2014"},{"issue":"Pt 3","key":"ref45","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1099\/00207713-49-3-1247","article-title":"<italic>Facklamia tabacinasalis<\/italic> sp. nov., from powdered tobacco","volume":"49","author":"MD Collins","year":"1999","journal-title":"Int J Syst Bacteriol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1556\/AMicr.61.2014.1.8","article-title":"Isolation of <italic>Kurthia gibsonii<\/italic> from non-gonorrheal urethritis: implications for the pathomechanism upon surveying the literature","volume":"61","author":"J Ongradi","year":"2014","journal-title":"Acta Microbiol Immunol Hung"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s11274-014-1764-3","article-title":". Highly effective bacterial agents against <italic>Cimbex quadrimaculatus<\/italic> (Hymenoptera: Cimbicidae): isolation of bacteria and their insecticidal activities","volume":"31","author":"FO Cakici","year":"2015","journal-title":"World J Microbiol Biotechnol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1128\/JCM.03076-13","article-title":"Identification and clinical significance of <italic>Helcococcus<\/italic> species, with description of <italic>Helcococcus seattlensis<\/italic> sp. nov. from a patient with urosepsis","volume":"52","author":"SK Chow","year":"2014","journal-title":"J Clin Microbiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.2527\/jas.2015-9190","article-title":"Effects of probiotics strain MA18\/5M and subsp. strain SB-CNCM I-1079 on fecal and intestinal microbiota of nursing and weanling piglets","volume":"93","author":"JP Brousseau","year":"2015","journal-title":"J Anim Sci"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"49","DOI":"10.3389\/fmicb.2016.00049","article-title":"Reservoirs of Non-baumannii Acinetobacter Species","volume":"7","author":"A Al Atrouni","year":"2016","journal-title":"Front Microbiol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1099\/00207713-47-1-115","article-title":"<italic>Moraxella boevrei<\/italic> sp. nov., a new <italic>Moraxella<\/italic> species found in goats","volume":"47","author":"A Kodjo","year":"1997","journal-title":"Int J Syst Bacteriol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e10598","DOI":"10.1371\/journal.pone.0010598","article-title":"The human nasal microbiota and <italic>Staphylococcus aureus<\/italic> carriage","volume":"5","author":"DN Frank","year":"2010","journal-title":"PLoS One"},{"key":"ref53","article-title":"The culturome of the human nose habitats reveals individual bacterial fingerprint patterns","author":"U Kaspar","year":"2015","journal-title":"Environ Microbiol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0160331","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T23:09:51Z","timestamp":1540336191000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0160331"}},"subtitle":[],"editor":[{"given":"Herminia","family":"de Lencastre","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,8,10]]},"references-count":53,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2016,8,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0160331","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,10]]}}}