{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T23:52:43Z","timestamp":1782172363261,"version":"3.54.5"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T00:00:00Z","timestamp":1606348800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T00:00:00Z","timestamp":1606348800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["1R01AI125562-01"],"award-info":[{"award-number":["1R01AI125562-01"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Although generally known as a human commensal,\n                      <jats:italic>Staphylococcus epidermidis<\/jats:italic>\n                      is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients\u2019 quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive.\n                    <\/jats:p>\n                    <jats:p>\n                      In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      communities.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Based on an assessment of &gt;\u2009800 genes from the\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico\n                      <jats:italic>,<\/jats:italic>\n                      and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      . The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of &lt;\u200910 copies\/\u03bcL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The Epidome method is designed for use on primary samples to obtain important information on\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of\n                      <jats:italic>S. epidermidis<\/jats:italic>\n                      communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-020-02041-w","type":"journal-article","created":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T06:04:57Z","timestamp":1606370697000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection"],"prefix":"10.1186","volume":"20","author":[{"given":"Amalie Katrine","family":"Rendboe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thor Bech","family":"Johannesen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna C\u00e4cilia","family":"Ingham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emeli","family":"M\u00e5nsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00f8ren","family":"Iversen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharmin","family":"Baig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofie","family":"Edslev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f8rgen Skov","family":"Jensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"S\u00f6derquist","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paal Skytt","family":"Andersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0321-1180","authenticated-orcid":false,"given":"Marc","family":"Stegger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,26]]},"reference":[{"issue":"3","key":"2041_CR1","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","volume":"16","author":"AL Byrd","year":"2018","unstructured":"Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol. 2018;16(3):143\u201355.","journal-title":"Nat Rev Microbiol"},{"issue":"6424","key":"2041_CR2","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1126\/science.aat4326","volume":"363","author":"A Stacy","year":"2019","unstructured":"Stacy A, Belkaid Y. Microbial guardians of skin health. Science. 2019;363(6424):227\u20138.","journal-title":"Science"},{"issue":"5","key":"2041_CR3","doi-asserted-by":"publisher","first-page":"2286","DOI":"10.1128\/JCM.43.5.2286-2290.2005","volume":"43","author":"E Heikens","year":"2005","unstructured":"Heikens E, Fleer A, Paauw A, Florijn A, Fluit AC. Comparison of genotypic and phenotypic methods for species-level identification of clinical isolates of coagulase-negative staphylococci. J Clin Microbiol. 2005;43(5):2286\u201390.","journal-title":"J Clin Microbiol"},{"issue":"4","key":"2041_CR4","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1128\/CMR.00109-13","volume":"27","author":"K Becker","year":"2014","unstructured":"Becker K, Heilmann C, Peters G. Coagulase-negative staphylococci. Clin Microbiol Rev. 2014;27(4):870\u2013926.","journal-title":"Clin Microbiol Rev"},{"issue":"2","key":"2041_CR5","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1302\/0301-620X.86B2.14129","volume":"86","author":"SS Mohanty","year":"2004","unstructured":"Mohanty SS, Kay PR. Infection in total joint replacements. Why we screen MRSA when MRSE is the problem? J Bone Joint Surg Br. 2004;86(2):266\u20138.","journal-title":"J Bone Joint Surg Br"},{"issue":"1","key":"2041_CR6","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.ijmm.2012.11.001","volume":"303","author":"B Hellmark","year":"2013","unstructured":"Hellmark B, Soderquist B, Unemo M, Nilsdotter-Augustinsson A. Comparison of Staphylococcus epidermidis isolated from prosthetic joint infections and commensal isolates in regard to antibiotic susceptibility, agr type, biofilm production, and epidemiology. Int J Med Microbiol. 2013;303(1):32\u20139.","journal-title":"Int J Med Microbiol"},{"issue":"7","key":"2041_CR7","doi-asserted-by":"publisher","first-page":"1679","DOI":"10.1128\/JCM.00743-16","volume":"54","author":"M Widerstrom","year":"2016","unstructured":"Widerstrom M. Significance of Staphylococcus epidermidis in health care-associated infections, from contaminant to clinically relevant pathogen: this is a wake-up call! J Clin Microbiol. 2016;54(7):1679\u201381.","journal-title":"J Clin Microbiol"},{"issue":"6","key":"2041_CR8","doi-asserted-by":"publisher","first-page":"e99045","DOI":"10.1371\/journal.pone.0099045","volume":"9","author":"E Ahlstrand","year":"2014","unstructured":"Ahlstrand E, Hellmark B, Svensson K, Soderquist B. Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies. PLoS One. 2014;9(6):e99045.","journal-title":"PLoS One"},{"issue":"16","key":"2041_CR9","doi-asserted-by":"publisher","first-page":"1645","DOI":"10.1056\/NEJMra040181","volume":"351","author":"W Zimmerli","year":"2004","unstructured":"Zimmerli W, Trampuz A, Ochsner PE. Prosthetic-joint infections. N Engl J Med. 2004;351(16):1645\u201354.","journal-title":"N Engl J Med"},{"issue":"8 Suppl","key":"2041_CR10","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.arth.2012.02.022","volume":"27","author":"SM Kurtz","year":"2012","unstructured":"Kurtz SM, Lau E, Watson H, Schmier JK, Parvizi J. Economic burden of periprosthetic joint infection in the United States. J Arthroplast. 2012;27(8 Suppl):61\u20135 e61.","journal-title":"J Arthroplast"},{"issue":"5","key":"2041_CR11","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1080\/23744235.2019.1572219","volume":"51","author":"T Puhto","year":"2019","unstructured":"Puhto T, Puhto AP, Vielma M, Syrjala H. Infection triples the cost of a primary joint arthroplasty. Infect Dis (Lond). 2019;51(5):348\u201355.","journal-title":"Infect Dis (Lond)"},{"issue":"12","key":"2041_CR12","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2015-009495","volume":"5","author":"AJ Moore","year":"2015","unstructured":"Moore AJ, Blom AW, Whitehouse MR, Gooberman-Hill R. Deep prosthetic joint infection: a qualitative study of the impact on patients and their experiences of revision surgery. BMJ Open. 2015;5(12):e009495.","journal-title":"BMJ Open"},{"issue":"10","key":"2041_CR13","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1038\/s41564-018-0230-7","volume":"3","author":"JYH Lee","year":"2018","unstructured":"Lee JYH, Monk IR. Goncalves da Silva a, Seemann T, Chua KYL, Kearns a, Hill R, Woodford N, Bartels MD, Strommenger B et al: global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nat Microbiol. 2018;3(10):1175\u201385.","journal-title":"Nat Microbiol"},{"issue":"Pt 4","key":"2041_CR14","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1099\/jmm.0.007567-0","volume":"58","author":"M Li","year":"2009","unstructured":"Li M, Wang X, Gao Q, Lu Y. Molecular characterization of Staphylococcus epidermidis strains isolated from a teaching hospital in Shanghai, China. J Med Microbiol. 2009;58(Pt 4):456\u201361.","journal-title":"J Med Microbiol"},{"issue":"6","key":"2041_CR15","doi-asserted-by":"publisher","first-page":"2540","DOI":"10.1128\/JB.01484-06","volume":"189","author":"M Miragaia","year":"2007","unstructured":"Miragaia M, Thomas JC, Couto I, Enright MC, de Lencastre H. Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing data. J Bacteriol. 2007;189(6):2540\u201352.","journal-title":"J Bacteriol"},{"issue":"9","key":"2041_CR16","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1093\/infdis\/jis218","volume":"205","author":"RJ Gordon","year":"2012","unstructured":"Gordon RJ, Miragaia M, Weinberg AD, Lee CJ, Rolo J, Giacalone JC, Slaughter MS, Pappas P, Naka Y, Tector AJ, et al. Staphylococcus epidermidis colonization is highly clonal across US cardiac centers. J Infect Dis. 2012;205(9):1391\u20138.","journal-title":"J Infect Dis"},{"issue":"3","key":"2041_CR17","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1093\/cid\/ciy089","volume":"67","author":"X Li","year":"2018","unstructured":"Li X, Arias CA, Aitken SL, Galloway Pena J, Panesso D, Chang M, Diaz L, Rios R, Numan Y, Ghaoui S, et al. Clonal emergence of invasive multidrug-resistant Staphylococcus epidermidis Deconvoluted via a combination of whole-genome sequencing and microbiome analyses. Clin Infect Dis. 2018;67(3):398\u2013406.","journal-title":"Clin Infect Dis"},{"issue":"7520","key":"2041_CR18","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature13786","volume":"514","author":"J Oh","year":"2014","unstructured":"Oh J, Byrd AL, Deming C, Conlan S, Program NCS, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514(7520):59\u201364.","journal-title":"Nature"},{"issue":"5","key":"2041_CR19","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1111\/j.1348-0421.1995.tb02207.x","volume":"39","author":"L Hu","year":"1995","unstructured":"Hu L, Umeda A, Amako K. Typing of Staphylococcus epidermidis colonizing in human nares by pulsed-field gel electrophoresis. Microbiol Immunol. 1995;39(5):315\u20139.","journal-title":"Microbiol Immunol"},{"issue":"12","key":"2041_CR20","doi-asserted-by":"publisher","first-page":"3766","DOI":"10.1128\/JCM.01018-15","volume":"53","author":"M De-la-Fuente","year":"2015","unstructured":"De-la-Fuente M, Martinez-Perez M, Gonzalez-Pallares I, Esteban J. Detection of Polyclonality among clinical isolates from prosthetic joint infections. J Clin Microbiol. 2015;53(12):3766\u201372.","journal-title":"J Clin Microbiol"},{"key":"2041_CR21","doi-asserted-by":"crossref","unstructured":"Byrd AL, Deming C, Cassidy SKB, Harrison OJ, Ng WI, Conlan S, Program NCS, Belkaid Y, Segre JA, Kong HH. Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis. Sci Transl Med. 2017;9(397):1\u201312.","DOI":"10.1126\/scitranslmed.aal4651"},{"issue":"3","key":"2041_CR22","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1086\/427240","volume":"191","author":"C Cespedes","year":"2005","unstructured":"Cespedes C, Said-Salim B, Miller M, Lo SH, Kreiswirth BN, Gordon RJ, Vavagiakis P, Klein RS, Lowy FD. The clonality of Staphylococcus aureus nasal carriage. J Infect Dis. 2005;191(3):444\u201352.","journal-title":"J Infect Dis"},{"issue":"4","key":"2041_CR23","doi-asserted-by":"publisher","first-page":"1192","DOI":"10.1128\/JCM.03254-13","volume":"52","author":"AA Votintseva","year":"2014","unstructured":"Votintseva AA, Miller RR, Fung R, Knox K, Godwin H, Peto TE, Crook DW, Bowden R, Walker AS. Multiple-strain colonization in nasal carriers of Staphylococcus aureus. J Clin Microbiol. 2014;52(4):1192\u2013200.","journal-title":"J Clin Microbiol"},{"issue":"2","key":"2041_CR24","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1099\/00222615-42-2-127","volume":"42","author":"L Hu","year":"1995","unstructured":"Hu L, Umeda A, Kondo S, Amako K. Typing of Staphylococcus aureus colonising human nasal carriers by pulsed-field gel electrophoresis. J Med Microbiol. 1995;42(2):127\u201332.","journal-title":"J Med Microbiol"},{"issue":"7","key":"2041_CR25","doi-asserted-by":"publisher","first-page":"2541","DOI":"10.1128\/JCM.39.7.2541-2547.2001","volume":"39","author":"F Martineau","year":"2001","unstructured":"Martineau F, Picard FJ, Ke D, Paradis S, Roy PH, Ouellette M, Bergeron MG. Development of a PCR assay for identification of staphylococci at genus and species levels. J Clin Microbiol. 2001;39(7):2541\u20137.","journal-title":"J Clin Microbiol"},{"issue":"12","key":"2041_CR26","doi-asserted-by":"publisher","first-page":"4296","DOI":"10.1128\/JCM.39.12.4296-4301.2001","volume":"39","author":"C Poyart","year":"2001","unstructured":"Poyart C, Quesne G, Boumaila C, Trieu-Cuot P. Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J Clin Microbiol. 2001;39(12):4296\u2013301.","journal-title":"J Clin Microbiol"},{"issue":"Pt 10","key":"2041_CR27","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1099\/jmm.0.47235-0","volume":"56","author":"T Iwase","year":"2007","unstructured":"Iwase T, Seki K, Shinji H, Mizunoe Y, Masuda S. Development of a real-time PCR assay for the detection and identification of Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri. J Med Microbiol. 2007;56(Pt 10):1346\u20139.","journal-title":"J Med Microbiol"},{"issue":"1","key":"2041_CR28","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/s00203-017-1415-9","volume":"200","author":"J Kim","year":"2018","unstructured":"Kim J, Hong J, Lim JA, Heu S, Roh E. Improved multiplex PCR primers for rapid identification of coagulase-negative staphylococci. Arch Microbiol. 2018;200(1):73\u201383.","journal-title":"Arch Microbiol"},{"issue":"5","key":"2041_CR29","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1093\/gbe\/evv066","volume":"7","author":"G Meric","year":"2015","unstructured":"Meric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, et al. Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. 2015;7(5):1313\u201328.","journal-title":"Genome Biol Evol"},{"issue":"5","key":"2041_CR30","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455\u201377.","journal-title":"J Comput Biol"},{"key":"2041_CR31","doi-asserted-by":"crossref","unstructured":"M\u00e5nsson E, Johannesen TB, Nilsdotter \u00c5, S\u00f6derquist B, Stegger M: Comparative genomics of Staphylococcus epidermidis from prosthetic joint infections and nares highlights genetic traits associated to antimicrobial resistance, not virulence. Submitted 2020.","DOI":"10.1099\/mgen.0.000504"},{"issue":"8","key":"2041_CR32","first-page":"e000074","volume":"2","author":"JW Sahl","year":"2016","unstructured":"Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD, Aziz M, Driebe EM, Drees KP, Hicks ND, Williamson CHD, et al. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom. 2016;2(8):e000074.","journal-title":"Microb Genom"},{"key":"2041_CR33","unstructured":"MacLea KS, Trachtenberg AM. Complete Genome Sequence of Staphylococcus epidermidis ATCC 12228 Chromosome and Plasmids, Generated by Long-Read Sequencing. Genome Announc. 2017;5(36):1\u20132."},{"issue":"3","key":"2041_CR34","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.","journal-title":"PLoS One"},{"issue":"14","key":"2041_CR35","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139.","journal-title":"Bioinformatics"},{"issue":"22","key":"2041_CR36","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691\u20133.","journal-title":"Bioinformatics"},{"issue":"1","key":"2041_CR37","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"LT Nguyen","year":"2015","unstructured":"Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268\u201374.","journal-title":"Mol Biol Evol"},{"key":"2041_CR38","first-page":"10","volume":"1","author":"M Martin","year":"2011","unstructured":"Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;1:10\u20132.","journal-title":"EMBnetjournal"},{"issue":"7","key":"2041_CR39","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581\u20133.","journal-title":"Nat Methods"},{"issue":"4","key":"2041_CR40","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.","journal-title":"PLoS One"},{"key":"2041_CR41","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.12688\/f1000research.16680.1","volume":"7","author":"GS Kandlikar","year":"2018","unstructured":"Kandlikar GS, Gold ZJ, Cowen MC, Meyer RS, Freise AC, Kraft NJB, Moberg-Parker J, Sprague J, Kushner DJ, Curd EE. ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Res. 2018;7:1734.","journal-title":"F1000Res"},{"key":"2041_CR42","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-Verlag; 2016."}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-020-02041-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12866-020-02041-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-020-02041-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,15]],"date-time":"2021-04-15T07:09:34Z","timestamp":1618470574000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/s12866-020-02041-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,26]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["2041"],"URL":"https:\/\/doi.org\/10.1186\/s12866-020-02041-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-66877\/v1","asserted-by":"object"}]},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,26]]},"assertion":[{"value":"31 August 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 November 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 November 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Collection of nasal and skin samples from healthy adults was approved by the local ethical committee (Videnskabetisk Komite Region-Hovedstaden, project id: H-16023435) and the Danish Data Protection Agency. All participants provided written informed consent.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that there is no conflict of interest regarding the publication of this paper.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"362"}}