Forgotten fungi—the gut mycobiome in human health and disease

FEMS Microbiology Reviews

Volumn 41, Issue 4, 2017, Pages

  Huseyin, Chloe E ^a,b,c   O’Toole, Paul W ^b,c   Cotter, Paul D ^a,b   Scanlan, Pauline D ^b  

^a TEAGASC FOOD RESEARCH CENTRE   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

fungi; gut microbiome; intestinal disease; mycobiome

Indexed keywords

BIOINFORMATICS; CANDIDA; COINFECTION; DIABETES MELLITUS; DIET; DNA EXTRACTION; ENTEROPATHY; FEEDING BEHAVIOR; FUNGUS; GENE SEQUENCE; GRAFT VERSUS HOST REACTION; HEPATITIS B; HOSPITAL INFECTION; HOST FUNGUS INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOCOMPROMISED PATIENT; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; MOUTH CAVITY; MYCOBIOME; OBESITY; RETT SYNDROME; REVIEW; VIRUS INFECTION; HOST PATHOGEN INTERACTION; MICROBIOLOGY; PHYSIOLOGY;

FUNGI; GASTROINTESTINAL MICROBIOME; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLAMMATORY BOWEL DISEASES; MYCOBIOME; OBESITY;

EID: 85026632014     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1093/FEMSRE/FUW047     Document Type: Review

References (372)

1. Abarenkov K, Henrik Nilsson R, Larsson K-H et al. The UNITE database for molecular identification of fungi—recent updates and future perspectives. New Phytol 2010;186:281–5.
2. Abbott DW, Martens EC, Gilbert HJ et al. Coevolution of yeast mannan digestion: convergence of the civilized human diet, distal gut microbiome, and host immunity. Gut Microbes 2015;6:334–9.
3. Adams RI, Miletto M, Taylor JW et al. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 2013;7:1262–73.
4. Agırbaslı H, Özcan SAK, Gedikoglu G. Fecal fungal flora of pediatric healthy volunteers and immunosuppressed patients. Mycopathologia 2005;159:515–20.
5. Akaza N, Akamatsu H, Sasaki Y et al. Cutaneous Malassezia microbiota of healthy subjects differ by sex, body part and season: malassezia microbiota in healthy subjects. J Dermatol 2010;37:786–92.
6. Albuquerque P, Casadevall A. Quorum sensing in fungi—a review. Med Mycol 2012;50:337–45.
7. Allison DL, Jayatilake JAMS, Shirtliff ME et al. Candida–bacteria interactions: their impact on human disease. Microbiol Spectr 2016;4, DOI: 10.1128/microbiolspec.VMBF-0030-2016.
8. Amend AS, Seifert KA, Bruns TD. Quantifying microbial communities with 454 pyrosequencing: does read abundance count?: quantitative pyrosequencing of microbes. Mol Ecol 2010;19:5555–65.
9. Amin R. The effect of chronic infection with Aspergillus fumigatus on lung function and hospitalization in patients with cystic fibrosis. Chest J 2010;137:171.
10. Andersen LO, Nielsen HV, Stensvold CR. Waiting for the human intestinal Eukaryotome. ISME J 2013;7:1253.
11. Anderson IC, Cairney JWG. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 2004;6: 769–79.
12. Araujo R. Towards the genotyping of fungi: methods, benefits and challenges. Curr Fungal Infect Rep 2014;8:203–10.
13. Arendrup MC. Update on antifungal resistance in Aspergillus and Candida. Clin Microbiol Infect 2014;20:42–8.
14. Ariizumi K, Shen GL, Shikano S et al. Identification of a novel, dendritic cell-associated molecule, dectin-1, by subtractive cDNA cloning. J Biol Chem 2000;275:20157–67.
15. Ashbee HR, Evans EGV. Immunology of diseases associated with Malassezia species. Clin Microbiol Rev 2002;15:21–57.
16. Back-Brito GN, da Mota AJ, de Souza Bernardes LÂ et al. Effects of eating disorders on oral fungal diversity. Oral Surg Oral Med O 2012;113:512–7.
17. Bahl MI, Bergström A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 2012;329:193–7.
18. Baley JE, Kliegman RM, Boxerbaum B et al. Fungal colonization in the very low birth weight infant. Pediatrics 1986;78:225–32.
19. Banjara N, Nickerson KW, Suhr MJ et al. Killer toxin from several food-derived Debaryomyces hansenii strains effective against pathogenic Candida yeasts. Int J Food Microbiol 2016;222:23–9.
20. Bates ST, Ahrendt S, Bik HM et al. Meeting report: fungal ITS workshop (October 2012). Stand Genomic Sci 2013;8:118–23.
21. Bazzicalupo AL, Bálint M, Schmitt I. Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities. Fungal Ecol 2013;6:102–9.
22. Begerow D, Nilsson H, Unterseher M et al. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biot 2010;87:99–108.
23. Bellemain E, Carlsen T, Brochmann C et al. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 2010;10:189.
24. Berry D, Ben Mahfoudh K, Wagner M et al. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microb 2011;77:7846–9.
25. Bik HM, Porazinska DL, Creer S et al. Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 2012;27:233–43.
26. Binladen J, Gilbert MTP, Bollback JP et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007;2:e197.
27. Blackwell M. The fungi: 1, 2, 3 ... 5.1 million species? Am J Bot 2011;98:426–38.
28. Blanco JL, Garcia ME. Immune response to fungal infections. Vet Immunol Immunop 2008;125:47–70.
29. Bliss JM, Basavegowda KP, Watson WJ et al. Vertical and horizontal transmission of Candida albicans in very low birth weight infants using DNA fingerprinting techniques. Pediatr Infect Dis J 2008;27:231–5.
30. Bokulich NA, Mills DA. Improved selection of internal transcribed spacer-specific primers enables quantitative, ultrahigh-throughput profiling of fungal communities. Appl Environ Microb 2013;79:2519–26.
31. Bokulich NA, Subramanian S, Faith JJ et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 2012;10:57–9.
32. Bor B, Cen L, Agnello M et al. Morphological and physiological changes induced by contact-dependent interaction between Candida albicans and Fusobacterium nucleatum. Sci Rep 2016;6:27956.
33. Borneman J, Hartin RJ. PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microb 2000;66:4356–60.
34. Bousbia S, Papazian L, Saux P et al. Repertoire of intensive care unit pneumonia microbiota. PLoS One 2012;7:e32486.
35. Brian Smith P, Steinbach WJ, Benjamin DK. Invasive Candida infections in the neonate. Drug Resist Update 2005;8: 147–62.
36. Brown GD, Denning DW, Levitz SM. Tackling human fungal infections. Science 2012;336:647.
37. Brown GD, Gordon S. Fungal β-glucans and mammalian immunity. Immunity 2003;19:311–5.
38. Brown SP, Callaham MA, Oliver AK et al. Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiol Ecol 2013;86:557–66.
39. Browne HP, Forster SC, Anonye BO et al. Culturing of “unculturable” human microbiota reveals novel taxa and extensive sporulation. Nature 2016;533:543–6.
40. Buée M, Reich M, Murat C et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity: research. New Phytol 2009;184:449–56.
41. Buermans HPJ, den Dunnen JT. Next generation sequencing technology: advances and applications. Biochim Biophys Acta 2014;1842:1932–41.
42. Bussey H. Host–microbe interactions: fungi. Curr Opin Microbiol 2005;8:359–61.
43. Calo-Mata P, Ageitos JM, Böhme K et al. Intestinal microbiota: first barrier against gut-affecting pathogens. In: Villa TG, Vinas M (eds). New Weapons to Control Bacterial Growth. Cham: Springer International Publishing, 2016, 281–314.
44. Campisi G, Pizzo G, Milici ME et al. Candidal carriage in the oral cavity of human immunodeficiency virus–infected subjects. Oral Surg Oral Med O 2002;93:281–6.
45. Caporaso JG, Kuczynski J, Stombaugh J et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335–6.
46. Carlsen T, Aas AB, Lindner D et al. Don’t make a mista (g) ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecol 2012;5:747–9.
47. Charlson ES, Diamond JM, Bittinger K et al. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Resp Crit Care 2012;186:536–45.
48. Chehoud C, Albenberg LG, Judge C et al. Fungal signature in the gut microbiota of Pediatric patients with inflammatory bowel disease. Inflamm Bowel Dis 2015;21:1948–56.
49. Chen Y, Chen Z, Guo R et al. Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagn Micr Infec Dis 2011;70:492–8.
50. Clemente JC, Ursell LK, Parfrey LW et al. The impact of the gut microbiota on human health: an integrative view. Cell 2012;148:1258–70.
51. Colucci F. An oral commensal associates with disease: chicken, egg, or red herring? Immunity 2015;42:208–10.
52. Crameri R, Blaser K. Allergy and immunity to fungal infections and colonization. Eur Respir J 2002;19:151–7.
53. Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med 2013;5:63.
54. Cutler JE, Deepe GS, Jr, Klein BS. Advances in combating fungal diseases: vaccines on the threshold. Nat Rev Microbiol 2007;5:13–28.
55. David LA, Maurice CF, Carmody RN et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2013;505:559–63.
56. De Brucker K, Tan Y, Vints K et al. Fungal β-1,3-Glucan increases Ofloxacin tolerance of Escherichia coli in a polymicrobial E. coli/Candida albicans biofilm. Antimicrob Agents Ch 2015;59:3052–8.
57. De Repentigny L, Phaneuf M, Mathieu L-G. Gastrointestinal colonization and systemic dissemination by Candida albicans and Candida tropicalis in intact and immunocompromised mice. Infect Immun 1992;60:4907–14.
58. Deeg HJ, Antin JH. The clinical spectrum of acute graft-versus-host disease. Semin Hematol 2006;43:24–31.
59. Delhaes L, Monchy S, Fréalle E et al. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community—implications for therapeutic management. PLoS One 2012;7:e36313.
60. Dollive S, Chen Y-Y, Grunberg S et al. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One 2013;8:e71806.
61. Dollive S, Peterfreund GL, Sherrill-Mix S et al. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol 2012;13:R60.
62. Drell T, Lillsaar T, Tummeleht L et al. Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age estonian women. PLoS One 2013;8:e54379.
63. Dridi B, Henry M, El Khéchine A et al. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 2009;4:e7063.
64. Duani H, Nunes VRT, Assumpção AB et al. Bilateral paracoccidioidomycotic iliopsoas abscess associated with ileo-colonic lesion. Rev Soc Bras Med Tro 2012;45:649–51.
65. Dupuy AK, David MS, Li L et al. Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of malassezia as a prominent commensal. PLoS One 2014;9:e90899.
66. Dynowska M, Roslon M, Góralska K. Saccharomyces cerevisiae in the respiratory system, digestive system and on the skin in humans. Acta Mycol 2006;41:139–44.
67. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5:113.
68. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10:996–8.
69. Edgar RC, Haas BJ, Clemente JC et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194–200.
70. Engelbrektson A, Kunin V, Wrighton KC et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 2010;4:642–7.
71. Eriksson M, Johannssen T, von Smolinski D et al. The C-type lectin receptor SIGNR3 binds to fungi present in commensal microbiota and influences immune regulation in experimental colitis. Front Immunol 2013;4, DOI: 10.3389/fimmu.2013.00196.
72. Esebelahie NO, Enweani IB, Omoregie R. Candida colonisation in asymptomatic HIV patients attending a tertiary hospital in Benin City, Nigeria. Libyan J Med 2013;8, DOI: 10.3402/ljm.v8i0.20322.
73. Everard A, Belzer C, Geurts L et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. P Natl Acad Sci USA 2013;110:9066–71.
74. Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One 2012;7:e42543.
75. Falagas ME, Betsi GI, Athanasiou S. Probiotics for prevention of recurrent vulvovaginal candidiasis: a review. J Antimicrob Chemoth 2006;58:266–72.
76. Feehery GR, Yigit E, Oyola SO et al. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS One 2013;8:e76096.
77. Feja KN, Wu F, Roberts K et al. Risk factors for Candidemia in critically ill infants: a matched case-control study. J Pediatr 2005;147:156–61.
78. Ferwerda B, Ferwerda G, Plantinga TS et al. Human Dectin-1 deficiency and mucocutaneous fungal infections. New Engl J Med 2009;361:1760–7.
79. Fidel PL. History and new insights into host defense against vaginal candidiasis. Trends Microbiol 2004;12:220–7.
80. Fierer N, Hamady M, Lauber CL et al. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. P Natl Acad Sci USA 2008;105:17994–9.
81. Findley K, Oh J, Yang J et al. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013;498:367–70.
82. Finegold SM, Attebery HR, Sutter VL. Effect of diet on human fecal flora: comparison of Japanese and American diets. Am J Clin Nutr 1974;27:1456–69.
83. Fonseca VG, Nichols B, Lallias D et al. Sample richness and genetic diversity as drivers of chimera formation in nSSU meta-genetic analyses. Nucleic Acids Res 2012;40:e66.
84. Ford EG, Baisden CE, Matteson ML et al. Sepsis after coronary bypass grafting: evidence for loss of the gut mucosal barrier. Ann Thorac Surg 1991;52:514–7.
85. Fouhy F, Deane J, Rea MC et al. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One 2015;10:e0119355.
86. Frykman PK, Nordenskjöld A, Kawaguchi A et al. Characterization of bacterial and fungal microbiome in children with Hirschsprung disease with and without a history of enterocolitis: a multicenter study. PLoS One 2015;10:e0124172.
87. Fujimura KE, Sitarik AR, Havstad S et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med 2016;22:1187–91.
88. Gadanho M, Sampaio JP. Microeukaryotic diversity in the extreme environments of the Iberian Pyrite Belt: a comparison between universal and fungi-specific primer sets, temperature gradient gel electrophoresis and cloning: microeukaryotic diversity in the IPB. FEMS Microbiol Ecol 2006;57: 139–48.
89. Gaetti-Jardim E, Marcelino SL, Feitosa ACR et al. Quantitative detection of periodontopathic bacteria in atherosclerotic plaques from coronary arteries. J Med Microbiol 2009;58:1568–75.
90. Gale D, Sandoval B. Response of mice to the inoculations of both Candida albicans and Escherichia coli I.: the enhancement phenomenon. J Bacteriol 1957;73:616.
91. Gantner BN, Simmons RM, Canavera SJ et al. Collaborative induction of inflammatory responses by Dectin-1 and toll-like Receptor 2. J Exp Med 2003;197:1107–17.
92. Gantner BN, Simmons RM, Underhill DM. Dectin-1 mediates macrophage recognition of Candida albicans yeast but not filaments. EMBO J 2005;24:1277–86.
93. Gao Y-D, Zhao Y, Huang J. Metabolic Modeling of common Escherichia coli strains in human gut microbiome. BioMed Res Int 2014;2014:1–11.
94. Gao Z, Perez-Perez GI, Chen Y et al. Quantitation of major human cutaneous bacterial and fungal populations. J Clin Microbiol 2010;48:3575–81.
95. Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 1993;2:113–8.
96. Gazis R, Rehner S, Chaverri P. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences: species delimitation in fungal endophytes. Mol Ecol 2011;20:3001–13.
97. Geramizadeh B, Foroughi R, Keshtkar-Jahromi M et al. Gastrointestinal basidiobolomycosis, an emerging infection in the immunocompetent host: a report of 14 patients. J Med Microbiol 2012;61:1770–4.
98. Gewolb IH, Schwalbe RS, Taciak VL et al. Stool microflora in extremely low birthweight infants. Arch Dis Child-Fetal 1999;80:F167–73.
99. Ghannoum MA, Jurevic RJ, Mukherjee PK et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010;6:e1000713.
100. Gionchetti P, Rizzello F, Helwig U et al. Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial. Gastroenterology 2003;124:1202–9.
101. Glenn TC. Field guide to next-generation DNA sequencers: field guide to next-gen sequencers. Mol Ecol Resour 2011;11:759–69.
102. Glocker E-O, Hennigs A, Nabavi M et al. A homozygous CARD9 mutation in a family with susceptibility to fungal infections. New Engl J Med 2009;361:1727–35.
103. Gonzalez GM, Sutton DA, Thompson E et al. In vitro activities of approved and investigational antifungal agents against 44 clinical isolates of Basidiomycetous fungi. Antimicrob Agents Ch 2001;45:633–5.
104. Gosiewski T, Salamon D, Szopa M et al. Quantitative evaluation of fungi of the genus Candida in the feces of adult patients with type 1 and 2 diabetes-a pilot study. Age 2014;27:17.
105. Gouba N, Raoult D, Drancourt M. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PLoS One 2013;8:e59474.
106. Gouba N, Raoult D, Drancourt M. Gut microeukaryotes during anorexia nervosa: a case report. BMC Res Notes 2014a;7:33.
107. Gouba N, Raoult D, Drancourt M. Eukaryote culturomics of the gut reveals new species. PLoS One 2014b;9:e106994.
108. Grice EA, Kong HH, Conlan S et al. Topographical and temporal diversity of the human skin microbiome. Science 2009;324:1190–2.
109. Griffith GW, Ozkose E, Theodorou MK et al. Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources. Fungal Ecol 2009;2:87–97.
110. Gulati M, Nobile CJ. Candida albicans biofilms: development, regulation, and molecular mechanisms. Microbes Infect 2016, DOI: 10.1016/j.micinf.2016.01.002.
111. Gumbo T, Isada CM, Hall G et al. Candida glabrata fungemia clinical features of 139 patients. Medicine (Baltimore) 1999;78: 220–7.
112. Gunsalus KT, Tornberg-Belanger SN, Matthan NR et al. Manipulation of host diet to reduce gastrointestinal colonization by the opportunistic pathogen Candida albicans. mSphere 2016;1:e00020–15.
113. Hallen-Adams HE, Kachman SD, Kim J et al. Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community. Fungal Ecol 2015;15:9–17.
114. Hamad I, Raoult D, Bittar F. Repertory of Eukaryotes (Eukaryome) in the human gastrointestinal tract: taxonomy and detection methods. Parasite Immunol 2016;38:12–36.
115. Hamad I, Sokhna C, Raoult D et al. Molecular detection of eukaryotes in a single human stool sample from senegal. PLoS One 2012;7:e40888.
116. Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 2009;19:1141–52.
117. Hamady M, Walker JJ, Harris JK et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008;5:235–7.
118. Hammoud MS, Al-Taiar A, Fouad M et al. Persistent candidemia in neonatal care units: risk factors and clinical significance. Int J Infect Dis 2013;17:e624–8.
119. Harrison MJ, Twomey KB, McCarthy Y et al. Fungal microbiota in the adult cystic fibrosis (CF) airway: characterization by second-generation sequencing and correlation with standard culture-based methods and clinical phenotype. Irish J Med Sci 2012;181: S411.
120. Hatoum R, Labrie S, Fliss I. Antimicrobial and probiotic properties of yeasts: from fundamental to novel applications. Front Microbiol 2012;3, DOI: 10.3389/fmicb.2012.00421.
121. Hawksworth DL. Fungal diversity and its implications for genetic resource collections. Stud Mycol 2004;50:9–18.
122. Hawksworth DL. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 2001;105:1422–32.
123. Hawksworth DL, Crous PW, Redhead SA et al. The Amsterdam declaration on fungal nomenclature. IMA Fungus 2011;2: 105–12.
124. Hawksworth DL, Rossman AY. Where are all the undescribed fungi? Phytopathology 1997;87:888–91.
125. Heisel T, Podgorski H, Staley CM et al. Complementary amplicon-based genomic approaches for the study of fungal communities in humans. PLoS One 2015;10:e0116705.
126. Henderson G, Cox F, Kittelmann S et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One 2013;8:e74787.
127. Hibbett DS, Ohman A, Glotzer D et al. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol Rev 2011;25:38–47.
128. Hilty M, Burke C, Pedro H et al. Disordered microbial communities in asthmatic airways. PLoS One 2010;5:e8578.
129. Hoarau G, Mukherjee PK, Gower-Rousseau C et al. Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn’s disease. mBio 2016;7:e01250–16.
130. Hoffmann C, Dollive S, Grunberg S et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 2013;8:e66019.
131. Hoffmann C, Minkah N, Leipzig J et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007;35:e91.
132. Hogan DA, Kolter R. Pseudomonas-Candida interactions: an ecological role for virulence factors. Science 2002;296:2229–32.
133. Hogan DA, Vik Å, Kolter R. A Pseudomonas aeruginosa quorum-sensing molecule influences Candida albicans morphology: pseudomonas inhibition of C. albicans filamentation. Mol Microbiol 2004;54:1212–23.
134. Hoog GS, Matos T, Sudhadham M et al. Intestinal prevalence of the neurotropic black yeast Exophiala (Wangiella) dermatitidis in healthy and impaired individuals. Mycoses 2005;48:142–5.
135. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science 2001;292:1115–8.
136. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science 2012;336:1268–73.
137. Horton TR, Bruns TD. The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 2001;10:1855–71.
138. Huber JA, Mark Welch DB, Morrison HG et al. Microbial population structures in the deep marine biosphere. Science 2007;318:97–100.
139. Huber JA, Morrison HG, Huse SM et al. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 2009;11: 1292–302.
140. Huffnagle GB, Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol 2013;21:334–41.
141. Hugenholtz P, Pace NR. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol 1996;14:190–7.
142. Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM et al. A catalog of reference genomes from the human microbiome. Science 2010;328:994–9.
143. Ihrmark K, Bödeker ITM, Cruz-Martinez K et al. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 2012;82:666–77.
144. Ikeda T, Suegara N, Abe S et al. Efficacy of antibacterial drugs in mice with complex infection by Candida albicans and Escherichia coli. J Antibiot (Tokyo) 1999;52:552–8.
145. Iliev ID, Funari VA, Taylor KD et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012;336:1314–7.
146. Iliev ID, Underhill DM. Striking a balance: fungal commensalism versus pathogenesis. Curr Opin Microbiol 2013;16:366–73.
147. Ishibashi K, Fukazawa R, Miura NN et al. Diagnostic potential of antibody titres against Candida cell wall β-glucan in Kawasaki disease: anti-β-glucan antibody and Kawasaki disease. Clin Exp Immunol 2014;177:161–7.
148. Ishii K, Fukui M. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl Environ Microb 2001;67:3753–5.
149. Iwen PC, Hinrichs SH, Rupp ME. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 2002;40:87–109.
150. Jawhara S, Thuru X, Standaert-Vitse A et al. Colonization of mice by Candida albicans is promoted by chemically induced colitis and augments inflammatory responses through Galectin-3. J Infect Dis 2008;197:972–80.
151. Jayaprakash AD, Jabado O, Brown BD et al. Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res 2011;39:e141–.
152. Jayshree RS, Shafiulla M, George J et al. Microscopic, cultural and molecular evidence of disseminated invasive aspergillosis involving the lungs and the gastrointestinal tract. J Med Microbiol 2006;55:961–4.
153. Jha AK, Uppal B, Chadha S et al. Clinical and microbiological profile of HIV/AIDS cases with diarrhea in North India. J Pathog 2012;2012:1–7.
154. Jobst D, Kraft K. Candida species in stool, symptoms and complaints in general practice–a cross-sectional study of 308 outpatients. Mycoses 2006;49:415–20.
155. Joossens S, Reinisch W, Vermeire S et al. The value of serologic markers in indeterminate colitis: a prospective followup study. Gastroenterology 2002;122:1242–7.
156. Jovel J, Patterson J, Wang W et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Evol Genomic Microbiol 2016:459.
157. Jumpponen A, Jones KL. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 2009;184:438–48.
158. Jumpponen A, Jones KL, David Mattox J et al. Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 2010;19:41–53.
159. Kalan L, Loesche M, Hodkinson BP et al. Redefining the chronic-wound microbiome: fungal communities are prevalent, dynamic, and associated with delayed healing. mBio 2016;7:e01058–16.
160. Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 2003;96:317–23.
161. Kashyap B, Bhalla P, Uppal B. Enteric pathogens in HIV/ AIDS from a tertiary care hospital. Indian J Community Med 2009;34:237.
162. Kemler M, Garnas J, Wingfield MJ et al. Ion torrent PGM as tool for fungal community analysis: a case study of Endophytes in Eucalyptus grandis reveals high taxonomic diversity. PLoS One 2013;8:e81718.
163. Kerr J. Inhibition of fungal growth by Pseudomonas aeruginosa and Pseudomonas cepacia isolated from patients with cystic fibrosis. J Infect 1994;28:305–10.
164. Khatib R, Riederer KM, Ramanathan J et al. Faecal fungal flora in healthy volunteers and inpatients. Mycoses 2001;44:151–6.
165. Kim Y-G, Udayanga KGS, Totsuka N et al. Gut dysbiosis promotes M2 macrophage polarization and allergic airway inflammation via fungi-induced PGE2. Cell Host Microbe 2014;15: 95–102.
166. Klaerner HG, Uknis ME, Acton RD et al. Candida albicans and Escherichia coli are synergistic pathogens during experimental microbial peritonitis. J Surg Res 1997;70:161–5.
167. Klingspor L, Jalal S. Molecular detection and identification of Candida and Aspergillus spp. from clinical samples using real-time PCR. Clin Microbiol Infect 2006;12:745–53.
168. Knights D, Lassen KG, Xavier RJ. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut 2013;62:1505–10.
169. Koenig JE, Spor A, Scalfone N et al. Succession of microbial consortia in the developing infant gut microbiome. P Natl Acad Sci USA 2011;108:4578–85.
170. Koetschan C, Forster F, Keller A et al. The ITS2 Database III–sequences and structures for phylogeny. Nucleic Acids Res 2010;38:D275–9.
171. Koetschan C, Hackl T, Müller T et al. ITS2 Database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Mol Phylogenet Evol 2012;63:585–8.
172. Kõljalg U, Larsson K-H, Abarenkov K et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi: methods. New Phytol 2005;166:1063–8.
173. Koren O, Spor A, Felin J et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. P Natl Acad Sci USA 2011;108:4592–8.
174. Korzenik JR. Past and current theories of etiology of IBD: toothpaste, worms, and refrigerators. J Clin Gastroenterol 2005;39:S59–65.
175. Kowalewska B, Zorena K, Szmigiero-Kawko M et al. Higher diversity in fungal species discriminates children with type 1 diabetes mellitus from healthy control. Patient Prefer Adherence 2016;10:591–9.
176. Krause R, Halwachs B, Thallinger GG et al. Characterisation of Candida within the mycobiome/microbiome of the lower respiratory tract of ICU patients. PLoS One 2016;11:e0155033.
177. Krom BP, Kidwai S, ten Cate JM. Candida and other fungal species: forgotten players of healthy oral microbiota. J Dent Res 2014, DOI: 10.1177/0022034514521814.
178. Krüger M, Stockinger H, Krüger C et al. DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytol 2009;183:212–23.
179. Kuhbacher T. Bacterial and fungal microbiota in relation to probiotic therapy (VSL#3) in pouchitis. Gut 2006;55:833–41.
180. Kumamoto CA. Inflammation and gastrointestinal Candida colonization. Curr Opin Microbiol 2011;14:386–91.
181. Kumamoto CA. The fungal mycobiota: small numbers, large impacts. Cell Host Microbe 2016;19:750–1.
182. Kunin V, Copeland A, Lapidus A et al. A bioinformatician’s guide to metagenomics. Microbiol Mol Biol R 2008;72:557–78.
183. Lagier J-C, Armougom F, Million M et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012;18:1185–93.
184. Landlinger C, Bašková L, Preuner S et al. Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region. Eur J Clin Microbiol 2009a;28:613–22.
185. Landlinger C, Preuner S, Willinger B et al. Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. J Clin Microbiol 2009b;47:1063–73.
186. LaTuga MS, Ellis JC, Cotton CM et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One 2011;6:e27858.
187. Lee J, Lee S, Young JPW. Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi: PCR primers for arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 2008;65:339–49.
188. Leeming JP, Notman FH Improved methods for isolation and enumeration of Malassezia furfur from human skin. J Clin Microbiol 1987;25:2017–9.
189. Lewis JD, Chen EZ, Baldassano RN et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 2015;18:489–500.
190. Li Q, Wang C, Tang C et al. Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J Clin Gastroenterol 2014;48:513.
191. Li Q, Wang C, Zhang Q et al. Use of 18S ribosomal DNA polymerase chain reaction–denaturing gradient gel electrophoresis to study composition of fungal community in 2 patients with intestinal transplants. Hum Pathol 2012;43:1273–81.
192. Liang W, Guan G, Dai Y et al. Lactic acid bacteria differentially regulate filamentation in two heritable cell types of the human fungal pathogen Candida albicans: Lactobacilli regulate filamentation in C. albicans. Mol Microbiol 2016, DOI: 10.1111/mmi.13475.
193. Liggenstoffer AS, Youssef NH, Couger MB et al. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 2010;4:1225–35.
194. Liguori G, Lamas B, Richard ML et al. Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients. J Crohns Colitis 2015, DOI: 10.1093/ecco-jcc/jjv209.
195. Lim ES, Zhou Y, Zhao G et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 2015;21:1228–34.
196. Lindahl BD, Nilsson RH, Tedersoo L et al. Fungal community analysis by high-throughput sequencing of amplified markers - a user’s guide. New Phytol 2013;199:288–99.
197. Lindner DL, Banik MT. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 2011;103:731–40.
198. Liu J, Yu Y, Cai Z et al. Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE. World J Microb Biot 2015, DOI: 10.1007/s11274-015-1890-6.
199. Liu K-L, Porras-Alfaro A, Kuske CR et al. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl Environ Microb 2012;78:1523–33.
200. Lo H-J, Köhler JR, DiDomenico B et al. Nonfilamentous C. albicans mutants are avirulent. Cell 1997;90:939–49.
201. Lo Russo L, Campisi G, Di Fede O et al. Oral manifestations of eating disorders: a critical review. Oral Dis 2008;14: 479–84.
202. Lozupone CA, Stombaugh J, Gonzalez A et al. Meta-analyses of studies of the human microbiota. Genome Res 2013;23:1704–14.
203. Lozupone CA, Stombaugh JI, Gordon JI et al. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220–30.
204. Luan C, Xie L, Yang X et al. Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Sci Rep 2015;5:7980.
205. Lutzoni F, Kauff F, Cox CJ et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 2004;91:1446–80.
206. McGovern DPB, Gardet A, Törkvist L et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 2010;42:332–7.
207. Main J, McKenzie H, Yeaman GR et al. Antibody to Saccharomyces cerevisiae (bakers’ yeast) in Crohn’s disease. BMJ 1988;297:1105.
208. Mar JS, LaMere BJ, Lin DL et al. Disease severity and immune activity relate to distinct interkingdom gut microbiome states in ethnically distinct ulcerative colitis patients. mBio 2016;7:e01072–16.
209. Mar Rodríguez M, Pérez D, Javier Chaves F et al. Obesity changes the human gut mycobiome. Sci Rep 2015;5:14600.
210. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genom Hum G 2008;9:387–402.
211. Mardis ER. Next-generation sequencing platforms. Annu Rev Anal Chem 2013;6:287–303.
212. Margulies M, Egholm M, Altman WE et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, DOI: 10.1038/nature03959.
213. Marsh AJ, O’Sullivan O, Hill C et al. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiol 2014;38:171–8.
214. Martin KJ, Rygiewicz PT. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 2005;5:28.
215. Martinez RCR, Seney SL, Summers KL et al. Effect of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 on the ability of Candida albicans to infect cells and induce inflammation. Microbiol Immunol 2009;53:487–95.
216. Mason KL, Erb Downward JR, Falkowski NR et al. Interplay between the gastric bacterial microbiota and Candida albicans during postantibiotic recolonization and gastritis. Infect Immun 2012a;80:150–8.
217. Mason KL, Erb Downward JR, Mason KD et al. Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun 2012b;80:3371–80.
218. Mello A, Napoli C, Murat C et al. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia 2011;103:1184–93.
219. Miceli MH, Díaz JA, Lee SA. Emerging opportunistic yeast infections. Lancet Infect Dis 2011;11:142–51.
220. Miranda TT, Vianna CR, Rodrigues L et al. Diversity and frequency of yeasts from the dorsum of the tongue and necrotic root canals associated with primary apical periodontitis. Int Endod J 2009;42:839–44.
221. Monteiro L, Bonnemaison D, Vekris A et al. Complex polysaccharides as PCR inhibitors in feces: helicobacter pylori model. J Clin Microbiol 1997;35:995–8.
222. Monteiro-da-Silva F, Sampaio-Maia B, Pereira M, de L et al. Characterization of the oral fungal microbiota in smokers and non-smokers. Eur J Oral Sci 2013;121:132–5.
223. Morace G, Perdoni F, Borghi E. Antifungal drug resistance in Candida species. J Glob Antimicrob Resist 2014;2:254–9.
224. Morris AJ, Byrne TC, Madden JF et al. Duration of incubation of fungal cultures. J Clin Microbiol 1996;34:1583–5.
225. Mowat AM, Viney JL. The anatomical basis of intestinal immunity. Immunol Rev 1997;156:145–66.
226. Moyes DL, Naglik JR. The mycobiome: influencing IBD severity. Cell Host Microbe 2012;11:551–2.
227. Mukherjee PK, Chandra J, Retuerto M et al. Oral Mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog 2014;10:e1003996.
228. Mukhopadhya I, Hansen R, Meharg C et al. The fungal microbiota of de-novo paediatric inflammatory bowel disease. Microbes Infect 2014, DOI: 10.1016/j.micinf.2014.12.001.
229. Nagata R, Nagano H, Ogishima D et al. Transmission of the major skin microbiota, Malassezia, from mother to neonate: transmission of Malassezia. Pediatr Int 2012;54:350–5.
230. Nam Y-D, Chang H-W, Kim K-H et al. Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people. J Microbiol 2008;46:491–501.
231. Neher DA, Weicht TR, Bates ST et al. Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times. PLoS One 2013;8:e79512.
232. Nelson A, De Soyza A, Bourke SJ et al. Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis: sample handling of CF sputum. Lett Appl Microbiol 2010;51:272–7.
233. Netea MG, Gow NAR, Munro CA et al. Immune sensing of Candida albicans requires cooperative recognition of mannans and glucans by lectin and Toll-like receptors. J Clin Invest 2006;116:1642–50.
234. Nguyen LDN, Viscogliosi E, Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol 2015;6, DOI: 10.3389/fmicb.2015.00089.
235. Nicholson MJ, McSweeney CS, Mackie RI et al. Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores. Anaerobe 2010;16:66–73.
236. Nilsson H, Tedersoo L, Abarenkov K et al. Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 2012;4:37–63.
237. Nilsson RH, Abarenkov K, Veldre V et al. An open source chimera checker for the fungal ITS region: computer program note. Mol Ecol Resour 2010;10:1076–81.
238. Nilsson RH, Ryberg M, Abarenkov K et al. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 2009;296:97–101.
239. Nilsson RH, Ryberg M, Kristiansson E et al. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 2006;1:e59.
240. Nilsson RH, Tedersoo L, Ryberg M et al. A comprehensive, automatically updated fungal its sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes Environ 2015, DOI: 10.1264/jsme2.ME14121.
241. Nobile CJ, Johnson AD. Candida albicans biofilms and human disease. Annu Rev Microbiol 2015;69:71–92.
242. Nordenfelt P, Waldemarson S, Linder A et al. Antibody orientation at bacterial surfaces is related to invasive infection. J Exp Med 2012;209:2367–81.
243. Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 2014;146:1459–69.
244. Noverr MC, Erb-Downward JR, Huffnagle GB. Production of Eicosanoids and other Oxylipins by pathogenic eukaryotic microbes. Clin Microbiol Rev 2003;16:517–33.
245. Noverr MC, Noggle RM, Toews GB et al. Role of antibiotics and fungal microbiota in driving pulmonary allergic responses. Infect Immun 2004;72:4996–5003.
246. O’Brien HE, Parrent JL, Jackson JA et al. Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microb 2005;71:5544–50.
247. Oever J ten, Netea MG. The bacteriome-mycobiome interaction and antifungal host defense: highlights. Eur J Immunol 2014;44:3182–91.
248. O’Meara TR, Veri AO, Ketela T et al. Global analysis of fungal morphology exposes mechanisms of host cell escape. Nat Com-mun 2015;6:6741.
249. Öpik M, Metsis M, Daniell TJ et al. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol 2009;184:424–37.
250. Ott SJ, El Mokhtari NE, Musfeldt M et al. Detection of diverse bacterial signatures in atherosclerotic lesions of patients with coronary heart disease. Circulation 2006;113:929–37.
251. Ott SJ, El Mokhtari NE, Rehman A et al. Fungal rDNA signatures in coronary atherosclerotic plaques. Environ Microbiol 2007;9:3035–45.
252. Ott SJ, Kühbacher T, Musfeldt M et al. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol 2008;43:831–41.
253. Ott SJ, Musfeldt M, Timmis KN et al. In vitro alterations of intestinal bacterial microbiota in fecal samples during storage. Diagn Micr Infec Dis 2004a;50:237–45.
254. Ott SJ, Musfeldt M, Wenderoth DF et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004b;53:685–93.
255. R Candida dans le diagnostic mycologique des levures. J Mycol Méd 2013;23:237–41.
256. Pagnoux C, Cohen P, Guillevin L. Vasculitides secondary to infections. Clin Exp Rheumatol 2006;24:S71.
257. Palmer C, Bik EM, DiGiulio DB et al. Development of the human infant intestinal microbiota. PLoS Biol 2007;5:e177.
258. Pandey PK, Siddharth J, Verma P et al. Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers. J Bioscience 2012;37:221–6.
259. Parameswaran P, Jalili R, Tao L et al. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 2007;35: e130.
260. Parfrey LW, Walters WA, Knight R. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol 2011;2, DOI: 10.3389/fmicb.2011.00153.
261. Parfrey LW, Walters WA, Lauber CL et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol 2014;5, DOI: 10.3389/fmicb.2014.00298.
262. Park BJ, Wannemuehler KA, Marston BJ et al. Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS: AIDS 2009;23:525–30.
263. Park HK, Ha M-H, Park S-G et al. Characterization of the fungal microbiota (mycobiome) in healthy and dandruff-afflicted human scalps. PLoS One 2012;7:e32847.
264. Peay KG, Kennedy PG, Bruns TD. Fungal community ecology: a hybrid beast with a molecular master. Bioscience 2008;58:799–810.
265. Peay KG, Kennedy PG, Talbot JM. Dimensions of biodiversity in the Earth mycobiome. Nat Rev Microbiol 2016;14:434–47.
266. Peleg AY, Hogan DA, Mylonakis E. Medically important bacterial–fungal interactions. Nat Rev Microbiol 2010;8:340–9.
267. Pfaller MA, Diekema DJ. Rare and emerging opportunistic fungal pathogens: concern for resistance beyond Candida albicans and Aspergillus fumigatus. J Clin Microbiol 2004;42: 4419–31.
268. Pirotta M, Gunn J, Chondros P et al. Effect of lactobacillus in preventing post-antibiotic vulvovaginal candidiasis: a randomised controlled trial. BMJ 2004;329:548.
269. Pitman RS, Blumberg RS. First line of defense: the role of the intestinal epithelium as an active component of the mucosal immune system. J Gastroenterol 2000;35:805–14.
270. Platt L, Easterbrook P, Gower E et al. Prevalence and burden of HCV co-infection in people living with HIV: a global systematic review and meta-analysis. Lancet Infect Dis 2016, DOI: 10.1016/S1473-3099(15)00485-5.
271. Plotkin BJ. Contribution of host signaling and virome to the mycobiome. Fungal Genomics Biol 2016;6, DOI: 10.4172/2165-8056.1000137.
272. Plotkin BJ, Sigar IM, Tiwari V et al. Herpes simplex virus (HSV) modulation of Staphylococcus aureus and Candida albicans initiation of HeLa 299 cell-associated biofilm. Curr Microbiol 2016;72:529–37.
273. Polvi EJ, Li X, O’Meara TR et al. Opportunistic yeast pathogens: reservoirs, virulence mechanisms, and therapeutic strategies. Cell Mol Life Sci 2015;72:2261–87.
274. Porter TM, Brian Golding G. Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytol 2011;192:775–82.
275. Poulain D, Jouault T. Candida albicans cell wall glycans, host receptors and responses: elements for a decisive crosstalk. Curr Opin Microbiol 2004;7:342–9.
276. Praneenararat S. Fungal infection of the colon. Clin Exp Gastroenterol 2014;7:415.
277. Primeggia J, Matsumoto CS, Fishbein TM et al. Infection among adult small bowel and multivisceral transplant recipients in the 30-day postoperative period. Transpl Infect Dis 2013;15:441–8.
278. Pruesse E, Quast C, Knittel K et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35:7188–96.
279. Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59–65.
280. Rajilić-Stojanović M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007;9:2125–36.
281. Ravel J, Gajer P, Abdo Z et al. Vaginal microbiome of reproductive-age women. P Natl Acad Sci USA 2011;108:4680–7.
282. Reales-Calderón JA, Sylvester M, Strijbis K et al. Candida albicans induces pro-inflammatory and anti-apoptotic signals in macrophages as revealed by quantitative proteomics and phosphoproteomics. J Proteomics 2013;91:106–35.
283. Richard ML, Lamas B, Liguori G et al. Gut fungal microbiota: the yin and yang of inflammatory bowel disease. Inflamm Bowel Dis 2015;21:656–65.
284. Rodríguez JM, Murphy K, Stanton C et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health D 2015;26, DOI: 10.3402/mehd.v26.26050.
285. Rowen JL. Fungal infections in the neonatal intensive care unit. Semin Pediatr Infect Dis 2001;12:107–14.
286. Salonen A, Nikkilä J, Jalanka-Tuovinen J et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 2010;81:127–34.
287. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. P Natl Acad Sci USA 1977;74: 5463–7.
288. Sanglard D, Odds FC. Resistance of Candida species to antifungal agents: molecular mechanisms and clinical consequences. Lancet Infect Dis 2002;2:73–85.
289. Sangster W, Hegarty JP, Schieffer KM et al. Bacterial and fungal microbiota changes distinguish C. difficile infection from other forms of diarrhea: results of a prospective inpatient study. Front Microbiol 2016;7, DOI: 10.3389/fmicb.2016.00789.
290. Santamaria M, Fosso B, Consiglio A et al. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 2012;13:682–95.
291. Sartor RB. Gut microbiota: optimal sampling of the intestinal microbiota for research. Nat Rev Gastroentero 2015;12:253–4.
292. Sauer S, Kliem M. Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol 2010;8:74–82.
293. Sboner A, Mu XJ, Greenbaum D et al. The real cost of sequencing: higher than you think. Genome Biol 2011;12:125.
294. Scanlan PD, Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces. ISME J 2008;2:1183–93.
295. Scanlan PD, Shanahan F, O’Mahony C et al. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn’s disease. J Clin Microbiol 2006;44:3980–8.
296. Schloss PD, Westcott SL, Ryabin T et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 2009;75:7537–41.
297. Schmidt P-A, Bálint M, Greshake B et al. Illumina metabarcoding of a soil fungal community. Soil Biol Biochem 2013;65:128–32.
298. Schoch CL, Robbertse B, Robert V et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database 2014;2014:bau061.
299. Schoch CL, Seifert KA, Huhndorf S et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci USA 2012;109:6241–6.
300. Schrader C, Schielke A, Ellerbroek L et al. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 2012;113:1014–26.
301. Schulze J, Sonnenborn U. Yeasts in the gut: from commensals to infectious agents. Dtsch Arztebl Int 2009;106:837–42.
302. Scupham AJ, Presley LL, Wei B et al. Abundant and diverse fungal microbiota in the murine intestine. Appl Environ Microb 2006;72:793–801.
303. Seed PC. The human mycobiome. Cold Spring Harb Perspect Med 2015;5:a019810.
304. Seifert KA. Progress towards DNA barcoding of fungi. Mol Ecol Resour 2009;9:83–9.
305. Shanahan F. The gut microbiota—a clinical perspective on lessons learned. Nat Rev Gastroentero 2012;9:609–14.
306. Shanahan F. Separating the microbiome from the hyperbolome. Genome Med 2015;7:17.
307. Shokralla S, Spall JL, Gibson JF et al. Next-generation sequencing technologies for environmental DNA research: next-generation sequencing for environmental DNA. Mol Ecol 2012;21:1794–805.
308. Smits G, Kapteyn JC, van den Ende H et al. Cell wall dynamics in yeast. Curr Opin Microbiol 1999;2:348–52.
309. Sobel JD. Gynecologic infections in human immunodeficiency virus-infected women. Clin Infect Dis 2000;31:1225–33.
310. Sobel JD, Faro S, Force RW et al. Vulvovaginal candidiasis: epidemiologic, diagnostic, and therapeutic considerations. Am J Obstet Gynecol 1998;178:203–11.
311. Sobel JD, Wiesenfeld HC, Martens M et al. Maintenance fluconazole therapy for recurrent vulvovaginal candidiasis. New Engl J Med 2004;351:876–83.
312. Sogin ML, Morrison HG, Huber JA et al. Microbial diversity in the deep sea and the underexplored “rare biosphere.” P Natl Acad Sci USA 2006;103:12115–20.
313. Sokol H, Leducq V, Aschard H et al. Fungal microbiota dysbiosis in IBD. Gut 2016, doi: gutjnl-2015-310746.
314. Soll DR, Galask R, Schmid J et al. Genetic dissimilarity of commensal strains of Candida spp. carried in different anatomical locations of the same healthy women. J Clin Microbiol 1991;29:1702–10.
315. Song SJ, Dominguez-Bello MG, Knight R. How delivery mode and feeding can shape the bacterial community in the infant gut. Can Med Assoc J 2013;185:373–4.
316. Soyucen E, Gulcan A, Aktuglu-Zeybek AC et al. Differences in the gut microbiota of healthy children and those with type 1 diabetes: gut microbiota and type 1 diabetes. Pediatr Int 2014;56:336–43.
317. Spear GT, Zariffard MR, Cohen MH et al. Vaginal IL-8 levels are positively associated with Candida albicans and inversely with lactobacilli in HIV-infected women. J Reprod Immunol 2008;78:76–9.
318. Stämpfli MR, Anderson GP. How cigarette smoke skews immune responses to promote infection, lung disease and cancer. Nat Rev Immunol 2009;9:377–84.
319. Standaert-Vitse A, Sendid B, Joossens M et al. Candida albicans colonization and ASCA in Familial Crohn’s disease. Am J Gastroenterol 2009;104:1745–53.
320. Stappenbeck TS, Virgin HW. Accounting for reciprocal host–microbiome interactions in experimental science. Nature 2016;534:191–9.
321. Steele C. Cytokine and chemokine production by human oral and vaginal Epithelial cells in response to Candida albicans. Infect Immun 2002;70:577–83.
322. Stewart CJ, Nelson A, Scribbins D et al. Bacterial and fungal viability in the preterm gut: NEC and sepsis. Arch Dis Child-Fetal 2013;98:F298–303.
323. Stockinger H, Krüger M, Schüßler A. DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 2010;187:461–74.
324. Strati F, Cavalieri D, Albanese D et al. Altered gut microbiota in Rett syndrome. Microbiome 2016a;4, DOI: 10.1186/s40168-016-0185-y.
325. Strati F, Di Paola M, Stefanini I et al. Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front Microbiol 2016b;7, DOI: 10.3389/fmicb.2016.01227.
326. Sugita T, Takashima M, Shinoda T et al. New yeast species, malassezia dermatis, isolated from patients with atopic dermatitis. J Clin Microbiol 2002;40:1363–7.
327. Suhr MJ, Banjara N, Hallen-Adams HE. Sequence-based methods for detecting and evaluating the human gut mycobiome. Lett Appl Microbiol 2016;62:209–15.
328. Suhr MJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials-a mycologist’s perspective. Mycologia 2015;107:1057–73.
329. Sutton CL, Yang H, Li Z et al. Familial expression of anti-Saccharomyces cerevisiae mannan antibodies in affected and unaffected relatives of patients with Crohn’s disease. Gut 2000;46:58–63.
330. Tajima M, Sugita T, Nishikawa A et al. Molecular analysis of Malassezia microflora in seborrheic dermatitis patients: comparison with other diseases and healthy subjects. J Invest Dermatol 2008;128:345–51.
331. Tang D, Kang R, Coyne CB et al. PAMPs and DAMPs: signal 0s that spur autophagy and immunity. Immunol Rev 2012;249: 158–75.
332. Tang J, Iliev ID, Brown J et al. Mycobiome: approaches to analysis of intestinal fungi. J Immunol Methods 2015;421:112–21.
333. Taylor GR, Kropp KD, Molina TC. Nine-year microflora study of an isolator-maintained immunodeficient child. Appl Environ Microb 1985;50:1349–56.
334. Taylor PR, Tsoni SV, Willment JA et al. Dectin-1 is required for β-glucan recognition and control of fungal infection. Nat Immunol 2007;8:31–8.
335. Tedersoo L, Abarenkov K, Nilsson RH et al. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi. PLoS One 2011;6:e24940.
336. Tedersoo L, Lindahl B. Fungal identification biases in microbiome projects: fungal identification biases in microbiome projects. Environ Microbiol Rep 2016, DOI: 10.1111/1758-2229.12438.
337. Thompson-Chagoyán OC, Maldonado J, Gil A. Aetiology of inflammatory bowel disease (IBD): role of intestinal microbiota and gut-associated lymphoid tissue immune response. Clin Nutr 2005;24:339–52.
338. Tierney L, Kuchler K, Rizzetto L et al. Systems biology of host–fungus interactions: turning complexity into simplicity. Curr Opin Microbiol 2012;15:440–6.
339. Toju H, Tanabe AS, Yamamoto S et al. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One 2012;7:e40863.
340. Trojanowska D, Konturek P, Pajdo R et al. Are probiotics effective in the treatment of fungal colonization of the gastrointestinal tract? Experimental and clinical studies. J Physiol Pharmacol 2006;57:35–49.
341. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol 2009;587:4153–8.
342. Underhill DM, Iliev ID. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol 2014;14:405–16.
343. Underhill DM, Pearlman E. Immune Interactions with Pathogenic and commensal fungi: a two-way street. Immunity 2015;43:845–58.
344. Ursell LK, Metcalf JL, Parfrey LW et al. Defining the human microbiome. Nutr Rev 2012;70:S38–44.
345. van der Velden WJFM, Netea MG, de Haan AFJ et al. Role of the mycobiome in human acute graft-versus-host disease. Biol Blood Marrow Tr 2013;19:329–32.
346. van Dijk EL, Auger H, Jaszczyszyn Y et al. Ten years of next-generation sequencing technology. Trends Genet 2014;30:418–26.
347. Vautier S, Drummond RA, Redelinghuys P et al. Dectin-1 is not required for controlling Candida albicans colonization of the gastrointestinal tract. Infect Immun 2012;80:4216–22.
348. Vilgalys R. Taxonomic misidentification in public DNA databases. New Phytol 2003;160:4–5.
349. Vylkova S, Carman AJ, Danhof HA et al. The fungal pathogen Candida albicans autoinduces hyphal morphogenesis by raising extracellular pH. MBio 2011;2:e00055–11.
350. Wade WG. The oral microbiome in health and disease. Pharmacol Res 2013;69:137–43.
351. Waggoner-Fountain LA, Walker MW, Hollis RJ et al. Vertical and horizontal transmission of unique Candida species to premature newborns. Clin Infect Dis 1996;22:803–8.
352. Walters W, Hyde ER, Berg-Lyons D et al. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems 2015;1:e00009–15..
353. Wang JE, Warris A, Ellingsen EA et al. Involvement of CD14 and toll-like receptors in activation of human monocytes by Aspergillus fumigatus hyphae. Infect Immun 2001;69:2402–6.
354. Wang T, Pan D, Zhou Z et al. Dectin-3 deficiency promotes colitis development due to impaired antifungal innate immune responses in the gut. PLoS Pathog 2016;12: e1005662.
355. Wargo MJ, Hogan DA. Fungal—bacterial interactions: a mixed bag of mingling microbes. Curr Opin Microbiol 2006;9:359–64.
356. Washington K, Jagasia M. Pathology of graft-versus-host disease in the gastrointestinal tract. Hum Pathol 2009;40:909–17.
357. Weindl G, Wagener J, Schaller M. Interaction of the mucosal barrier with accessory immune cells during fungal infection. Int J Med Microbiol 2011;301:431–5.
358. Westbrook SD, Kirkpatrick WR, Freytes CO et al. Candida krusei sepsis secondary to oral colonization in a hemopoietic stem cell transplant recipient. Med Mycol 2007;45:187–90.
359. Wheeler ML, Limon JJ, Bar AS et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe 2016;19:865–73.
360. White JR, Maddox C, White O et al. CloVR-ITS: automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome 2013;1:6.
361. White SJ, Rosenbach A, Lephart P et al. Self-regulation of Candida albicans population size during GI colonization. PLoS Pathog 2007;3:e184.
362. White TJ, Bruns T, Lee S et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, in Innis MA, Gelfand DH, Sninsky JJ et al., (eds). PCR protocols: a guide to methods and applications. New York: Academic Press, Inc. 1990, pp. 315–322.
363. Whiteley AS, Jenkins S, Waite I et al. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 2012;91:80–8.
364. Wingard JR, Dick JD, Merz WG et al. Pathogenicity of Candida tropicalis and Candida albicans after gastrointestinal inoculation in mice. Infect Immun 1980;29:808–13.
365. van Woerden HC, Gregory C, Brown R et al. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infect Dis 2013;13:69.
366. Wu GD, Lewis JD, Hoffmann C et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 2010;10:206.
367. Yahr R, Schoch CL, Dentinger BTM. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos T R Soc B 2016;371:20150336.
368. Yamaguchi N, Sugita R, Miki A et al. Gastrointestinal Candida colonisation promotes sensitisation against food antigens by affecting the mucosal barrier in mice. Gut 2006;55:954–60.
369. Yu Z, Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 2004;36:808–13.
370. Zhang E, Tanaka T, Tajima M et al. Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects: skin fungal microbiota & atopic dermatitis. Microbiol Immunol 2011;55:625–32.
371. Zoll J, Snelders E, Verweij PE et al. Next-generation sequencing in the mycology lab. Curr Fungal Infect Rep 2016, DOI: 10.1007/s12281-016-0253-6.
372. Zwolinska-Wcislo M, Brzozowski T, Budak A et al. Effect of Candida colonization on human ulcerative colitis and the healing of inflammatory changes of the colon in the experimental model of colitis ulcerosa. Acta Physiol Pol 2009;60:107.