{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T14:15:25Z","timestamp":1781187325497,"version":"3.54.1"},"reference-count":73,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T00:00:00Z","timestamp":1552608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2019.00512","type":"journal-article","created":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T04:22:07Z","timestamp":1552623727000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":41,"title":["Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis"],"prefix":"10.3389","volume":"10","author":[{"given":"Lisa R.","family":"McTaggart","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia K.","family":"Copeland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anuradha","family":"Surendra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline W.","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahid","family":"Husain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Coburn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David S.","family":"Guttman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julianne V.","family":"Kus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,3,15]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"5555","DOI":"10.1111\/j.1365-294X.2010.04898.x","article-title":"Quantifying microbial communities with 454 pyrosequencing: does read abundance count?","volume":"19","author":"Amend","year":"2010","journal-title":"Mol. Ecol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3897\/mycokeys.39.28109","article-title":"Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.","volume":"39","author":"Anslan","year":"2018","journal-title":"MycoKeys"},{"key":"B4","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1128\/CMR.00091-13","article-title":"Molecular and nonmolecular diagnostic methods for invasive fungal infections.","volume":"27","author":"Arvanitis","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"B5","doi-asserted-by":"publisher","first-page":"3204","DOI":"10.1128\/JCM.00673-11","article-title":"Detection of Blastomyces dermatitidis and Histoplasma capsulatum from culture isolates and clinical specimens by use of real-time PCR.","volume":"49","author":"Babady","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-10-189","article-title":"ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases.","volume":"10","author":"Bellemain","year":"2010","journal-title":"BMC Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.tree.2011.11.010","article-title":"Sequencing our way towards understanding global eukaryotic biodiversity.","volume":"27","author":"Bik","year":"2012","journal-title":"Trends Ecol. Evol."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0487-y","article-title":"Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.","volume":"15","author":"Bittinger","year":"2014","journal-title":"Genome Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"2519","DOI":"10.1128\/AEM.03870-12","article-title":"Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities.","volume":"79","author":"Bokulich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1007\/s11046-017-0185-x","article-title":"Fungal and bacterial diversity of airway microbiota in adults with cystic fibrosis: concordance between conventional methods and ultra-deep sequencing, and their practical use in the clinical laboratory.","volume":"183","author":"Botterel","year":"2018","journal-title":"Mycopathologia"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0032486","article-title":"Repertoire of intensive care unit pneumonia microbiota.","volume":"7","author":"Bousbia","year":"2012","journal-title":"PLoS One"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-2063-6","article-title":"Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.","volume":"16","author":"Bowers","year":"2015","journal-title":"BMC Genomics"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-015-0351-6","article-title":"The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.","volume":"15","author":"Brooks","year":"2015","journal-title":"BMC Microbiol."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden killers: human fungal infections.","volume":"4","author":"Brown","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"B15","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data.","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"B16","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1164\/rccm.201204-0693OC","article-title":"Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.","volume":"186","author":"Charlson","year":"2012","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1038\/srep16350","article-title":"Sample storage conditions significantly influence faecal microbiome profiles.","volume":"5","author":"Choo","year":"2015","journal-title":"Sci. Rep."},{"key":"B18","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1086\/500405","article-title":"Hospitalizations for endemic mycoses: a population-based national study.","volume":"42","author":"Chu","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1086\/378901","article-title":"Partitioning species diversity across landscapes and regions: a hierarchical analysis of alpha, beta, and gamma diversity.","volume":"162","author":"Crist","year":"2003","journal-title":"Am. Nat."},{"key":"B20","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1164\/rccm.201409-1583OC","article-title":"Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease.","volume":"191","author":"Cui","year":"2015","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1186\/gm467","article-title":"The human mycobiome in health and disease.","volume":"5","author":"Cui","year":"2013","journal-title":"Genome Med."},{"key":"B22","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1007\/978-1-4939-6515-1_14","article-title":"Broad-spectrum molecular detection of fungal nucleic acids by PCR-based amplification techniques.","volume":"1508","author":"Czurda","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1002\/jobm.201200507","article-title":"Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS).","volume":"54","author":"Dannemiller","year":"2014","journal-title":"J. Basic Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"AEM.905","DOI":"10.1128\/AEM.00905-17","article-title":"Different amplicon targets for sequencing-based studies of fungal diversity.","volume":"83","author":"De Filippis","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"B25","first-page":"2949","article-title":"\u201c265 - Histoplasma capsulatum (Histoplasmosis),\u201d in","author":"Deepe","year":"2015","journal-title":"Principles and Practice of Infectious Diseases, 7th edition"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0036313","article-title":"The airway microbiota in cystic fibrosis: a complex fungal and bacterial community\u2013implications for therapeutic management.","volume":"7","author":"Delhaes","year":"2012","journal-title":"PLoS One"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0090899","article-title":"Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.","volume":"9","author":"Dupuy","year":"2014","journal-title":"PLoS One"},{"key":"B28","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads.","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"B29","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/nature12171","article-title":"Topographic diversity of fungal and bacterial communities in human skin.","volume":"498","author":"Findley","year":"2013","journal-title":"Nature"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-016-0738-z","article-title":"16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform.","volume":"16","author":"Fouhy","year":"2016","journal-title":"BMC Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1016\/j.jaci.2017.09.039","article-title":"Corticosteroid treatment is associated with increased filamentous fungal burden in allergic fungal disease.","volume":"143","author":"Fraczek","year":"2018","journal-title":"J. Allergy Clin. Immunol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1128\/CMR.00021-11","article-title":"The Malassezia genus in skin and systemic diseases.","volume":"25","author":"Gaitanis","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3114\/sim.2007.59.01","article-title":"The current status of species recognition and identification in Aspergillus.","volume":"59","author":"Geiser","year":"2007","journal-title":"Stud. Mycol."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00180","article-title":"Critical issues in mycobiota analysis.","volume":"8","author":"Halwachs","year":"2017","journal-title":"Front. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-018-1359-5","article-title":"Sample storage conditions induce post-collection biases in microbiome profiles.","volume":"18","author":"Jenkins","year":"2018","journal-title":"BMC Microbiol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s13225-018-0403-y","article-title":"Phylogeny, ecology and taxonomy of systemic pathogens and their relatives in ajellomycetaceae (onygenales): blastomyces, emergomyces, emmonsia, emmonsiellopsis.","volume":"90","author":"Jiang","year":"2018","journal-title":"Fungal Divers."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005308","article-title":"Global analysis of the fungal microbiome in cystic fibrosis patients reveals loss of function of the transcriptional repressor Nrg1 as a mechanism of pathogen adaptation.","volume":"11","author":"Kim","year":"2015","journal-title":"PLoS Pathog."},{"key":"B38","doi-asserted-by":"publisher","first-page":"2900","DOI":"10.1128\/JCM.01094-15","article-title":"Cohort study of airway mycobiome in adult cystic fibrosis patients: differences in community structure between fungi and bacteria reveal predominance of transient fungal elements.","volume":"53","author":"Kramer","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0155033","article-title":"Characterisation of candida within the mycobiome\/microbiome of the lower respiratory tract of ICU patients.","volume":"11","author":"Krause","year":"2016","journal-title":"PLoS One"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.02169","article-title":"Mycobiome in the lower respiratory tract-a clinical perspective.","volume":"7","author":"Krause","year":"2017","journal-title":"Front. Microbiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.humimm.2014.12.016","article-title":"Impact of three illumina library construction methods on GC bias and HLA genotype calling.","volume":"76","author":"Lan","year":"2015","journal-title":"Hum. Immunol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1111\/nph.12243","article-title":"Fungal community analysis by high-throughput sequencing of amplified markers\u2013a user\u2019s guide.","volume":"199","author":"Lindahl","year":"2013","journal-title":"New Phytol."},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0110808","article-title":"Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data.","volume":"9","author":"Lusk","year":"2014","journal-title":"PLoS One"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-4428-5","article-title":"Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing.","volume":"19","author":"MacConaill","year":"2018","journal-title":"BMC Genomics"},{"key":"B45","author":"Martinez-Arbizu","year":"2017","journal-title":"pairwiseAdonis: Pairwise Multilevel Comparison Using Adonis. R Package Version"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1186\/gm485","article-title":"Metagenomics for pathogen detection in public health.","volume":"5","author":"Miller","year":"2013","journal-title":"Genome Med."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00238","article-title":"Fungal ITS1 deep-sequencing strategies to reconstruct the composition of a 26-species community and evaluation of the gut mycobiota of healthy japanese individuals.","volume":"8","author":"Motooka","year":"2017","journal-title":"Front. Microbiol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1111\/nph.12923","article-title":"Parsing ecological signal from noise in next generation amplicon sequencing.","volume":"205","author":"Nguyen","year":"2015","journal-title":"New Phytol."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1186\/1751-0473-4-1","article-title":"A software pipeline for processing and identification of fungal ITS sequences.","volume":"4","author":"Nilsson","year":"2009","journal-title":"Source Code Biol. Med."},{"key":"B50","author":"Oksanen","year":"2017","journal-title":"Vegan: Community Ecology Package. R Package Version 2.2-0"},{"key":"B51","doi-asserted-by":"publisher","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3109\/10408410903241444","article-title":"Epidemiology of invasive mycoses in North America.","volume":"36","author":"Pfaller","year":"2010","journal-title":"Crit. Rev. Microbiol."},{"key":"B53","author":"Pohlert","year":"2014","journal-title":"The Pairwise Multiple Comparison of Mean Ranks Package (PMCMR). R Package"},{"key":"B54","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1038\/ismej.2016.117","article-title":"Absolute quantification of microbial taxon abundances.","volume":"11","author":"Props","year":"2017","journal-title":"ISME J."},{"key":"B55","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1128\/CMR.00056-09","article-title":"Clinical and laboratory update on blastomycosis.","volume":"23","author":"Saccente","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-014-0087-z","article-title":"Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.","volume":"12","author":"Salter","year":"2014","journal-title":"BMC Biol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"6241","DOI":"10.1073\/pnas.1117018109","article-title":"Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.","volume":"109","author":"Schoch","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B58","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1017\/S0953756298007904","article-title":"Phylogenetic analysis of nucleotide sequences from the ITS region of terverticillate Penicillium species.","volume":"103","author":"Skouboe","year":"1999","journal-title":"Mycol. Res."},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-016-0175-0","article-title":"Adjusting microbiome profiles for differences in microbial load by spike-in bacteria.","volume":"4","author":"Stammler","year":"2016","journal-title":"Microbiome"},{"key":"B60","doi-asserted-by":"publisher","first-page":"7217","DOI":"10.1128\/AEM.02576-16","article-title":"Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for illumina amplicon sequencing.","volume":"82","author":"Taylor","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"B61","doi-asserted-by":"publisher","first-page":"113","DOI":"10.5598\/imafungus.2011.02.02.01","article-title":"One fungus = one name: DNA and fungal nomenclature twenty years after PCR.","volume":"2","author":"Taylor","year":"2011","journal-title":"IMA Fungus"},{"key":"B62","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1080\/21505594.2016.1235671","article-title":"The lung mycobiome in the next-generation sequencing era.","volume":"8","author":"Tipton","year":"2017","journal-title":"Virulence"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0148676","article-title":"Comparison of sample preparation methods used for the next-generation sequencing of mycobacterium tuberculosis.","volume":"11","author":"Tyler","year":"2016","journal-title":"PLoS One"},{"key":"B64","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00488-17","article-title":"Novel ITS1 fungal primers for characterization of the mycobiome.","volume":"2","author":"Usyk","year":"2017","journal-title":"mSphere"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1038\/srep26314","article-title":"Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene.","volume":"6","author":"Van den Hoecke","year":"2016","journal-title":"Sci. Rep."},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-13-69","article-title":"Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study.","volume":"13","author":"van Woerden","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"B67","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1093\/bioinformatics\/btr087","article-title":"PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.","volume":"27","author":"Walters","year":"2011","journal-title":"Bioinformatics"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0564-2","article-title":"Tracking down the sources of experimental contamination in microbiome studies.","volume":"15","author":"Weiss","year":"2014","journal-title":"Genome Biol."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0237-y","article-title":"Normalization and microbial differential abundance strategies depend upon data characteristics.","volume":"5","author":"Weiss","year":"2017","journal-title":"Microbiome"},{"key":"B70","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.idc.2015.10.009","article-title":"Histoplasmosis.","volume":"30","author":"Wheat","year":"2016","journal-title":"Infect. Dis. Clin. North Am."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","author":"Wickham","year":"2009","journal-title":"Ggplot2: Elegant Graphics for Data Analysis"},{"key":"B72","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-40","article-title":"Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.","volume":"2","author":"Willger","year":"2014","journal-title":"Microbiome"},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0034605","article-title":"Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples.","volume":"7","author":"Willner","year":"2012","journal-title":"PLoS One"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.00512\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T04:22:09Z","timestamp":1552623729000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.00512\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,15]]},"references-count":73,"alternative-id":["10.3389\/fmicb.2019.00512"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2019.00512","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,15]]},"article-number":"512"}}