{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T22:26:56Z","timestamp":1791498416312,"version":"4.3.4"},"reference-count":95,"publisher":"Frontiers Media SA","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2015.00089","type":"journal-article","created":{"date-parts":[[2015,2,13]],"date-time":"2015-02-13T10:12:59Z","timestamp":1423822379000},"source":"Crossref","is-referenced-by-count":217,"title":["The lung mycobiome: an emerging field of the human respiratory microbiome"],"prefix":"10.3389","volume":"6","author":[{"given":"Linh D. N.","family":"Nguyen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Viscogliosi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Delhaes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2015,2,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"5721","DOI":"10.1128\/JCM.43.11.5721-5732.2005","article-title":"Defining the normal bacterial flora of the oral cavity","volume":"43","author":"Aas","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1378\/chest.09-1103","article-title":"The effect of chronic infection with Aspergillus fumigatus on lung function and hospitalization in patients with cystic fibrosis","volume":"137","author":"Amin","year":"2010","journal-title":"Chest"},{"key":"B3","doi-asserted-by":"publisher","first-page":"e98502","DOI":"10.1371\/journal.pone.0098502","article-title":"Multi-country estimate of different manifestations of aspergillosis in cystic fibrosis","volume":"9","author":"Armstead","year":"2014","journal-title":"PLoS ONE"},{"key":"B4","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1186\/1471-2180-13-303","article-title":"The murine lung microbiome in relation to the intestinal and vaginal bacterial communities","volume":"13","author":"Barfod","year":"2013","journal-title":"BMC Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"e2908","DOI":"10.1371\/journal.pone.0002908","article-title":"Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients","volume":"3","author":"Bittar","year":"2008","journal-title":"PLoS ONE"},{"key":"B6","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/1471-2334-13-210","article-title":"The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection","volume":"13","author":"Boase","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"B7","doi-asserted-by":"publisher","first-page":"O7","DOI":"10.1111\/1469-0691.12294","article-title":"An 8-year survey of strains identified in blood cultures in a clinical haematology unit","volume":"20","author":"Bousquet","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"B8","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1513\/AnnalsATS.201211-107OC","article-title":"Changes in cystic fibrosis airway microbiota at pulmonary exacerbation","volume":"10","author":"Carmody","year":"2013","journal-title":"Ann. Am. Thorac. Soc."},{"key":"B9","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1111\/j.1567-1364.2010.00698.x","article-title":"Pneumocystis: from a doubtful unique entity to a group of highly diversified fungal species","volume":"11","author":"Chab\u00c3\u00a9","year":"2011","journal-title":"FEMS Yeast Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e42786","DOI":"10.1371\/journal.pone.0042786","article-title":"Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts","volume":"7","author":"Charlson","year":"2012a","journal-title":"PLoS ONE"},{"key":"B11","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":"2012b","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B12","doi-asserted-by":"publisher","first-page":"e15216","DOI":"10.1371\/journal.pone.0015216","article-title":"Disordered microbial communities in the upper respiratory tract of cigarette smokers","volume":"5","author":"Charlson","year":"2010","journal-title":"PLoS ONE"},{"key":"B13","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1080\/mmy.40.4.333.357","article-title":"A review of nucleic acid-based diagnostic tests for systemic mycoses with an emphasis on polymerase chain reaction-based assays","volume":"40","author":"Chen","year":"2002","journal-title":"Med. Mycol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1016\/j.kjms.2011.11.011","article-title":"Fluconazole exposure rather than clonal spreading is correlated with the emergence of Candida glabrata with cross-resistance to triazole antifungal agents","volume":"28","author":"Chen","year":"2012","journal-title":"Kaohsiung J. Med. Sci."},{"key":"B15","doi-asserted-by":"publisher","first-page":"4038","DOI":"10.1021\/es4055725","article-title":"Differential resistance of drinking water bacterial populations to monochloramine disinfection","volume":"48","author":"Chiao","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1186","DOI":"10.1378\/chest.09-2996","article-title":"Sputum Candida albicans presages FEV decline and hospital-treated exacerbations in cystic fibrosis","volume":"138","author":"Chotirmall","year":"2010","journal-title":"Chest"},{"key":"B17","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1002\/alr.21297","article-title":"The fungal microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes and patient outcomes: fungal microbiome in CRS","volume":"4","author":"Cleland","year":"2014","journal-title":"Int. Forum Allergy Rhinol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1165\/rcmb.2012-0059PS","article-title":"Cystic fibrosis therapy: a community ecology perspective","volume":"48","author":"Conrad","year":"2013","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/gm467","article-title":"The human mycobiome in health and disease","volume":"5","author":"Cui","year":"2013","journal-title":"Genome Med."},{"key":"B20","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.jcf.2014.10.004","article-title":"Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses","author":"Cuthbertson","year":"2014","journal-title":"J. Cyst. Fibros."},{"key":"B21","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1093\/infdis\/jit473","article-title":"complications and associated bacterial coinfections among children hospitalized with seasonal or pandemic influenza, United States, 2003\u00e2\u20ac\u201c2010","volume":"209","author":"Dawood","year":"2014","journal-title":"J. Infect. Dis."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02016-14","article-title":"Name changes in medically important fungi and their implications for clinical practice","author":"de Hoog","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"e36313","DOI":"10.1371\/journal.pone.0036313","article-title":"The airway microbiota in cystic fibrosis: a complex fungal and bacterial community\u00e2\u20ac\u201dimplications for therapeutic management","volume":"7","author":"Delhaes","year":"2012","journal-title":"PLoS ONE"},{"key":"B24","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/2045-7022-4-14","article-title":"Fungal allergy in asthma-state of the art and research needs","volume":"4","author":"Denning","year":"2014","journal-title":"Clin. Transl. Allergy"},{"key":"B25","doi-asserted-by":"publisher","first-page":"101","DOI":"10.3389\/fcimb.2014.00101","article-title":"Fungal\u00e2\u20ac\u201cbacterial interactions and their relevance to oral health: linking the clinic and the bench","volume":"4","author":"Diaz","year":"2014","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1128\/IAI.05896-11","article-title":"Synergistic interaction between Candida albicans and commensal oral streptococci in a novel in vitro mucosal model","volume":"80","author":"Diaz","year":"2012","journal-title":"Infect. Immun."},{"key":"B27","doi-asserted-by":"publisher","first-page":"e90899","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":"1659","DOI":"10.1038\/ismej.2014.23","article-title":"Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis","volume":"8","author":"Duran-Pinedo","year":"2014","journal-title":"ISME J."},{"key":"B29","doi-asserted-by":"publisher","first-page":"e28438","DOI":"10.1371\/journal.pone.0028438","article-title":"Correlation network analysis applied to complex biofilm communities","volume":"6","author":"Duran-Pinedo","year":"2011","journal-title":"PLoS ONE"},{"key":"B30","doi-asserted-by":"publisher","first-page":"8015","DOI":"10.1128\/AEM.05933-11","article-title":"Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings","volume":"77","author":"Duytschaever","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"e16384","DOI":"10.1371\/journal.pone.0016384","article-title":"Analysis of the lung microbiome in the \u00e2\u20ac\u0153healthy\u00e2\u20ac\u009d smoker and in COPD","volume":"6","author":"Erb-Downward","year":"2011","journal-title":"PLoS ONE"},{"key":"B32","doi-asserted-by":"publisher","first-page":"e1002606","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial co-occurrence relationships in the human microbiome","volume":"8","author":"Faust","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"4709","DOI":"10.1128\/JB.00566-12","article-title":"Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability","volume":"194","author":"Filkins","year":"2012","journal-title":"J. Bacteriol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"842","DOI":"10.3109\/00365548.2012.695454","article-title":"Assessment of Aspergillus sensitization or persistent carriage as a factor in lung function impairment in cystic fibrosis patients","volume":"44","author":"Fillaux","year":"2012","journal-title":"Scand. J. Infect. Dis."},{"key":"B35","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":"B36","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/nature10947","article-title":"Emerging fungal threats to animal, plant and ecosystem health","volume":"484","author":"Fisher","year":"2012","journal-title":"Nature"},{"key":"B37","doi-asserted-by":"publisher","first-page":"S221","DOI":"10.1513\/AnnalsATS.201401-041PL","article-title":"Infections in \u00e2\u20ac\u0153noninfectious\u00e2\u20ac\u009d lung diseases","volume":"11","author":"Fitzpatrick","year":"2014","journal-title":"Ann. Am. Thorac. Soc."},{"key":"B38","doi-asserted-by":"publisher","first-page":"e45001","DOI":"10.1371\/journal.pone.0045001","article-title":"The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations","volume":"7","author":"Fodor","year":"2012","journal-title":"PLoS ONE"},{"key":"B39","doi-asserted-by":"publisher","first-page":"5122","DOI":"10.1128\/JCM.43.10.5122-5128.2005","article-title":"Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR","volume":"43","author":"Fredricks","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"e1000713","DOI":"10.1371\/journal.ppat.1000713","article-title":"Characterization of the oral fungal microbiome (Mycobiome) in healthy individuals","volume":"6","author":"Ghannoum","year":"2010","journal-title":"PLoS Pathog."},{"key":"B41","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.jcv.2014.02.005","article-title":"Virus and cystic fibrosis: rhinoviruses are associated with exacerbations in adult patients","volume":"60","author":"Goffard","year":"2014","journal-title":"J. Clin. Virol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"e94886","DOI":"10.1371\/journal.pone.0094886","article-title":"Enzymatic treatment of specimens before dna extraction directly influences molecular detection of infectious agents","volume":"9","author":"Goldschmidt","year":"2014","journal-title":"PLoS ONE"},{"key":"B43","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1099\/jmm.0.46510-0","article-title":"Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR","volume":"55","author":"Griffiths","year":"2006","journal-title":"J. Med. Microbiol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1016\/S1569-1993(13)60046-6","article-title":"The role of second-generation sequencing in describing the fungal microbiota in the adult cystic fibrosis (CF) airway and its correlation with clinical phenotype","volume":"12","author":"Harrison","year":"2013","journal-title":"J. Cyst. Fibros."},{"key":"B45","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1126\/science.291.5505.881","article-title":"Molecular analysis of commensal host\u00e2\u20ac\u201cmicrobial relationships in the intestine","volume":"291","author":"Hooper","year":"2001","journal-title":"Science"},{"key":"B46","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.3109\/13693786.2010.529304","article-title":"Fungal respiratory infections in cystic fibrosis: a growing problem","volume":"48","author":"Horr\u00c3\u00a9","year":"2010","journal-title":"Med. Mycol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1007\/s11882-013-0355-y","article-title":"Asthma microbiome studies and the potential for new therapeutic strategies","volume":"13","author":"Huang","year":"2013","journal-title":"Curr. Allergy Asthma Rep."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1164\/rccm.201303-0488WS","article-title":"The role of the lung microbiome in health and disease. a national heart, lung, and blood institute workshop report","volume":"187","author":"Huang","year":"2013","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B49","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1016\/j.tim.2013.04.002","article-title":"The emerging world of the fungal microbiome","volume":"21","author":"Huffnagle","year":"2013","journal-title":"Trends Microbiol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.ijheh.2012.02.011","article-title":"Positive associations between respiratory outcomes and fungal index in rural inhabitants of a representative sample of French dwellings","volume":"216","author":"Hulin","year":"2013","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"B51","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"Huttenhower","year":"2012","journal-title":"Nature"},{"key":"B52","doi-asserted-by":"crossref","first-page":"4565","DOI":"10.2174\/13816128113196660723","article-title":"Role of yeasts in healthy and impaired gut microbiota: the gut mycome","volume":"20","author":"Ianiro","year":"2014","journal-title":"Curr. Pharm. Des."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1126\/science.1221789","article-title":"Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis","volume":"336","author":"Iliev","year":"2012","journal-title":"Science"},{"key":"B54","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature12198","article-title":"Gut metagenome in European women with normal, impaired and diabetic glucose control","volume":"498","author":"Karlsson","year":"2013","journal-title":"Nature"},{"key":"B55","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1378\/chest.12-0954","article-title":"High rhinovirus burden in lower airways of children with cystic fibrosis","volume":"143","author":"Kieninger","year":"2013","journal-title":"Chest"},{"key":"B56","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1016\/j.jaci.2011.12.970","article-title":"Fungi and allergic lower respiratory tract diseases","volume":"129","author":"Knutsen","year":"2012","journal-title":"J. Allergy Clin. Immunol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"e90702","DOI":"10.1371\/journal.pone.0090702","article-title":"Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals","volume":"9","author":"Korpela","year":"2014","journal-title":"PLoS ONE"},{"key":"B58","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1128\/JCM.02204-13","article-title":"Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis","volume":"52","author":"Lim","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.jcf.2012.07.009","article-title":"Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities","volume":"12","author":"Lim","year":"2013","journal-title":"J. Cyst. Fibros."},{"key":"B60","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1111\/j.1439-0507.2011.02108.x","article-title":"Reverse line blot hybridisation screening of Pseudallescheria\/Scedosporium species in patients with cystic fibrosis: RLB of Scedosporium spp. in cystic fibrosis","volume":"54","author":"Lu","year":"2011","journal-title":"Mycoses"},{"key":"B61","doi-asserted-by":"publisher","first-page":"e00251\u00e2\u20ac\u201c12","DOI":"10.1128\/mBio.00251-12","article-title":"Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures","volume":"3","author":"Madan","year":"2012","journal-title":"mBio"},{"key":"B62","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.mmcr.2012.08.004","article-title":"Clinical and microbiological efficacy of micafungin on Geosmithia argillacea infection in a cystic fibrosis patient","volume":"1","author":"Marguet","year":"2012","journal-title":"Med. Mycol. Case Rep."},{"key":"B63","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1038\/nri3769","article-title":"Host\u00e2\u20ac\u201cmicroorganism interactions in lung diseases","volume":"14","author":"Marsland","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1128\/IAI.05162-11","article-title":"Interplay between the gastric bacterial microbiota and Candida albicans during postantibiotic recolonization and gastritis","volume":"80","author":"Mason","year":"2012","journal-title":"Infect. Immun."},{"key":"B65","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/nrmicro3231","article-title":"The co-pathogenesis of influenza viruses with bacteria in the lung","volume":"12","author":"McCullers","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/s12275-014-3425-5","article-title":"Use of denaturing high-performance liquid chromatography (DHPLC) to characterize the bacterial and fungal airway microbiota of cystic fibrosis patients","volume":"52","author":"Mounier","year":"2014","journal-title":"J. Microbiol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"e1003996","DOI":"10.1371\/journal.ppat.1003996","article-title":"Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi","volume":"10","author":"Mukherjee","year":"2014","journal-title":"PLoS Pathog."},{"key":"B68","doi-asserted-by":"publisher","first-page":"59","DOI":"10.2436\/20.1501.01.111","article-title":"Discrimination between live and dead cells in bacterial communities from environmental water samples analyzed by 454 pyrosequencing","volume":"13","author":"Nocker","year":"2010","journal-title":"Int. Microbiol."},{"key":"B69","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1128\/IAI.73.1.30-38.2005","article-title":"Development of allergic airway disease in mice following antibiotic therapy and fungal microbiota increase: role of host genetics, antigen and interleukin-13","volume":"73","author":"Noverr","year":"2005","journal-title":"Infect. Immun."},{"key":"B70","doi-asserted-by":"publisher","first-page":"4996","DOI":"10.1128\/IAI.72.9.4996-5003.2004","article-title":"Role of antibiotics and fungal microbiota in driving pulmonary allergic responses","volume":"72","author":"Noverr","year":"2004","journal-title":"Infect. Immun."},{"key":"B71","doi-asserted-by":"publisher","first-page":"73","DOI":"10.3390\/d5010073","article-title":"454 Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome","volume":"5","author":"Orgiazzi","year":"2013","journal-title":"Diversity"},{"key":"B72","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1111\/j.1439-0507.2012.02184.x","article-title":"Lobomycosis: an emerging disease in humans and delphinidae","volume":"55","author":"Paniz-Mondolfi","year":"2012","journal-title":"Mycoses"},{"key":"B73","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.funbio.2011.11.004","article-title":"DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology","volume":"116","author":"Pashley","year":"2012","journal-title":"Fungal Biol."},{"key":"B74","doi-asserted-by":"publisher","first-page":"e44279","DOI":"10.1371\/journal.pone.0044279","article-title":"Evaluation of the ISO Standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure","volume":"7","author":"Plassart","year":"2012","journal-title":"PLoS ONE"},{"key":"B75","doi-asserted-by":"publisher","first-page":"e1003371","DOI":"10.1371\/journal.ppat.1003371","article-title":"Asthma and the diversity of fungal spores in air","volume":"9","author":"Pringle","year":"2013","journal-title":"PLoS Pathog."},{"key":"B76","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/1471-2180-14-130","article-title":"Polymicrobial airway bacterial communities in adult bronchiectasis patients","volume":"14","author":"Purcell","year":"2014","journal-title":"BMC Microbiol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1016\/j.jaci.2012.05.030","article-title":"Infant origins of childhood asthma associated with specific molds","volume":"130","author":"Reponen","year":"2012","journal-title":"J. Allergy Clin. Immunol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.anai.2011.04.018","article-title":"High environmental relative moldiness index during infancy as a predictor of asthma at 7 years of age","volume":"107","author":"Reponen","year":"2011","journal-title":"Ann. Allergy Asthma Immunol."},{"key":"B79","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1038\/ismej.2012.145","article-title":"Reducing bias in bacterial community analysis of lower respiratory infections","volume":"7","author":"Rogers","year":"2013","journal-title":"ISME J."},{"key":"B80","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1513\/AnnalsATS.201310-335OC","article-title":"A novel microbiota stratification system predicts future exacerbations in bronchiectasis","volume":"11","author":"Rogers","year":"2014","journal-title":"Ann. Am. Thorac. Soc."},{"key":"B81","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.1097\/CCM.0b013e31819629d2","article-title":"Candida albicans impairs macrophage function and facilitates Pseudomonas aeruginosa pneumonia in rat","volume":"37","author":"Roux","year":"2009","journal-title":"Crit. Care Med."},{"key":"B82","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":"B83","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1097\/MCP.0b013e328358d50b","article-title":"Effects of Aspergillus fumigatus colonization on lung function in cystic fibrosis","volume":"18","author":"Speirs","year":"2012","journal-title":"Curr. Opin. Pulm. Med."},{"key":"B84","doi-asserted-by":"publisher","first-page":"2317","DOI":"10.1101\/gr.096651.109","article-title":"The NIH Human Microbiome Project","volume":"19","author":"Peterson","year":"2009","journal-title":"Genome Res."},{"key":"B85","doi-asserted-by":"publisher","first-page":"4153","DOI":"10.1113\/jphysiol.2009.174136","article-title":"The core gut microbiome, energy balance and obesity","volume":"587","author":"Turnbaugh","year":"2009","journal-title":"J. Physiol."},{"key":"B86","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/nri3684","article-title":"The mycobiota: interactions between commensal fungi and the host immune system","volume":"14","author":"Underhill","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"B87","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1097\/QCO.0000000000000005","article-title":"Azole resistance in Aspergillus fumigatus: a growing public health concern","volume":"26","author":"Vermeulen","year":"2013","journal-title":"Curr. Opin. Infect. Dis."},{"key":"B88","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1016\/j.mib.2006.06.001","article-title":"Fungal\u00e2\u20ac\u201cbacterial interactions: a mixed bag of mingling microbes","volume":"9","author":"Wargo","year":"2006","journal-title":"Curr. Opin. Microbiol."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1164\/rccm.201312-2129PP","article-title":"The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. parallels from island biogeography","volume":"189","author":"Whiteson","year":"2014","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B90","doi-asserted-by":"publisher","first-page":"40","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":"B91","doi-asserted-by":"publisher","first-page":"4547","DOI":"10.1073\/pnas.1000089107","article-title":"Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity","volume":"108","author":"Willner","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B92","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1165\/rcmb.2011-0253OC","article-title":"Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung","volume":"46","author":"Willner","year":"2012","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"69","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":"B94","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciu225","article-title":"Adenovirus species c is associated with chronic suppurative lung diseases in children","author":"Wurzel","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"B95","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1111\/cmi.12216","article-title":"Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response: Candida-streptococcal synergy in oral thrush","volume":"16","author":"Xu","year":"2014","journal-title":"Cell. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"deposited":{"date-parts":[[2017,6,23]],"date-time":"2017-06-23T01:30:15Z","timestamp":1498181415000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/Article\/10.3389\/fmicb.2015.00089\/abstract"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,13]]},"references-count":95,"URL":"https:\/\/doi.org\/10.3389\/fmicb.2015.00089","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,2,13]]}}}