Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis

Microbiome

Volumn 2, Issue 1, 2014, Pages

  Willger, Sven D ^a   Grim, Sharon L ^b,d   Dolben, Emily L ^a   Shipunova, Anna ^b   Hampton, Thomas H ^a   Morrison, Hilary G ^b   Filkins, Laura M ^a   O'Toole, George A ^a   Moulton, Lisa A ^c   Ashare, Alix ^c   Sogin, Mitchell L ^b   Hogan, Deborah A ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

^b MARINE BIOLOGICAL LABORATORY   (United States)

^c DARTMOUTH HITCHCOCK MEDICAL CENTER   (United States)

^d UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMICROBIAL THERAPY; ARTICLE; CANDIDA; CLINICAL ARTICLE; CYSTIC FIBROSIS; FUNGAL COMMUNITY; GENE SEQUENCE; HUMAN; MALASSEZIA; MICROBIOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; SPUTUM ANALYSIS;

BACTERIA (MICROORGANISMS); CANDIDA; FUNGI; MALASSEZIA;

EID: 84923101545     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-2-40     Document Type: Article

References (104)

1. Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF, McGrath SJ, Muhlebach MS, Boucher RC, Cardwell C, Doering G, Elborn JS, Wolfgang MC. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011, 66(7):579-584. 10.1136/thx.2010.137281, 21270069.
2. Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O'Toole GA. Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol 2012, 194(17):4709-4717. 10.1128/JB.00566-12, 3415522, 22753064.
3. Spilker T, Vandamme P, Lipuma JJ. A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J Clin Microbiol 2012, 50(9):3010-3015. 10.1128/JCM.00814-12, 3421806, 22785192.
4. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A 2012, 109(15):5809-5814. 10.1073/pnas.1120577109, 3326496, 22451929.
5. Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci U S A 2008, 105(39):15070-15075. 10.1073/pnas.0804326105, 2567494, 18812504.
6. Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, Wolfgang MC. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One 2012, 7(9):e45001. 10.1371/journal.pone.0045001, 3458854, 23049765.
7. Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, Hoffman L, Daniels TW, Patel N, Forbes B, Bruce KD. Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax 2012, 67(10):867-873. 10.1136/thoraxjnl-2011-200932, 22707521.
8. Leclair LW, Hogan DA. Mixed bacterial-fungal infections in the CF respiratory tract. Med Mycol 2010, 48(O1):S125-S132. 10.3109/13693786.2010.521522, 21067324.
9. Morales DK, Hogan DA. Candida albicans interactions with bacteria in the context of human health and disease. PLoS Pathog 2010, 6(4):e1000886. 10.1371/journal.ppat.1000886, 2861711, 20442787.
10. Peleg AY, Hogan DA, Mylonakis E. Medically important bacterial-fungal interactions. Nat Rev Microbiol 2010, 8(5):340-349. 10.1038/nrmicro2313, 20348933.
11. Hoppe JE, Theurer-Mainka U, Stern M. Comparison of three methods for culturing throat swabs from cystic fibrosis patients. J Clin Microbiol 1995, 33(7):1896-1898. 228293, 7665666.
12. Bakare N, Rickerts V, Bargon J, Just-Nubling G. Prevalence of Aspergillus fumigatus and other fungal species in the sputum of adult patients with cystic fibrosis. Mycoses 2003, 46(1-2):19-23.
13. Haase G, Skopnik H, Groten T, Kusenbach G, Posselt HG. Long-term fungal cultures from sputum of patients with cystic fibrosis. Mycoses 1991, 34(9-10):373-376.
14. Hughes WT, Kim HK. Mycoflora in cystic fibrosis: some ecologic aspects of Pseudomonas aeruginosa and Candida albicans. Mycopathol Mycol Appl 1973, 50(3):261-269. 10.1007/BF02053377, 4199669.
15. Bauernfeind A, Bertele RM, Harms K, Horl G, Jungwirth R, Petermuller C, Przyklenk B, Weisslein-Pfister C. Qualitative and quantitative microbiological analysis of sputa of 102 patients with cystic fibrosis. Infection 1987, 15(4):270-277. 10.1007/BF01644137, 3117700.
16. Chotirmall SH, O'Donoghue E, Bennett K, Gunaratnam C, O'Neill SJ, McElvaney NG. Sputum Candida albicans presages FEV1 decline and hospitalized exacerbations in cystic fibrosis. Chest 2010, 138(5):1186-1195. 10.1378/chest.09-2996, 20472859.
17. Doern GV, Brogden-Torres B. Optimum use of selective plated media in primary processing of respiratory tract specimens from patients with cystic fibrosis. J Clin Microbiol 1992, 30(10):2740-2742. 270512, 1400978.
18. Güngör O, Tamay Z, Güler N, Erturan Z. Frequency of fungi in respiratory samples from Turkish cystic fibrosis patients. Mycoses 2012, 56(2):123-129.
19. Delhaes L, Monchy S, Frealle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E, Sime-Ngando T, Chabe M, Viscogliosi E. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community-implications for therapeutic management. PLoS One 2012, 7(4):e36313. 10.1371/journal.pone.0036313, 3338676, 22558432.
20. Navarro J, Rainisio M, Harms HK, Hodson ME, Koch C, Mastella G, Strandvik B, McKenzie SG. Factors associated with poor pulmonary function: cross-sectional analysis of data from the ERCF. European Epidemiologic Registry of Cystic Fibrosis. Eur Respir J 2001, 18(2):298-305. 10.1183/09031936.01.00068901, 11529288.
21. Storey DG, Ujack EE, Rabin HR, Mitchell I. Pseudomonas aeruginosa lasR transcription correlates with the transcription of lasA, lasB, and toxA in chronic lung infections associated with cystic fibrosis. Infect Immun 1998, 66(6):2521-2528. 108233, 9596711.
22. Amin R, Dupuis A, Aaron SD, Ratjen F. The effect of chronic infection with Aspergillus fumigatus on lung function and hospitalization in patients with cystic fibrosis. Chest 2010, 137(1):171-176. 10.1378/chest.09-1103, 19567494.
23. Masoud-Landgraf L, Badura A, Eber E, Feierl G, Marth E, Buzina W. Modified culture method detects a high diversity of fungal species in cystic fibrosis patients. Med Mycol 2013, 52(2):179-186.
24. Parize P, Billaud S, Bienvenu AL, Bourdy S, le Pogam MA, Reix P, Picot S, Robert R, Lortholary O, Bouchara JP, Durieu I. Impact of Scedosporium apiospermum complex seroprevalence in patients with cystic fibrosis. J Cyst Fibros 2014, doi:10.1016/j.jcf.2014.01.011.
25. Bernhardt A, Sedlacek L, Wagner S, Schwarz C, Wurstl B, Tintelnot K. Multilocus sequence typing of Scedosporium apiospermum and Pseudallescheria boydii isolates from cystic fibrosis patients. J Cyst Fibros 2013, 12(6):592-598. 10.1016/j.jcf.2013.05.007, 23764085.
26. Packeu A, Lebecque P, Rodriguez-Villalobos H, Boeras A, Hendrickx M, Bouchara JP, Symoens F. Molecular typing and antifungal susceptibility of Exophiala isolates from patients with cystic fibrosis. J Med Microbiol 2012, 61(Pt 9):1226-1233.
27. Hickey PW, Sutton DA, Fothergill AW, Rinaldi MG, Wickes BL, Schmidt HJ, Walsh TJ. Trichosporon mycotoxinivorans, a novel respiratory pathogen in patients with cystic fibrosis. J Clin Microbiol 2009, 47(10):3091-3097. 10.1128/JCM.00460-09, 2756937, 19656976.
28. Nagano Y, Elborn JS, Millar BC, Walker JM, Goldsmith CE, Rendall J, Moore JE. Comparison of techniques to examine the diversity of fungi in adult patients with cystic fibrosis. Med Mycol 2010, 48(1):166-76 e1. 10.3109/13693780903127506, 19672783.
29. Respiratory cultures from Cystic Fibrosis patients, in Clinical Microbiology Procedures Handbook 2010, ASM Press, Garcia L.
30. Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O'Toole GA. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome 2013, 1(1):27. 10.1186/2049-2618-1-27, 3971630, 24451123.
31. Jubin V, Ranque S, Stremler N, Le B, Sarles J, Dubus JC. Risk factors for Aspergillus colonization and allergic bronchopulmonary aspergillosis in children with cystic fibrosis. Pediatr Pulmonol 2010, 45(8):764-771. 10.1002/ppul.21240, 20597074.
32. Burns J, Van Dalfsen J, Shawar R, Otto K, Garber R, Quan J, Montgomery A, Albers G, Ramsey B, Smith A. Effect of intermittent administration of inhaled tobramycin on respiratory microbial flora in patients with cystic fibrosis. J Infect Dis 1999, 179:1190-1196. 10.1086/314727, 10191222.
33. Cheer SM, Waugh J, Noble S. Inhaled tobramycin (TOBI): a review of its use in the management of Pseudomonas aeruginosa infections in patients with cystic fibrosis. Drugs 2003, 63(22):2501-2520. 10.2165/00003495-200363220-00015, 14609360.
34. Sudfeld CR, Dasenbrook EC, Merz WG, Carroll KC, Boyle MP. Prevalence and risk factors for recovery of filamentous fungi in individuals with cystic fibrosis. J Cyst Fibros 2010, 9(2):110-116. 10.1016/j.jcf.2009.11.010, 4113956, 20045384.
35. Kerr J. Inhibition of fungal growth by Pseudomonas aeruginosa and Pseudomonas cepacia isolated from patients with cystic fibrosis. J Infect 1994, 28:305-310. 10.1016/S0163-4453(94)91943-7, 7522262.
36. Mastella G, Rainisio M, Harms HK, Hodson ME, Koch C, Navarro J, Strandvik B, McKenzie SG. Allergic bronchopulmonary aspergillosis in cystic fibrosis. A European epidemiological study. Epidemiologic Registry of Cystic Fibrosis. Eur Respir J 2000, 16(3):464-471. 10.1034/j.1399-3003.2000.016003464.x, 11028661.
37. Krcmery V, Matejicka F, Pichnova E, Jurga L, Sulcova M, Kunova A, West D. Documented fungal infections after prophylaxis or therapy with wide spectrum antibiotics: relationship between certain fungal pathogens and particular antimicrobials?. J Chemother 1999, 11(5):385-390. 10.1179/joc.1999.11.5.385, 10632385.
38. Hebert C, Villaran R, Tolentino J, Best L, Boonlayangoor S, Pitrak D, Lin M, Weber SG. Prior antimicrobial exposure and the risk for bloodstream infection with fluconazole-non-susceptible Candida strains. Scand J Infect Dis 2010, 42(6-7):506-509.
39. Wey SB, Mori M, Pfaller MA, Woolson RF, Wenzel RP. Risk factors for hospital-acquired candidemia. A matched case-control study. Arch Intern Med 1989, 149(10):2349-2353. 10.1001/archinte.1989.00390100145030, 2802900.
40. Charles PE, Dalle F, Aube H, Doise JM, Quenot JP, Aho LS, Chavanet P, Blettery B. Candida spp. colonization significance in critically ill medical patients: a prospective study. Intensive Care Med 2005, 31(3):393-400. 10.1007/s00134-005-2571-y, 15711782.
41. Soysa NS, Samaranayake LP, Ellepola AN. Antimicrobials as a contributory factor in oral candidosis-a brief overview. Oral Dis 2008, 14(2):138-143. 10.1111/j.1601-0825.2006.01357.x, 18302673.
42. Xu J, Schwartz K, Bartoces M, Monsur J, Severson RK, Sobel JD. Effect of antibiotics on vulvovaginal candidiasis: a MetroNet study. J Am Board Fam Med 2008, 21(4):261-268. 10.3122/jabfm.2008.04.070169, 18612052.
43. Samonis G, Anastassiadou H, Dassiou M, Tselentis Y, Bodey GP. Effects of broad-spectrum antibiotics on colonization of gastrointestinal tracts of mice by Candida albicans. Antimicrob Agents Chemother 1994, 38(3):602-603. 10.1128/AAC.38.3.602, 284504, 8203861.
44. Samonis G, Gikas A, Toloudis P, Maraki S, Vrentzos G, Tselentis Y, Tsaparas N, Bodey G. Prospective study of the impact of broad-spectrum antibiotics on the yeast flora of the human gut. Eur J Clin Microbiol Infect Dis 1994, 13(8):665-667. 10.1007/BF01973996, 7813500.
45. Giuliano M, Barza M, Jacobus NV, Gorbach SL. Effect of broad-spectrum parenteral antibiotics on composition of intestinal microflora of humans. Antimicrob Agents Chemother 1987, 31(2):202-206. 10.1128/AAC.31.2.202, 174692, 3566249.
46. Leaw SN, Chang HC, Sun HF, Barton R, Bouchara JP, Chang TC. Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions. J Clin Microbiol 2006, 44(3):693-699. 10.1128/JCM.44.3.693-699.2006, 1393093, 16517841.
47. Pryce TM, Palladino S, Kay ID, Coombs GW. Rapid identification of fungi by sequencing the ITS1 and ITS2 regions using an automated capillary electrophoresis system. Med Mycol 2003, 41(5):369-381. 10.1080/13693780310001600435, 14653513.
48. 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(1):e1000713. 10.1371/journal.ppat.1000713, 2795202, 20072605.
49. Ferrer C, Colom F, Frases S, Mulet E, Abad JL, Alio JL. Detection and identification of fungal pathogens by PCR and by ITS2 and 5.8S ribosomal DNA typing in ocular infections. J Clin Microbiol 2001, 39(8):2873-2879. 10.1128/JCM.39.8.2873-2879.2001, 88253, 11474006.
50. Borman AM, Linton CJ, Miles SJ, Johnson EM. Molecular identification of pathogenic fungi. J Antimicrob Chemother 2008, 61(Suppl 1):i7-i12.
51. Spiess B, Seifarth W, Hummel M, Frank O, Fabarius A, Zheng C, Morz H, Hehlmann R, Buchheidt D. DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. J Clin Microbiol 2007, 45(11):3743-3753. 10.1128/JCM.00942-07, 2168469, 17715373.
52. Kittelmann S, Naylor GE, Koolaard JP, Janssen PH. A proposed taxonomy of anaerobic fungi (class neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis. PLoS One 2012, 7(5):e36866. 10.1371/journal.pone.0036866, 3353986, 22615827.
53. Huse SM, Mark DB, Welch A, Voorhis A, Shipunova HG, Morrison AM, Eren, Sogin ML. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics 2014, 15(1):41. 10.1186/1471-2105-15-41, 3922339, 24499292.
54. Huse SM, Dethlefsen L, Huber JA, Mark D, Welch DA, Relman, Sogin ML. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 2008, 4(11):e1000255. 10.1371/journal.pgen.1000255, 2577301, 19023400.
55. Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 2010, 12(7):1889-1898. 10.1111/j.1462-2920.2010.02193.x, 2909393, 20236171.
56. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML. Microbial population structures in the deep marine biosphere. Science 2007, 318(5847):97-100. 10.1126/science.1146689, 17916733.
57. Madan JC, Koestler DC, Stanton BA, Davidson L, Moulton LA, Housman ML, Moore JH, Guill MF, Morrison HG, Sogin ML, Hampton TH, Karagas MR, Palumbo PE, Foster JA, Hibberd PL, O'Toole GA. Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. MBio 2012, 3(4):e00251-12.
58. Koljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Duenas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lucking R, Martin MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, et al. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 2013, 22(21):5271-5277. 10.1111/mec.12481, 24112409.
59. Bruns T, White T, Taylor J. Fungal molecular systematics. Annu Rev Ecol Syst 1991, 22:525-564.
60. Yao C, Frederiksen RA, Magill CW. Length heterogeneity in ITS 2 and the methylation status of CCGG and GCGC sites in the rRNA genes of the genus Peronosclerospora. Curr Genet 1992, 22(5):415-420. 10.1007/BF00352443, 1423729.
61. Longo AV, Rodriguez D, Da Silva D, Leite LF, Toledo C, Mendoza A, Burrowes PA, Zamudio KR. ITS1 copy number varies among Batrachochytrium dendrobatidis strains: implications for qPCR estimates of infection intensity from field-collected amphibian skin swabs. PLoS One 2013, 8(3):e59499. 10.1371/journal.pone.0059499, 3605245, 23555682.
62. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform Online 2008, 4:193-201. 2614188, 19204817.
63. Bittar F, Rolain JM. Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 2010, 16(7):809-820. 10.1111/j.1469-0691.2010.03236.x, 20880410.
64. Sibley CD, Rabin H, Surette MG. Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol 2006, 1(1):53-61. 10.2217/17460913.1.1.53, 17661685.
65. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013, 8(4):e62917. 10.1371/journal.pone.0062917, 3639911, 23646159.
66. Hirschi S, Letscher-Bru V, Pottecher J, Lannes B, Jeung MY, Degot T, Santelmo N, Sabou AM, Herbrecht R, Kessler R. Disseminated Trichosporon mycotoxinivorans, Aspergillus fumigatus, and Scedosporium apiospermum coinfection after lung and liver transplantation in a cystic fibrosis patient. J Clin Microbiol 2012, 50(12):4168-4170. 10.1128/JCM.01928-12, 3503015, 23035187.
67. Kothavade RJ, Kura MM, Valand AG, Panthaki MH. Candida tropicalis: its prevalence, pathogenicity and increasing resistance to fluconazole. J Med Microbiol 2010, 59(Pt 8):873-880.
68. Davies AN, Brailsford S, Broadley K, Beighton D. Oral yeast carriage in patients with advanced cancer. Oral Microbiol Immunol 2002, 17(2):79-84. 10.1046/j.0902-0055.2001.00095.x, 11929553.
69. Xu J, Mitchell TG. Geographical differences in human oral yeast flora. Clin Infect Dis 2003, 36(2):221-224. 10.1086/345672, 12522756.
70. Silva S, Negri M, Henriques M, Oliveira R, Williams DW, Azeredo J. Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. FEMS Microbiol Rev 2012, 36(2):288-305. 10.1111/j.1574-6976.2011.00278.x, 21569057.
71. Mounier J, Gouello A, Keravec M, Le Gal S, Pacini G, Debaets S, Nevez G, Rault G, Barbier G, Hery-Arnaud G. Use of denaturing high-performance liquid chromatography (DHPLC) to characterize the bacterial and fungal airway microbiota of cystic fibrosis patients. J Microbiol 2014, 52(4):307-314. 10.1007/s12275-014-3425-5, 24535743.
72. Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, Kong HH, Segre JA. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013, 498(7454):367-370. 10.1038/nature12171, 3711185, 23698366.
73. Hauser PM, Bernard T, Greub G, Jaton K, Pagni M, Hafen GM. Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS One 2014, 9(3):e90934. 10.1371/journal.pone.0090934, 3944733, 24599149.
74. Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med 2012, 186(6):536-545. 10.1164/rccm.201204-0693OC, 3480531, 22798321.
75. Hogan DA, Vik A, Kolter R. A Pseudomonas aeruginosa quorum-sensing molecule influences Candida albicans morphology. Mol Microbiol 2004, 54(5):1212-1223. 10.1111/j.1365-2958.2004.04349.x, 15554963.
76. Morales DK, Grahl N, Okegbe C, Dietrich LE, Jacobs NJ, Hogan DA. Control of Candida albicans metabolism and biofilm formation by Pseudomonas aeruginosa phenazines. MBio 2013, 4(1):e00526-12. 3560528, 23362320.
77. Hogan DA, Kolter R. Pseudomonas-Candida interactions: an ecological role for virulence factors. Science 2002, 296(5576):2229-2232. 10.1126/science.1070784, 12077418.
78. Gibson J, Sood A, Hogan DA. Pseudomonas aeruginosa-Candida albicans interactions: localization and fungal toxicity of a phenazine derivative. Appl Environ Microbiol 2009, 75(2):504-513. 10.1128/AEM.01037-08, 2620721, 19011064.
79. Lindsay AK, Morales DK, Liu Z, Grahl N, Zhang A, Willger SD, Myers LC, Hogan DA. Analysis of Candida albicans mutants defective in the Cdk8 module of mediator reveal links between metabolism and biofilm formation. PLoS Genet 2014, 10(10):e1004567. 10.1371/journal.pgen.1004567, 4183431, 25275466.
80. Cugini C, Morales DK, Hogan DA. Candida albicans-produced farnesol stimulates Pseudomonas quinolone signal production in LasR-defective Pseudomonas aeruginosa strains. Microbiology 2010, 156(Pt 10):3096-3107. 3068698, 20656785.
81. McAlester G, O'Gara F, Morrissey JP. Signal-mediated interactions between Pseudomonas aeruginosa and Candida albicans. J Med Microbiol 2008, 57(Pt 5):563-569.
82. Samonis G, Gikas A, Anaissie EJ, Vrenzos G, Maraki S, Tselentis Y, Bodey GP. Prospective evaluation of effects of broad-spectrum antibiotics on gastrointestinal yeast colonization of humans. Antimicrob Agents Chemother 1993, 37(1):51-53. 10.1128/AAC.37.1.51, 187603, 8431017.
83. Mulligan ME, Citron DM, McNamara BT, Finegold SM. Impact of cefoperazone therapy on fecal flora. Antimicrob Agents Chemother 1982, 22(2):226-230. 10.1128/AAC.22.2.226, 183716, 6927284.
84. Abbott J. Clinical and microscopic diagnosis of vaginal yeast infection: a prospective analysis. Ann Emerg Med 1995, 25(5):587-591. 10.1016/S0196-0644(95)70168-0, 7741332.
85. Oksala E. Factors predisposing to oral yeast infections. Acta Odontol Scand 1990, 48(1):71-74. 10.3109/00016359009012736, 2181813.
86. Leyden JJ, Marples RR. Ecologic principles and antibiotic therapy in chronic dermatoses. Arch Dermatol 1973, 107(2):208-211. 10.1001/archderm.1973.01620170020006, 4265456.
87. Ben-Ami R, Olshtain-Pops K, Krieger M, Oren I, Bishara J, Dan M, Wiener-Well Y, Weinberger M, Zimhony O, Chowers M, Weber G, Potasman I, Chazan B, Kassis I, Shalit I, Block C, Keller N, Kontoyiannis DP, Giladi M. Antibiotic exposure as a risk factor for fluconazole-resistant Candida bloodstream infection. Antimicrob Agents Chemother 2012, 56(5):2518-2523. 10.1128/AAC.05947-11, 3346668, 22314534.
88. Bow EJ, Louie TJ. Changes in endogenous microflora among febrile granulocytopenic patients receiving empiric antibiotic therapy: implications for fungal superinfection. CMAJ 1987, 137(5):397-403. 1492778, 3304600.
89. Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One 2013, 8(8):e71806. 10.1371/journal.pone.0071806, 3747063, 23977147.
90. Rogers GB, Cuthbertson L, Hoffman LR, Wing PA, Pope C, Hooftman DA, Lilley AK, Oliver A, Carroll MP, Bruce KD, van der Gast CJ. Reducing bias in bacterial community analysis of lower respiratory infections. ISME J 2013, 7(4):697-706. 10.1038/ismej.2012.145, 3603400, 23190732.
91. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome 2013, 1(1):9. 10.1186/2049-2618-1-9, 3971607, 24451366.
92. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
93. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200. 10.1093/bioinformatics/btr381, 3150044, 21700674.
94. Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE. Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Microbiome 2014, 2(1):5. 10.1186/2049-2618-2-5, 3931571, 24529162.
95. Eren AM, Vineis JH, Morrison HG, Sogin ML. A filtering method to generate high quality short reads using illumina paired-end technology. PLoS One 2013, 8(6):e66643. 10.1371/journal.pone.0066643, 3684618, 23799126.
96. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013, 41(Database issue):D590-D596. 3531112, 23193283.
97. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460-2461. 10.1093/bioinformatics/btq461, 20709691.
98. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26(2):266-267. 10.1093/bioinformatics/btp636, 2804299, 19914921.
99. Jacobs J. Individual Based Rarefaction using R-package 2011,
100. Liu CM, Kachur S, Dwan MG, Abraham AG, Aziz M, Hsueh PR, Huang YT, Busch JD, Lamit LJ, Gehring CA, Keim P, Price LB. FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. BMC Microbiol 2012, 12:255. 10.1186/1471-2180-12-255, 3565980, 23136846.
101. Horz HP, Vianna ME, Gomes BP, Conrads G. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol 2005, 43(10):5332-5337. 10.1128/JCM.43.10.5332-5337.2005, 1248440, 16208011.
102. Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, Arai H, Tanimoto I, Nishimura F, Takashiba S. Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol 2003, 39(1):81-86. 10.1016/S0928-8244(03)00224-4, 14557000.
103. Goslee SC, Urban DL. The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 2007, 22:1-19.
104. Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci 2003, 14(6):927-930.