Hassall A: On the development of Torulæ in the urine, and on the relation of these fungi to albuminous and saccharine urine. Med Chir Trans 1853, 36: 23-78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chiene J, Ewart JC: Do bacteria or their germs exist in the organs of healthy living animals? J Anat Physiol 1878, 12: 448-453.
CAS
PubMed
PubMed Central
Google Scholar
Relman DA: New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J Infect Dis 2002, 186: S254-S258. 10.1086/344935
Article
PubMed
Google Scholar
Mitreva M: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486: 207-214. 10.1038/nature11234
Article
Google Scholar
Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C: The NIH human microbiome project. Genome Res 2009, 19: 2317-2323.
Article
PubMed
PubMed Central
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464: 59-65. 10.1038/nature08821
Article
CAS
PubMed
PubMed Central
Google Scholar
Moyes DL, Naglik JR: The mycobiome: influencing IBD severity. Cell Host Microbe 2012, 11: 551-552. 10.1016/j.chom.2012.05.009
Article
CAS
PubMed
Google Scholar
Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM: Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010, 6: e1000713. 10.1371/journal.ppat.1000713
Article
PubMed
PubMed Central
Google Scholar
Perfect JR, Casadevall A: Fungal molecular pathogenesis: what can it do and why do we need it? In Molecular Principles of Fungal Pathogenesis. Edited by: Heitman J, Filler SG, Edwards JE, Mitchell AP. Washington DC: ASM Press; 2006:3-12.
Chapter
Google Scholar
Chen Y, Chen Z, Guo R, Chen N, Lu H, Huang S, Wang J, Li L: Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagn Micr Infec Dis 2011, 70: 492-498. 10.1016/j.diagmicrobio.2010.04.005
Article
Google Scholar
Nelson A, De Soyza A, Bourke S, Perry J, Cummings S: Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis. Lett Appl Microbiol 2010, 51: 272-277. 10.1111/j.1472-765X.2010.02891.x
Article
CAS
PubMed
Google Scholar
Harrison MJ, Twomey KB, McCarthy Y, O'Connell OJ, Alston M, Febrer M, Murphy DM, Ryan RP, Plant BJ: Fungal microbiota in the adult cystic fibrosis (CF) airway: characterization by second-generation sequencing and correlation with standard culture-based methods and clinical phenotype. Ir J Med Sci 2012, 181: S369-S437.
Google Scholar
Kuehbacher T, Ott SJ, Helwig U, Mimura T, Rizzello F, Kleessen B, Gionchetti P, Blaut M, Campieri M, Fölsch UR, Kamm MA, Schreiber S: Bacterial and fungal microbiota in relation to probiotic therapy (VSL# 3) in pouchitis. Gut 2006, 55: 833-841. 10.1136/gut.2005.078303
Article
CAS
Google Scholar
Ott SJ, Kühbacher T, Musfeldt M, Rosenstiel P, Hellmig S, Rehman A, Drews O, Weichert W, Timmis KN, Schreiber S: Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol 2008, 43: 831-841. 10.1080/00365520801935434
Article
CAS
PubMed
Google Scholar
Deborah AH, Roberto K: Fungal-bacterial interactions. In Molecular Principles of Fungal Pathogenesis. Edited by: Heitman J, Filler SG, Edwards JE, Mitchell AP. Washington DC: ASM Press; 2006:261-269.
Google Scholar
Cutler JE, Deepe GS Jr, Klein BS: Advances in combating fungal diseases: vaccines on the threshold. Nat Rev Microbiol 2007, 5: 13-28. 10.1038/nrmicro1537
Article
CAS
PubMed
PubMed Central
Google Scholar
Marloth RH: An apparatus for the study of matforming fungi in culture solutions. Science 1929, 69: 524-525. 10.1126/science.69.1794.524
Article
CAS
PubMed
Google Scholar
Beck JM, Young VB, Huffnagle GB: The microbiome of the lung. Transl Res 2012, 160: 258-266. 10.1016/j.trsl.2012.02.005
Article
CAS
PubMed
PubMed Central
Google Scholar
Delhaes L, Monchy S, Fréalle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E: The airway microbiota in cystic fibrosis: a complex fungal and bacterial community-implications for therapeutic management. PLoS One 2012, 7: e36313. 10.1371/journal.pone.0036313
Article
CAS
PubMed
PubMed Central
Google Scholar
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci USA 2012, 109: 6241-6246. 10.1073/pnas.1117018109
Article
CAS
PubMed
PubMed Central
Google Scholar
Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel C, Hill DA, Artis D, Bachman MA: A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol 2012, 13: R60. 10.1186/gb-2012-13-7-r60
Article
PubMed
PubMed Central
Google Scholar
Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, NIH Intramural Sequencing Center Comparative Sequencing Program, Kong HH, Segre JA: Topographic diversity of fungal and bacterial communities in human skin. Nature 2013, 498: 367-370. 10.1038/nature12171
Article
CAS
PubMed
PubMed Central
Google Scholar
Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H: ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 2010, 10: 189-197. 10.1186/1471-2180-10-189
Article
PubMed
PubMed Central
Google Scholar
Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, DeSantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z: Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol 2010, 16: 4135-4144. 10.3748/wjg.v16.i33.4135
Article
CAS
PubMed
PubMed Central
Google Scholar
Jumpstart Consortium Human Microbiome Project Data Generation Working Group: Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One 2012, 7: e39315. 10.1371/journal.pone.0039315
Article
PubMed Central
Google Scholar
Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD: Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol 2011, 77: 3846-3852. 10.1128/AEM.02772-10
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R: Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012, 6: 1621-1624. 10.1038/ismej.2012.8
Article
CAS
PubMed
PubMed Central
Google Scholar
Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A: Microbial 16S rRNA ion tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 2012, 91: 80-88. 10.1016/j.mimet.2012.07.008
Article
CAS
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7: 335-336. 10.1038/nmeth.f.303
Article
CAS
PubMed
PubMed Central
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009, 75: 7537-7541. 10.1128/AEM.01541-09
Article
CAS
PubMed
PubMed Central
Google Scholar
White JR, Maddox C, White O, Angiuoli SV, Fricke WF: CloVR-ITS: automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome 2013, 1: 1-11. 10.1186/2049-2618-1-1
Article
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013, 41: D590-D596. 10.1093/nar/gks1219
Article
CAS
PubMed
PubMed Central
Google Scholar
Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T: The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol 2010, 186: 281-285. 10.1111/j.1469-8137.2009.03160.x
Article
PubMed
Google Scholar
Matsen F, Kodner R, Armbrust EV: pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 2010, 11: 538. 10.1186/1471-2105-11-538
Article
PubMed
PubMed Central
Google Scholar
Sellart-Altisent M, Torres-Rodríguez JM, Gómez de Ana S, Alvarado-Ramírez E: Nasal fungal microbiota in allergic and healthy subjects. Rev Iberoam Micol 2007, 24: 125-130. 10.1016/S1130-1406(07)70027-X
Article
PubMed
Google Scholar
Noverr MC, Falkowski NR, McDonald RA, McKenzie AN, Huffnagle GB: Development of allergic airway disease in mice following antibiotic therapy and fungal microbiota increase: role of host genetics, antigen, and interleukin-13. Infect Immun 2005, 73: 30-38. 10.1128/IAI.73.1.30-38.2005
Article
CAS
PubMed
PubMed Central
Google Scholar
Brenchley JM, Price DA, Schacker TW, Asher TE, Silvestri G, Rao S, Kazzaz Z, Bornstein E, Lambotte O, Altmann D, Blazar BR, Rodriguez B, Teixeira-Johnson L, Landay A, Martin JN, Hecht FM, Picker LJ, Lederman MM, Deeks SG, Douek DC: Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med 2006, 12: 1365-1371.
Article
CAS
PubMed
Google Scholar
Morris A, Hillenbrand M, Finkelman M, George MP, Singh V, Kessinger C, Lucht L, Busch M, McMahon D, Weinman R: Serum (1→3)-β-D-Glucan levels in HIV-infected individuals are associated with immunosuppression, inflammation, and cardiopulmonary function. J Acquir Immune Defic Syndr 2012, 61: 462-468. 10.1097/QAI.0b013e318271799b
Article
CAS
PubMed
PubMed Central
Google Scholar
Darling WM: Co-cultivation of mycobacteria and fungus. Lancet 1976, 2: 740.
Article
CAS
PubMed
Google Scholar
Kerr J: Inhibition of fungal growth by Pseudomonas aeruginosa and Pseudomonas cepacia isolated from patients with cystic fibrosis. J Infect 1994, 28: 305-310.
Article
CAS
PubMed
Google Scholar
Adam B, Baillie GS, Douglas LJ: Mixed species biofilms of Candida albicans and Staphylococcus epidermidis . J Med Microbiol 2002, 51: 344-349.
Article
PubMed
Google Scholar
Grice EA, Segre JA: The skin microbiome. Nat Rev Microbiol 2011, 9: 244-253. 10.1038/nrmicro2537
Article
CAS
PubMed
PubMed Central
Google Scholar
Jacobs PH: An overview: antifungal treatment. In Fungal Disease: Biology, Immunology, and Diagnosis. Edited by: Jacobs PH, Nall L. New York: CRC Press; 1997:1-5.
Google Scholar
Nagata R, Nagano H, Ogishima D, Nakamura Y, Hiruma M, Sugita T: Transmission of the major skin microbiota, Malassezia , from mother to neonate. Pediatr Int 2012, 54: 350-355. 10.1111/j.1442-200X.2012.03563.x
Article
CAS
PubMed
Google Scholar
Jawhara S, Mogensen E, Maggiotto F, Fradin C, Sarazin A, Dubuquoy L, Maes E, Guérardel Y, Janbon G, Poulain D: A murine model of dextran sulfate sodium-induced colitis reveals Candida glabrata virulence and contribution of β-mannosyltransferases. J Biol Chem 2012, 287: 11313-11324. 10.1074/jbc.M111.329300
Article
CAS
PubMed
PubMed Central
Google Scholar
Netea MG, Gow NA, Munro CA, Bates S, Collins C, Ferwerda G, Hobson RP, Bertram G, Hughes HB, Jansen T, Jacobs L, Buurman ET, Gijzen K, Williams DL, Torensma R, McKinnon A, MacCallum DM, Odds FC, Van der Meer JW, Brown AJ, Kullberg BJ: Immune sensing of Candida albicans requires cooperative recognition of mannans and glucans by lectin and Toll-like receptors. J Clin Invest 2006, 116: 1642-1650. 10.1172/JCI27114
Article
CAS
PubMed
PubMed Central
Google Scholar
Saijo S, Ikeda S, Yamabe K, Kakuta S, Ishigame H, Akitsu A, Fujikado N, Kusaka T, Kubo S, Chung S-h, Komatsu R, Miura N, Adachi Y, Ohno N, Shibuya K, Yamamoto N, Kawakami K, Yamasaki S, Saito T, Akira S, Iwakura Y: Dectin-2 recognition of α-mannans and induction of Th17 cell differentiation is essential for host defense against Candida albicans . Immunity 2010, 32: 681-691. 10.1016/j.immuni.2010.05.001
Article
CAS
PubMed
Google Scholar
Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M: Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012, 336: 1314-1317. 10.1126/science.1221789
Article
CAS
PubMed
PubMed Central
Google Scholar
van der Velden WJ, Netea MG, de Haan AF, Huls GA, Donnelly JP, Blijlevens N: The role of the mycobiome in human acute graft-versus-host disease. Biol Blood Marrow Transplant 2013, 19: 329-332. 10.1016/j.bbmt.2012.11.008
Article
CAS
PubMed
Google Scholar
Zhang E, Tanaka T, Tajima M, Tsuboi R, Nishikawa A, Sugita T: Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects. Microbiol Immunol 2011, 55: 625-632. 10.1111/j.1348-0421.2011.00364.x
Article
CAS
PubMed
Google Scholar
Paulino LC, Tseng CH, Blaser MJ: Analysis of Malassezia microbiota in healthy superficial human skin and in psoriatic lesions by multiplex real-time PCR. FEMS Yeast Res 2008, 8: 460-471. 10.1111/j.1567-1364.2008.00359.x
Article
CAS
PubMed
Google Scholar
McFarland L, Bernasconi P: Saccharomyces boulardii : a review of an innovative biotherapeutic agent. Microb Ecol Health Dis 1993, 6: 157-171. 10.3109/08910609309141323
Article
Google Scholar
Romani L: Immunity to fungal infections. Nat Rev Immunol 2011, 11: 275-288. 10.1038/nri2939
Article
CAS
PubMed
Google Scholar
Cho I, Blaser MJ: The human microbiome: at the interface of health and disease. Nat Rev Genet 2012, 13: 260-270.
CAS
PubMed
PubMed Central
Google Scholar
Ostrosky-Zeichner L, Casadevall A, Galgiani JN, Odds FC, Rex JH: An insight into the antifungal pipeline: selected new molecules and beyond. Nat Rev Drug Discov 2010, 9: 719-727. 10.1038/nrd3074
Article
CAS
PubMed
Google Scholar
Fleuridor R, Zhong Z, Pirofski L: A human IgM monoclonal antibody prolongs survival of mice with lethal cryptococcosis. J Infect Dis 1998, 178: 1213-1216. 10.1086/515688
Article
CAS
PubMed
Google Scholar
Moragues MD, Omaetxebarria MJ, Elguezabal N, Sevilla MJ, Conti S, Polonelli L, Pontón J: A monoclonal antibody directed against a Candida albicans cell wall mannoprotein exerts three anti- C. albicans activities. Infect Immun 2003, 71: 5273-5279. 10.1128/IAI.71.9.5273-5279.2003
Article
CAS
PubMed
PubMed Central
Google Scholar
Nosanchuk JD, Steenbergen JN, Shi L, Deepe GS, Casadevall A: Antibodies to a cell surface histone-like protein protect against Histoplasma capsulatum . J Clin Invest 2003, 112: 1164-1175.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaturvedi AK, Kavishwar A, Keshava GS, Shukla P: Monoclonal immunoglobulin G1 directed against Aspergillus fumigatus cell wall glycoprotein protects against experimental murine aspergillosis. Clin Diagn Lab Immunol 2005, 12: 1063-1068.
CAS
PubMed
PubMed Central
Google Scholar
Korabečná M, Liška V, Fajfrlik K: PrimersITS1, ITS2 andITS4 detect the intraspecies variability in the internal transcribed spacers and 5.8 S rRNA gene region in clinical isolates of fungi. Folia Microbiol 2003, 48: 233-238. 10.1007/BF02930961
Article
Google Scholar
Esteve-Zarzoso B, Belloch C, Uruburu F, Querol A: Identification of yeasts by RFLP analysis of the 5.8 S rRNA gene and the two ribosomal internal transcribed spacers. Int J Syst Bacteriol 1999, 49: 329-337. 10.1099/00207713-49-1-329
Article
CAS
PubMed
Google Scholar
Scupham AJ, Presley LL, Wei B, Bent E, Griffith N, McPherson M, Zhu F, Oluwadara O, Rao N, Braun J: Abundant and diverse fungal microbiota in the murine intestine. Appl Environ Microbiol 2006, 72: 793-801. 10.1128/AEM.72.1.793-801.2006
Article
CAS
PubMed
PubMed Central
Google Scholar
Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, Väin E, Saarma I, Salumets A, Donders GG, Metsis M: Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age Estonian women. PLoS One 2013, 8: e54379. 10.1371/journal.pone.0054379
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M: Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012, 2012: 1-11.
PubMed
Google Scholar
Amend AS, Seifert KA, Samson R, Bruns TD: Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci USA 2010, 107: 13748-13753. 10.1073/pnas.1000454107
Article
CAS
PubMed
PubMed Central
Google Scholar
Park HK, Ha M-H, Park S-G, Kim MN, Kim BJ, Kim W: Characterization of the fungal microbiota (mycobiome) in healthy and dandruff-afflicted human scalps. PLoS One 2012, 7: e32847. 10.1371/journal.pone.0032847
Article
CAS
PubMed
PubMed Central
Google Scholar
Bosco VL, Birman EG, Cury AE, Paula CR: Yeasts from the oral cavity of children with AIDS: exoenzyme production and antifungal resistance. Pediatr Dent 2003, 17: 217-222.
Google Scholar
Paulino LC, Tseng C-H, Strober BE, Blaser MJ: Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol 2006, 44: 2933-2941. 10.1128/JCM.00785-06
Article
CAS
PubMed
PubMed Central
Google Scholar
Purim K, Bordignon G, Queiroz-Telles F: Fungal infection of the feet in soccer players and non-athlete individuals. Rev Iberoam Micol 2005, 22: 34-38. 10.1016/S1130-1406(05)70004-8
Article
PubMed
Google Scholar
Santos PM, Melo CM, Martins SA, Chaves Ade A, Sá DSP, Santos RC: Study of ocular fungal microbiota in patients with Hansen's disease and in individuals who deal with them. Arq Bras Oftalmol 2006, 69: 915-918. 10.1590/S0004-27492006000600022
Article
PubMed
Google Scholar
Thomas JG, Ramage G, Lopez-Ribot JL: Biofilms and implant infections. In Microbial Biofilms. Edited by: Ghannoum MA, O'Toole GA. Washington DC: ASM Press; 2004:269-293.
Chapter
Google Scholar
Grimaudo N, Nesbitt W: Coaggregation of Candida albicans with oral Fusobacterium species. Oral Microbiol Immunol 1997, 12: 168-173. 10.1111/j.1399-302X.1997.tb00374.x
Article
CAS
PubMed
Google Scholar
Holmes AR, McNAB R, Jenkinson HF: Candida albicans binding to the oral bacterium Streptococcus gordonii involves multiple adhesin-receptor interactions. Infect Immun 1996, 64: 4680-4685.
CAS
PubMed
PubMed Central
Google Scholar
Branting C, Sund M-L, Linder L: The influence of Streptococcus mutans on adhesion of Candida albicans to acrylic surfaces in vitro . Arch Oral Biol 1989, 34: 347-353. 10.1016/0003-9969(89)90108-8
Article
CAS
PubMed
Google Scholar
Wagner RD, Pierson C, Warner T, Dohnalek M, Hilty M, Balish E: Probiotic effects of feeding heat-killed Lactobacillus acidophilus and Lactobacillus casei to Candida albicans -colonized immunodeficient mice. J Food Prot 2000, 63: 638-644.
CAS
PubMed
Google Scholar
Boris S, Barbés C: Role played by Lactobacilli in controlling the population of vaginal pathogens. Microbes Infect 2000, 2: 543-546. 10.1016/S1286-4579(00)00313-0
Article
CAS
PubMed
Google Scholar