Referanslar

• Anderson, H.W. (1917). Yeast-like fungi of the human intestinal tract. J Infect Dis 21 (4):341-354. https://doi. org/10.1093/infdis/21.4.341. google scholar
• Arrieta, M. C., Arevalo, A., Stiemsma, L., Dimitriu, P., Chico, M. E., Loor, S., Vaca, M., Boutin, R. C. T., Morien, E., Jin, M., Turvey, S. E., Walter, J., Parfrey, L. W., Cooper, P. J., & Finlay, B. (2018). Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting. The Journal of allergy and clinical immunology, 142(2), 424-434.e10. https://doi.org/10.1016/jjaci.2017.08.041 google scholar
• Aykut, B., Pushalkar, S., Chen, R., Li, Q., Abengozar, R., Kim, J. I., Shadaloey, S. A., Wu, D., Preiss, P., Verma, N., Guo, Y., Saxena, A., Vardhan, M., Diskin, B., Wang, W., Leinwand, J., Kurz, E., Kochen Rossi, J. A., Hundeyin, M., Zambrinis, C., .. Miller, G. (2019). The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature, 574(7777), 264-267. https://doi.org/10.1038/s41586-019-1608-2 google scholar
• Azevedo, M. M., Teixeira-Santos, R., Silva, A. P., Cruz, L., Ricardo, E., Pina-Vaz, C., & Rodrigues, A. G. (2015). The effect of antibacterial and non-antibacterial compounds alone or associated with antifugals upon fun-gi. Frontiers in microbiology, 6, 669. https://doi.org/10.3389/fmicb.2015.00669 google scholar
• Bacher, P., Hohnstein, T., Beerbaum, E., Röcker, M., Blango, M. G., Kaufmann, S., Röhmel, J., Eschenhagen, P., Grehn, C., Seidel, K., Rickerts, V., Lozza, L., Stervbo, U., Nienen, M., Babel, N., Milleck, J., Assenma-cher, M., Cornely, O. A., Ziegler, M., Wisplinghoff, H., ... Scheffold, A. (2019). Human Anti-fungal Th17 Immunity and Pathology Rely on Cross-Reactivity against Candida albicans. Cell, 176(6), 1340-1355.e15. https://doi.org/10.1016/j.cell.2019.01.041 google scholar
• Bamford, C. V., Nobbs, A. H., Barbour, M. E., Lamont, R. J., & Jenkinson, H. F. (2015). Functional regions of Candida albicans hyphal cell wall protein Als3 that determine interaction with the oral bacterium Streptococ-cus gordonii. Microbiology (Reading, England), 161 (Pt 1), 18-29. https://doi.org/10.1099/mic.0.083378-0 google scholar
• Bandara, H. M., Cheung, B. P., Watt, R. M., Jin, L. J., & Samaranayake, L. P. (2013). Secretory products of Esc-herichia coli biofilm modulate Candida biofilm formation and hyphal development. Journal of investigative and clinical dentistry, 4(3), 186-199. https://doi.org/10.1111/jicd.12048 google scholar
• Becker, H. M., Apladas, A., Scharl, M., Fried, M., & Rogler, G. (2014). Probiotic Escherichia coli Nissle 1917 and commensal E. coli K12 differentially affect the inflammasome in intestinal epithelial cells. Digesti-on, 89(2), 110-118. https://doi.org/10.1159/000357521 google scholar
• Behnsen, J., Jellbauer, S., Wong, C. P., Edwards, R. A., George, M. D., Ouyang, W., & Raffatellu, M. (2014). The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria. Immu-nity, 40(2), 262-273. https://doi.org/10.1016/j.immuni.2014.01.003 google scholar
• Bianchi, C. M., Bianchi, H. A., Tadano, T., Paula, C. R., Hoffmann-Santos, H. D., Leite, D. P., Jr, & Hahn, R. C. (2016). FACTORS RELATED TO ORAL CANDIDIASIS IN ELDERLY USERS AND NON-USERS OF REMOVABLE DENTAL PROSTHESES. Revista do Instituto de Medicina Tropical de Sao Paulo, 58, 17. https://doi.org/10.1590/S1678-9946201658017 google scholar
• Bien, J., Palagani, V., & Bozko, P. (2013). The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease?. Therapeutic advances in gastroenterology, 6(1), 53-68. https://doi.org/10.1177/1756283X12454590 google scholar
• Bliss, J. M., Basavegowda, K. P., Watson, W. J., Sheikh, A. U., & Ryan, R. M. (2008). Vertical and horizontal transmission of Candida albicans in very low birth weight infants using DNA fingerprinting techniques. The Pediatric infectious disease journal, 27(3), 231-235. https://doi.org/10.1097/INF.0b013e31815bb69d google scholar
• Bouza, E., Burillo, A., Munoz, P., Guinea, J., Marin, M., & Rodriguez-Creixems, M. (2013). Mixed bloodst-ream infections involving bacteria and Candida spp. The Journal of antimicrobial chemotherapy, 68(8), 1881-1888. https://doi.org/10.1093/jac/dkt099 google scholar
• Böhm, L., Torsin, S., Tint, S. H., Eckstein, M. T., Ludwig, T., & Perez, J. C. (2017). The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice. PLoS pathogens, 13(10), e1006699. https://doi.org/10.1371/journal.ppat.1006699 google scholar
• Brandl, K., Plitas, G., Mihu, C. N., Ubeda, C., Jia, T., Fleisher, M., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2008). Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Natu-re, 455(7214), 804-807. https://doi.org/10.1038/nature07250 google scholar
• Brown, A. J., Brown, G. D., Netea, M. G., & Gow, N. A. (2014). Metabolism impacts upon Candida im-munogenicity and pathogenicity at multiple levels. Trends in microbiology, 22(11), 614-622. https://doi. org/10.1016/j.tim.2014.07.001 google scholar
• Brown, G. D., Denning, D. W., Gow, N. A., Levitz, S. M., Netea, M. G., & White, T. C. (2012). Hidden killers: human fungal infections. Science translational medicine, 4(165), 165rv13. https://doi.org/10.1126/scitrans-lmed.3004404 google scholar
• Buffie, C. G., & Pamer, E. G. (2013). Microbiota-mediated colonization resistance against intestinal pat-hogens. Nature reviews. Immunology, 13(11), 790-801. https://doi.org/10.1038/nri3535 google scholar
• Burke, K. E., & Lamont, J. T. (2014). Clostridium difficile infection: a worldwide disease. Gut and liver, 8(1), 1-6. https://doi.org/10.5009/gnl.2014.8.1.1 google scholar
• Cabral, D. J., Penumutchu, S., Norris, C., Morones-Ramirez, J. R., & Belenky, P. (2018). Microbial competition between Escherichia coli and Candida albicans reveals a soluble fungicidal factor. Microbial cell (Graz, Austria), 5(5), 249-255. https://doi.org/10.15698/mic2018.05.631 google scholar
• Calderone R. A. & Clancy C. J. (2012). Candida and candidiasis (2nd ed.). ASM Press. https://doi. org/10.1128/9781555817176 google scholar
• Carlson E. (1983a). Effect of strain of Staphylococcus aureus on synergism with Candida albicans resul-ting in mouse mortality and morbidity. Infection and immunity, 42(1), 285-292. https://doi.org/10.1128/ iai.42.1.285-292.1983 google scholar
• Carlson E. (1983b). Enhancement by Candida albicans of Staphylococcus aureus, Serratia marcescens, and Streptococcus faecalis in the establishment of infection in mice. Infection and immunity, 39(1), 193-197. https://doi.org/10.1128/iai.39.1.193-197.1983 google scholar
• Carruba, G., Pontieri, E., De Bernardis, F., Martino, P., & Cassone, A. (1991). DNA fingerprinting and elect-rophoretic karyotype of environmental and clinical isolates of Candida parapsilosis. Journal of clinical microbiology, 29(5), 916-922. https://doi.org/10.1128/jcm.29.5.916-922.1991 google scholar
• Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006). Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science (New York, N.Y.), 313(5790), 1126-1130. https://doi.org/10.1126/ science.1127119 google scholar
• Chacon, M. R., Lozano-Bartolome, J., Portero-Otm, M., Rodriguez, M. M., Xifra, G., Puig, J., Blasco, G., Ricart, W., Chaves, F. J., & Fernandez-Real, J. M. (2018). The gut mycobiome composition is linked to carotid atherosclerosis. Beneficial microbes, 9(2), 185-198. https://doi.org/10.3920/BM2017.0029 google scholar
• Chambers, P. J., & Pretorius, I. S. (2010). Fermenting knowledge: the history of winemaking, science and yeast research. EMBO reports, 11(12), 914-920. https://doi.org/10.1038/embor.2010.179 google scholar
• Chassaing, B., Compher, C., Bonhomme, B., Liu, Q., Tian, Y., Walters, W., Nessel, L., Delaroque, C., Hao, F., Gershuni, V., Chau, L., Ni, J., Bewtra, M., Albenberg, L., Bretin, A., McKeever, L., Ley, R. E., Patterson, A. D., Wu, G. D., Gewirtz, A. T., ... Lewis, J. D. (2022). Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolo-me. Gastroenterology, 162(3), 743-756. https://doi.org/10.1053/j.gastro.2021.11.006 google scholar
• Chen, C., Pande, K., French, S. D., Tuch, B. B., & Noble, S. M. (2011). An iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis. Cell host & microbe, 10(2), 118-135. https://doi.org/10.1016/j.chom.2011.07.005 google scholar
• Chen, Y., Chen, Z., Guo, R., Chen, N., Lu, H., Huang, S., Wang, J., & Li, L. (2011). Correlation between gast-rointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagnostic microbiology and infectious disease, 70(4), 492-498. https://doi.org/10.1016/j.diagmicrobio.2010.04.005 google scholar
• Chenault, S. S., & Earhart, C. F. (1992). Identification of hydrophobic proteins FepD and FepG of the Esche-richia coli ferrienterobactin permease. Journal of general microbiology, 138(10), 2167-2171. https://doi. org/10.1099/00221287-138-10-2167 google scholar
• Chin, S. F., Megat Mohd Azlan, P. I. H., Mazlan, L., & Neoh, H. M. (2018). Identification of Schizosaccha-romyces pombe in the guts of healthy individuals and patients with colorectal cancer: preliminary evidence from a gut microbiome secretome study. Gut pathogens, 10, 29. https://doi.org/10.1186/s13099-018-0258-5 google scholar
• Chin, V. K., Yong, V. C., Chong, P. P., Amin Nordin, S., Basir, R., & Abdullah, M. (2020). Mycobiome in the Gut: A Multiperspective Review. Mediators of inflammation, 2020, 9560684. https://doi.org/10.1155/2020/9560684 google scholar
• Chu, H., Duan, Y., Lang, S., Jiang, L., Wang, Y., Llorente, C., Liu, J., Mogavero, S., Bosques-Padilla, F., Abral-des, J. G., Vargas, V., Tu, X. M., Yang, L., Hou, X., Hube, B., Stârkel, P., & Schnabl, B. (2020). The Candida albicans exotoxin candidalysin promotes alcohol-associated liver disease. Journal of hepatology, 72(3), 391-400. https://doi.org/10.1016/j.jhep.2019.09.029 google scholar
• Corbin, B. D., Seeley, E. H., Raab, A., Feldmann, J., Miller, M. R., Torres, V. J., Anderson, K. L., Dattilo, B. M., Dunman, P. M., Gerads, R., Caprioli, R. M., Nacken, W., Chazin, W. J., & Skaar, E. P. (2008). Metal chela-tion and inhibition of bacterial growth in tissue abscesses. Science (New York, N.Y.), 319(5865), 962-965. https://doi.org/10.1126/science.1152449 google scholar
• Corthier, G., Dubos, F., & Ducluzeau, R. (1986). Prevention of Clostridium difficile induced mortality in gnoto-biotic mice by Saccharomyces boulardii. Canadian journal of microbiology, 32(11), 894-896. https://doi. org/10.1139/m86-164 google scholar
• Cruz, M. R., Graham, C. E., Gagliano, B. C., Lorenz, M. C., & Garsin, D. A. (2013). Enterococcus faecalis inhibits hyphal morphogenesis and virulence of Candida albicans. Infection and immunity, 81(1), 189-200. https://doi.org/10.1128/IAI.00914-12 google scholar
• David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559-563. https://doi.org/10.1038/ nature12820 google scholar
• de Sablet, T., Chassard, C., Bernalier-Donadille, A., Vareille, M., Gobert, A. P., & Martin, C. (2009). Human mic-robiota-secreted factors inhibit shiga toxin synthesis by enterohemorrhagic Escherichia coli O157:H7. Infe-ction and immunity, 77(2), 783-790. https://doi.org/10.1128/IAI.01048-08 google scholar
• De Vuyst, L., & Leroy, F. (2007). Bacteriocins from lactic acid bacteria: production, purification, and food applications. Journal of molecular microbiology and biotechnology, 13(4), 194-199. https://doi. org/10.1159/000104752 google scholar
• Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. International journal of systematic and evolutionary microbiology, 54(Pt 5), 1469-1476. https://doi.org/10.1099/ijs.0.02873-0 google scholar
• Dijkshoorn, L., Nemec, A., & Seifert, H. (2007). An increasing threat in hospitals: multidrug-resistant Acine-tobacter baumannii. Nature reviews. Microbiology, 5(12), 939-951. https://doi.org/10.1038/nrmicro1789 google scholar
• Doron, I., Leonardi, I., Li, X. V., Fiers, W. D., Semon, A., Bialt-DeCelie, M., Migaud, M., Gao, I. H., Lin, W. Y., Kusakabe, T., Puel, A., & Iliev, I. D. (2021). Human gut mycobiota tune immunity via CARD9-de-pendent induction of anti-fungal IgG antibodies. Cell, 184(4), 1017-1031.e14. https://doi.org/10.1016/j. cell.2021.01.016 google scholar
• Doron, I., Mesko, M., Li, X. V., Kusakabe, T., Leonardi, I., Shaw, D. G., Fiers, W. D., Lin, W. Y., Bialt-DeCelie, M., Roman, E., Longman, R. S., Pla, J., Wilson, P. C., & Iliev, I. D. (2021). Mycobiota-induced IgA anti-bodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease. Nature microbio-logy, 6(12), 1493-1504. https://doi.org/10.1038/s41564-021-00983-z google scholar
• Eggimann, P., Que, Y. A., Revelly, J. P., & Pagani, J. L. (2015). Preventing invasive candida infections. Where could we do better?. The Journal of hospital infection, 89(4), 302-308. https://doi.org/10.1016/j. jhin.2014.11.006 google scholar
• Enaud, R., Vandenborght, L. E., Coron, N., Bazin, T., Prevel, R., Schaeverbeke, T., Berger, P., Fayon, M., La-mireau, T., & Delhaes, L. (2018). The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis. Microorganisms, 6(1), 22. https://doi.org/10.3390/microorganisms6010022 google scholar
• Ene, I. V., Brunke, S., Brown, A. J., & Hube, B. (2014). Metabolism in fungal pathogenesis. Cold Spring Harbor perspectives in medicine, 4(12), a019695. https://doi.org/10.1101/cshperspect.a019695 google scholar
• Erb Downward, J. R., Falkowski, N. R., Mason, K. L., Muraglia, R., & Huffnagle, G. B. (2013). Modulation of post-antibiotic bacterial community reassembly and host response by Candida albicans. Scientific reports, 3, 2191. https://doi.org/10.1038/srep02191 google scholar
• Evans, C. C., LePard, K. J., Kwak, J. W., Stancukas, M. C., Laskowski, S., Dougherty, J., Moulton, L., Glawe, A., Wang, Y., Leone, V., Antonopoulos, D. A., Smith, D., Chang, E. B., & Ciancio, M. J. (2014). Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PloS one, 9(3), e92193. https://doi.org/10.1371/journal.pone.0092193 google scholar
• Falsetta, M. L., Klein, M. I., Colonne, P. M., Scott-Anne, K., Gregoire, S., Pai, C. H., Gonzalez-Begne, M., Watson, G., Krysan, D. J., Bowen, W. H., & Koo, H. (2014). Symbiotic relationship between Streptococcus mutans and Candida albicans synergizes virulence of plaque biofilms in vivo. Infection and immunity, 82(5), 1968-1981. https://doi.org/10.1128/IAI.00087-14 google scholar
• Fan, D., Coughlin, L. A., Neubauer, M. M., Kim, J., Kim, M. S., Zhan, X., Simms-Waldrip, T. R., Xie, Y., Ho-oper, L. V, & Koh, A. Y. (2015). Activation of HIF-1a and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nature medicine, 21(7), 808-814. https://doi.org/10.1038/nm.3871 google scholar
• Fiers, W. D., Gao, I. H., & Iliev, I. D. (2019). Gut mycobiota under scrutiny: fungal symbionts or environmental transients?. Current opinion in microbiology, 50, 79-86. https://doi.org/10.1016/j.mib.2019.09.010 google scholar
• Fischbach, M. A., & Sonnenburg, J. L. (2011). Eating for two: how metabolism establishes interspecies interac-tions in the gut. Cell host & microbe, 10(4), 336-347. https://doi.org/10.1016/j.chom.2011.10.002 google scholar
• Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012). Microbial degradation of complex car-bohydrates in the gut. Gut microbes, 3(4), 289-306. https://doi.org/10.4161/gmic.19897 google scholar
• Fox, E. P., Cowley, E. S., Nobile, C. J., Hartooni, N., Newman, D. K., & Johnson, A. D. (2014). Anaerobic ba-cteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures. Current biology : CB, 24(20), 2411-2416. https://doi.org/10.1016/j.cub.2014.08.057 google scholar
• Fujimura, K. E., Sitarik, A. R., Havstad, S., Lin, D. L., Levan, S., Fadrosh, D., Panzer, A. R., LaMere, B., Racka-ityte, E., Lukacs, N. W., Wegienka, G., Boushey, H. A., Ownby, D. R., Zoratti, E. M., Levin, A. M., Johnson, C. C., & Lynch, S. V. (2016). Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nature medicine, 22(10), 1187-1191. https://doi.org/10.1038/nm.4176 google scholar
• Gabaldon, T., & Carrete, L. (2016). The birth of a deadly yeast: tracing the evolutionary emergence of virulen-ce traits in Candida glabrata. FEMS yeast research, 16(2), fov110. https://doi.org/10.1093/femsyr/fov110 google scholar
• Gaboriau-Routhiau, V., Rakotobe, S., Lecuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., Eberl, G., Snel, J., Kelly, D., & Cerf-Bensussan, N. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity, 31(4), 677-689. https://doi.org/10.1016/j.immuni.2009.08.020 google scholar
• Gadanho, M., & Sampaio, J. P. (2005). Occurrence and diversity of yeasts in the mid-atlantic ridge hydrothermal fields near the Azores Archipelago. Microbial ecology, 50(3), 408-417. https://doi.org/10.1007/s00248-005-0195-y google scholar
• Gaddy, J. A., Tomaras, A. P., & Actis, L. A. (2009). The Acinetobacter baumannii 19606 OmpA protein plays a role in biofilm formation on abiotic surfaces and in the interaction of this pathogen with eukaryotic cel-ls. Infection and immunity, 77(8), 3150-3160. https://doi.org/10.1128/IAI.00096-09 google scholar
• Gagnon, M., Kheadr, E. E., Le Blay, G., & Fliss, I. (2004). In vitro inhibition of Escherichia coli O157:H7 by bifidobacterial strains of human origin. International journal of food microbiology, 92(1), 69-78. https:// doi.org/10.1016/j.ijfoodmicro.2003.07.010 google scholar
• Gao, R., Kong, C., Li, H., Huang, L., Qu, X., Qin, N., & Qin, H. (2017). Dysbiosis signature of mycobiota in colon polyp and colorectal cancer. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 36(12), 2457-2468. https://doi.org/10.1007/ s10096-017-3085-6 google scholar
• Ghannoum, M. A., Jurevic, R. J., Mukherjee, P. K., Cui, F., Sikaroodi, M., Naqvi, A., & Gillevet, P. M. (2010). Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS pathogens, 6(1), e1000713. https://doi.org/10.1371/journal.ppat.1000713 google scholar
• Giaffer, M. H., Clark, A., & Holdsworth, C. D. (1992). Antibodies to Saccharomyces cerevisiae in patients with Crohn’s disease and their possible pathogenic importance. Gut, 33(8), 1071-1075. https://doi.org/10.1136/ gut.33.8.1071 google scholar
• Gil, M. L., & Gozalbo, D. (2009). Role of Toll-like receptors in systemic Candida albicans infections. Frontiers in bioscience (Landmark edition), 14(2), 570-582. https://doi.org/10.2741/3263 google scholar
• Goddard M. R. (2008). Quantifying the complexities of Saccharomyces cerevisiae’s ecosystem engineering via fermentation. Ecology, 89(8), 2077-2082. https://doi.org/10.1890/07-2060.1 google scholar
• Godinez, I., Haneda, T., Raffatellu, M., George, M. D., Paixâo, T. A., Rolan, H. G., Santos, R. L., Dandekar, S., Tsolis, R. M., & Bâumler, A. J. (2008). T cells help to amplify inflammatory responses induced by Salmo-nella enterica serotype Typhimurium in the intestinal mucosa. Infection and immunity, 76(5), 2008-2017. https://doi.org/10.1128/IAI.01691-07 google scholar
• Gosiewski, T., Salamon, D., Szopa, M., Sroka, A., Malecki, M. T., & Bulanda, M. (2014). Quantitative evaluation of fungi of the genus Candida in the feces of adult patients with type 1 and 2 diabetes- a pilot study. Gut pathogens, 6(1), 43. https://doi.org/10.1186/s13099-014-0043-z google scholar
• Gouba, N., Raoult, D., & Drancourt, M. (2014). Gut microeukaryotes during anorexia nervosa: a case re-port. BMC research notes, 7, 33. https://doi.org/10.1186/1756-0500-7-33 google scholar
• Gouba, N., Raoult, D., & Drancourt, M. (2013). Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PloS one, 8(3), e59474. https://doi.org/10.1371/journal.pone.0059474 google scholar
• Graham, C. E., Cruz, M. R., Garsin, D. A., & Lorenz, M. C. (2017). Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans. Proceedings of the National Academy of Sciences of the United States of America, 114(17), 4507-4512. https://doi.org/10.1073/ pnas.1620432114 google scholar
• Hallen-Adams, H.E., Kachman, S.D., Kim, J., Legge, R.M., Martinez, I., 2015. Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community. Fungal Ecol. 15, 9-17. https://doi.or-g/10.1016/j.funeco.2015.01.006. google scholar
• Harriott, M. M., & Noverr, M. C. (2010). Ability of Candida albicans mutants to induce Staphylococcus au-reus vancomycin resistance during polymicrobial biofilm formation. Antimicrobial agents and chemothe-rapy, 54(9), 3746-3755. https://doi.org/10.1128/AAC.00573-10 google scholar
• Hayashi, H., Takahashi, R., Nishi, T., Sakamoto, M., & Benno, Y. (2005). Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restri-ction fragment length polymorphism. Journal of medical microbiology, 54(Pt 11), 1093-1101. https://doi. org/10.1099/jmm.0.45935-0 google scholar
• Hermann, C., Hermann, J., Munzel, U., & Rüchel, R. (1999). Bacterial flora accompanying Candida yeasts in clinical specimens. Mycoses, 42(11-12), 619-627. https://doi.org/10.1046/j.1439-0507.1999.00519.x google scholar
• Hernandez-Santos, N., & Gaffen, S. L. (2012). Th17 cells in immunity to Candida albicans. Cell host & micro-be, 11(5), 425-435. https://doi.org/10.1016/j.chom.2012.04.008 google scholar
• Herwald, S. E., & Kumamoto, C. A. (2014). Candida albicans Niche Specialization: Features That Distin-guish Biofilm Cells from Commensal Cells. Current fungal infection reports, 8(2), 179-184. https://doi. org/10.1007/s12281-014-0178-x google scholar
• Hickman, M. A., Zeng, G., Forche, A., Hirakawa, M. P., Abbey, D., Harrison, B. D., Wang, Y. M., Su, C. H., Bennett, R. J., Wang, Y., & Berman, J. (2013). The ‘obligate diploid’ Candida albicans forms mating-com-petent haploids. Nature, 494(7435), 55-59. https://doi.org/10.1038/nature11865 google scholar
• Hoarau, G., Mukherjee, P. K., Gower-Rousseau, C., Hager, C., Chandra, J., Retuerto, M. A., Neut, C., Vermeire, S., Clemente, J., Colombel, J. F., Fujioka, H., Poulain, D., Sendid, B., & Ghannoum, M. A. (2016). Bacteri-ome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio, 7(5), e01250-16. https://doi.org/10.1128/mBio.01250-16 google scholar
• Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013). Ar-chaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PloS one, 8(6), e66019. https://doi.org/10.1371/journal.pone.0066019 google scholar
• Hohmann E. L. (2001). Nontyphoidal salmonellosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 32(2), 263-269. https://doi.org/10.1086/318457 google scholar
• Holcombe, L. J., McAlester, G., Munro, C. A., Enjalbert, B., Brown, A. J. P., Gow, N. A. R., Ding, C., Butler, G., O’Gara, F., & Morrissey, J. P. (2010). Pseudomonas aeruginosa secreted factors impair biofilm develop-ment in Candida albicans. Microbiology (Reading, England), 156(Pt 5), 1476-1486. https://doi.org/10.1099/ mic.0.037549-0 google scholar
• Horsley, H., Malone-Lee, J., Holland, D., Tuz, M., Hibbert, A., Kelsey, M., Kupelian, A., & Rohn, J. L. (2013). Enterococcus faecalis subverts and invades the host urothelium in patients with chronic urinary tract infec-tion. PloS one, 8(12), e83637. https://doi.org/10.1371/journal.pone.0083637 google scholar
• Huang, J., Wu, Q., Lin, Z., Liu, S., Su, Q., & Pan, Y. (2020). Therapeutic effects of chitin from Pleurotus ery-ngii on high-fat diet induced obesity in rats. Acta scientiarum polonorum. Technologia alimentaria, 19(3), 279-289. https://doi.org/10.17306/J.AFS.0775 google scholar
• Ianiro, G., Tilg, H., & Gasbarrini, A. (2016). Antibiotics as deep modulators of gut microbiota: between good and evil. Gut, 65(11), 1906-1915. https://doi.org/10.1136/gutjnl-2016-312297 google scholar
• Iliev, I. D., Funari, V. A., Taylor, K. D., Nguyen, Q., Reyes, C. N., Strom, S. P., Brown, J., Becker, C. A., Fleshner, P. R., Dubinsky, M., Rotter, J. I., Wang, H. L., McGovern, D. P., Brown, G. D., & Underhill, D. M. (2012). Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science (New York, N.Y.), 336(6086), 1314-1317. https://doi.org/10.1126/science.1221789 google scholar
• Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., Tanoue, T., Imaoka, A., Itoh, K., Takeda, K., Umesaki, Y., Honda, K., & Littman, D. R. (2009). Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell, 139(3), 485-498. https:// doi.org/10.1016/j.cell.2009.09.033 google scholar
• Jain, U., Ver Heul, A. M., Xiong, S., Gregory, M. H., Demers, E. G., Kern, J. T., Lai, C. W., Muegge, B. D., Barisas, D. A. G., Leal-Ekman, J. S., Deepak, P., Ciorba, M. A., Liu, T. C., Hogan, D. A., Debbas, P., Braun, J., McGovern, D. P. B., Underhill, D. M., & Stappenbeck, T. S. (2021). Debaryomyces is enriched in Cro-hn’s disease intestinal tissue and impairs healing in mice. Science (New York, N.Y.), 371(6534), 1154-1159. https://doi.org/10.1126/science.abd0919 google scholar
• Jiang, T. T., Shao, T. Y., Ang, W. X. G., Kinder, J. M., Turner, L. H., Pham, G., Whitt, J., Alenghat, T., & Way, S. S. (2017). Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria. Cell host & microbe, 22(6), 809-816.e4. https://doi.org/10.1016/j.chom.2017.10.013 google scholar
• Juyal, D., Sharma, M., Pal, S., Rathaur, V. K., & Sharma, N. (2013). Emergence of non-albicans Candida species in neonatal candidemia. North American journal of medical sciences, 5(9), 541-545. https://doi. org/10.4103/1947-2714.118919 google scholar
• Kagami, S., Rizzo, H. L., Kurtz, S. E., Miller, L. S., & Blauvelt, A. (2010). IL-23 and IL-17A, but not IL-12 and IL-22, are required for optimal skin host defense against Candida albicans. Journal of immunology (Baltimore, Md. : 1950), 185(9), 5453-5462. https://doi.org/10.4049/jimmunol.1001153 google scholar
• Kamada, N., Kim, Y. G., Sham, H. P., Vallance, B. A., Puente, J. L., Martens, E. C., & Nunez, G. (2012). Regu-lated virulence controls the ability of a pathogen to compete with the gut microbiota. Science (New York, N.Y.), 336(6086), 1325-1329. https://doi.org/10.1126/science.1222195 google scholar
• Kang, D., , Su, M., , Duan, Y., , & Huang, Y., (2019). Eurotium cristatum, a potential probiotic fungus from Fuz-huan brick tea, alleviated obesity in mice by modulating gut microbiota. Food & function, 10(8), 5032-5045. https://doi.org/10.1039/c9fo00604d google scholar
• Kankainen, M., Paulin, L., Tynkkynen, S., von Ossowski, I., Reunanen, J., Partanen, P., Satokari, A., Vesterlund, S., Hendrickx, A. P., Lebeer, S., de Keersmaecker, S. C., Vanderleyden, J., Hâmâlâinen, T., Laukkanen, S., Salovuori, N., Ritari, J., Alatalo, E., Korpela, R., Mattila-Sandholm, T., ... de Vos, W. M. (2009). Compa-rative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proceedings of the National Academy of Sciences of the United States of America, 106(40), 1719317198. https://doi.org/10.1073/pnas.0908876106 google scholar
• Kapitan, M., Niemiec, M. J., Steimle, A., Frick, J. S., & Jacobsen, I. D. (2019). Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria. Current topics in microbiology and immunology, 422, 265-301. https://doi.org/10.1007/82_2018_117 google scholar
• Kasper, L., König, A., Koenig, P. A., Gresnigt, M. S., Westman, J., Drummond, R. A., Lionakis, M. S., GroB, O., Ruland, J., Naglik, J. R., & Hube, B. (2018). The fungal peptide toxin Candidalysin activates the NLRP3 inflammasome and causes cytolysis in mononuclear phagocytes. Nature communications, 9(1), 4260. https:// doi.org/10.1038/s41467-018-06607-1 google scholar
• Katagiri, H., Fukui, K., Nakamura, K., & Tanaka, A. (2018). Systemic hematogenous dissemination of mouse oral candidiasis is induced by oral mucositis. Odontology, 106(4), 389-397. https://doi.org/10.1007/s10266-018-0366-1 google scholar
• Kelesidis, T., & Pothoulakis, C. (2012). Efficacy and safety of the probiotic Saccharomyces boulardii for the pre-vention and therapy of gastrointestinal disorders. Therapeutic advances in gastroenterology, 5(2), 111-125. https://doi.org/10.1177/1756283X11428502 google scholar
• Khutoryanskiy V. V. (2015). Supramolecular materials: Longer and safer gastric residence. Nature materi-als, 14(10), 963-964. https://doi.org/10.1038/nmat4432 google scholar
• Kim, S. H., Yoon, Y. K., Kim, M. J., & Sohn, J. W. (2013). Risk factors for and clinical implications of mixed Candida/bacterial bloodstream infections. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 19(1), 62-68. https://doi.or-g/10.1111/j.1469-0691.2012.03906.x google scholar
• Kim, Y., & Mylonakis, E. (2011). Killing of Candida albicans filaments by Salmonella enterica serovar Typhi-murium is mediated by sopB effectors, parts of a type III secretion system. Eukaryotic cell, 10(6), 782-790. https://doi.org/10.1128/EC.00014-11 google scholar
• Klaerner, H. G., Uknis, M. E., Acton, R. D., Dahlberg, P. S., Carlone-Jambor, C., & Dunn, D. L. (1997). Can-dida albicans and Escherichia coli are synergistic pathogens during experimental microbial peritonitis. The Journal of surgical research, 70(2), 161-165. https://doi.org/10.1006/jsre.1997.5110 google scholar
• Klastersky, J., & Aoun, M. (2004). Opportunistic infections in patients with cancer. Annals of oncology : official journal of the European Society for Medical Oncology, 15 Suppl 4, iv329-iv335. https://doi.org/10.1093/ annonc/mdh947 google scholar
• Klotz, S. A., Chasin, B. S., Powell, B., Gaur, N. K., & Lipke, P. N. (2007). Polymicrobial bloodstream infections involving Candida species: analysis of patients and review of the literature. Diagnostic microbiology and infectious disease, 59(4), 401-406. https://doi.org/10.1016/j.diagmicrobio.2007.07.001 google scholar
• Kobayashi, C., Watanabe, Y., Oshima, M., Hirose, T., Yamasaki, M., Iwamoto, M., Iwatsuki, M., Asami, Y., Kuramochi, K., Wakae, K., Aizaki, H., Muramatsu, M., Sureau, C., Sunazuka, T., & Watashi, K. (2022). Fungal Secondary Metabolite Exophillic Acid Selectively Inhibits the Entry of Hepatitis B and D Viru-ses. Viruses, 14(4), 764. https://doi.org/10.3390/v14040764 google scholar
• Koc, A. N., Silici, S., MUTLU-SARIGUZEL, F., & Sagdic, O., (2007). Antifungal activity of propolis in four different fruit juices. Food Technology And Biotechnology , vol.45, no.1, 57-61. google scholar
• Komiyama, E. Y., Lepesqueur, L. S., Yassuda, C. G., Samaranayake, L. P., Parahitiyawa, N. B., Balducci, I., & Koga-Ito, C. Y. (2016). Enterococcus Species in the Oral Cavity: Prevalence, Virulence Factors and Anti-microbial Susceptibility. PloS one, 11(9), e0163001. https://doi.org/10.1371/journal.pone.0163001 google scholar
• Kong, H. H., & Segre, J. A. (2020). Cultivating fungal research. Science (New York, N.Y.), 368(6489), 365-366. https://doi.org/10.1126/science.aaz8086 google scholar
• Kong, E. F., Tsui, C., Kucharikova, S., Andes, D., Van Dijck, P., & Jabra-Rizk, M. A. (2016). Commensal Pro-tection of Staphylococcus aureus against Antimicrobials by Candida albicans Biofilm Matrix. mBio, 7(5), e01365-16. https://doi.org/10.1128/mBio.01365-16 google scholar
• Kowalewska, B., Zorena, K., Szmigiero-Kawko, M., W^z, P., & Mysliwiec, M. (2016). Higher diversity in fungal species discriminates children with type 1 diabetes mellitus from healthy control. Patient preference and adherence, 10, 591-599. https://doi.org/10.2147/PPA.S97852 google scholar
• Krause, J., Geginat, G., & Tammer, I. (2015). Prostaglandin E2 from Candida albicans Stimulates the Growth of Staphylococcus aureus in Mixed Biofilms. PloS one, 10(8), e0135404. https://doi.org/10.1371/journal. pone.0135404 google scholar
• Kurtzman, C. P., & Robnett, C. J. (1998). Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek, 73(4), 331-371. https://doi.org/10.1023/a:1001761008817 google scholar
• Lam, S., Zuo, T., Ho, M., Chan, F. K. L., Chan, P. K. S., & Ng, S. C. (2019). Review article: fungal alterations in inflammatory bowel diseases. Alimentary pharmacology & therapeutics, 50(11-12), 1159-1171. https:// doi.org/10.1111/apt.15523 google scholar
• Lang, S., Duan, Y., Liu, J., Torralba, M. G., Kuelbs, C., Ventura-Cots, M., Abraldes, J. G., Bosques-Padilla, F., Verna, E. C., Brown, R. S., Jr, Vargas, V, Altamirano, J., Caballeria, J., Shawcross, D., Lucey, M. R., Louvet, A., Mathurin, P., Garcia-Tsao, G., Ho, S. B., Tu, X. M., ... Schnabl, B. (2020). Intestinal Fungal Dysbiosis and Systemic Immune Response to Fungi in Patients With Alcoholic Hepatitis. Hepatology (Baltimore, Md.), 71(2), 522-538. https://doi.org/10.1002/hep.30832 google scholar
• Lebwohl, B., Sanders, D. S., & Green, P. H. R. (2018). Coeliac disease. Lancet (London, England), 391(10115), 70-81. https://doi.org/10.1016/S0140-6736(17)31796-8 google scholar
• Lee, J. S., Tato, C. M., Joyce-Shaikh, B., Gulen, M. F., Cayatte, C., Chen, Y., Blumenschein, W. M., Judo, M., Ayanoglu, G., McClanahan, T. K., Li, X., & Cua, D. J. (2015). Interleukin-23-Independent IL-17 Pro-duction Regulates Intestinal Epithelial Permeability. Immunity, 43(4), 727-738. https://doi.org/10.1016/j. immuni.2015.09.003 google scholar
• Lee, N. Y., Lee, H. C., Ko, N. Y., Chang, C. M., Shih, H. I., Wu, C. J., & Ko, W. C. (2007). Clinical and economic impact of multidrug resistance in nosocomial Acinetobacter baumannii bacteremia. Infection control and hospital epidemiology, 28(6), 713-719. https://doi.org/10.1086/517954 google scholar
• Lemoinne, S., Kemgang, A., Ben Belkacem, K., Straube, M., Jegou, S., Corpechot, C., Saint-Antoine IBD Network, Chazouilleres, O., Housset, C., & Sokol, H. (2020). Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. Gut, 69(1), 92-102. https://doi.org/10.1136/ gutjnl-2018-317791 google scholar
• Levison, M. E., & Pitsakis, P. G. (1987). Susceptibility to experimental Candida albicans urinary tract infection in the rat. The Journal of infectious diseases, 155(5), 841-846. https://doi.org/10.1093/infdis/155.5.841 google scholar
• Leonardi, I., Gao, I. H., Lin, W. Y., Allen, M., Li, X. V., Fiers, W. D., De Celie, M. B., Putzel, G. G., Yantiss, R. K., Johncilla, M., Colak, D., & Iliev, I. D. (2022). Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity. Cell, 185(5), 831-846.e14. https://doi.org/10.1016/j.cell.2022.01.017 google scholar
• Leonardi, I., Li, X., Semon, A., Li, D., Doron, I., Putzel, G., Bar, A., Prieto, D., Rescigno, M., McGovern, D. P. B., Pla, J., & Iliev, I. D. (2018). CX3CR1+ mononuclear phagocytes control immunity to intestinal fun-gi. Science (New York, N.Y.), 359(6372), 232-236. https://doi.org/10.1126/science.aao1503 google scholar
• Li, Q., Wang, C., Tang, C., He, Q., Li, N., & Li, J. (2014). Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. Journal of clinical gastroenterology, 48(6), 513-523. https://doi. org/10.1097/MCG.0000000000000035 google scholar
• Li, X. V., Leonardi, I., Putzel, G. G., Semon, A., Fiers, W. D., Kusakabe, T., Lin, W. Y., Gao, I. H., Doron, I., Gutierrez-Guerrero, A., DeCelie, M. B., Carriche, G. M., Mesko, M., Yang, C., Naglik, J. R., Hube, B., Scherl, E.J., & Iliev, I.D. (2022). Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature, 603(7902), 672-678. https://doi.org/10.1038/s41586-022-04502-w google scholar
• Li, X.V., Leonardi, I., & Iliev, I.D. (2019). Gut Mycobiota in Immunity and Inflammatory Disease. Immu-nity, 50(6), 1365-1379. https://doi.org/10.1016/j.immuni.2019.05.023 google scholar
• Li, Y., Komai-Koma, M., Gilchrist, D. S., Hsu, D. K., Liu, F. T., Springall, T., & Xu, D. (2008). Galectin-3 is a negative regulator of lipopolysaccharide-mediated inflammation. Journal of immunology (Baltimore, Md. : 1950), 181(4), 2781-2789. https://doi.org/10.4049/jimmunol.181.4.2781 google scholar
• Liguori, G., Lamas, B., Richard, M. L., Brandi, G., da Costa, G., Hoffmann, T. W., Di Simone, M. P., Calab-rese, C., Poggioli, G., Langella, P., Campieri, M., & Sokol, H. (2016). Fungal Dysbiosis in Mucosa-asso-ciated Microbiota of Crohn’s Disease Patients. Journal of Crohn’s & colitis, 10(3), 296-305. https://doi. org/10.1093/ecco-jcc/jjv209 google scholar
• Limon, J. J., Tang, J., Li, D., Wolf, A. J., Michelsen, K. S., Funari, V., Gargus, M., Nguyen, C., Sharma, P., May-mi, V. I., Iliev, I. D., Skalski, J. H., Brown, J., Landers, C., Borneman, J., Braun, J., Targan, S. R., McGovern, D. P. B., & Underhill, D. M. (2019). Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell host & microbe, 25(3), 377-388.e6. https://doi.org/10.1016/j.chom.2019.01.007 google scholar
• Limon, J. J., Skalski, J. H., & Underhill, D. M. (2017). Commensal Fungi in Health and Disease. Cell host & microbe, 22(2), 156-165. https://doi.org/10.1016/j.chom.2017.07.002 google scholar
• Ling, Z., Zhu, M., Liu, X., Shao, L., Cheng, Y., Yan, X., Jiang, R., & Wu, S. (2021). Fecal Fungal Dysbiosis in Chinese Patients With Alzheimer’s Disease. Frontiers in cell and developmental biology, 8, 631460. https:// doi.org/10.3389/fcell.2020.631460 google scholar
• Lo, H. J., Köhler, J. R., DiDomenico, B., Loebenberg, D., Cacciapuoti, A., & Fink, G. R. (1997). Nonfilamentous C. albicans mutants are avirulent. Cell, 90(5), 939-949. https://doi.org/10.1016/s0092-8674(00)80358-x google scholar
• Lopez-Garda, B., Lee, P. H., Yamasaki, K., & Gallo, R. L. (2005). Anti-fUngal activity of cathelicidins and their potential role in Candida albicans skin infection. The Journal of investigative dermatology, 125(1), 108-115. https://doi.org/10.1111/j.0022-202X.2005.23713.x google scholar
• Louis, P., Young, P., Holtrop, G., & Flint, H. J. (2010). Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environmental microbiology, 12(2), 304-314. https://doi.org/10.1111/j.1462-2920.2009.02066.x google scholar
• Luan, C., Xie, L., Yang, X., Miao, H., Lv, N., Zhang, R., Xiao, X., Hu, Y., Liu, Y., Wu, N., Zhu, Y., & Zhu, B. (2015). Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Scien-tific reports, 5, 7980. https://doi.org/10.1038/srep07980 google scholar
• Malani, A. N., Psarros, G., Malani, P. N., & Kauffman, C. A. (2011). Is age a risk factor for Candida glabrata colonisation?. Mycoses, 54(6), 531-537. https://doi.org/10.1111/j.1439-0507.2010.01941.x google scholar
• Mar Rodriguez, M., Perez, D., Javier Chaves, F., Esteve, E., Marin-Garcia, P., Xifra, G., Vendrell, J., Jove, M., Pamplona, R., Ricart, W., Portero-Otin, M., Chacon, M. R., & Fernandez Real, J. M. (2015). Obesity chan-ges the human gut mycobiome. Scientific reports, 5, 14600. https://doi.org/10.1038/srep14600 google scholar
• Markey, L., Shaban, L., Green, E. R., Lemon, K. P., Mecsas, J., & Kumamoto, C. A. (2018). Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infecti-on. Gut microbes, 9(6), 497-509. https://doi.org/10.1080/19490976.2018.1465158 google scholar
• Mason, K. L., Erb Downward, J. R., Falkowski, N. R., Young, V. B., Kao, J. Y., & Huffnagle, G. B. (2012a). Interplay between the gastric bacterial microbiota and Candida albicans during postantibiotic recolonization and gastritis. Infection and immunity, 80(1), 150-158. https://doi.org/10.1128/IAI.05162-11 google scholar
• Mason, K. L., Erb Downward, J. R., Mason, K. D., Falkowski, N. R., Eaton, K. A., Kao, J. Y., Young, V. B., & Huffnagle, G. B. (2012b). Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infection and immunity, 80(10), 3371-3380. https://doi.org/10.1128/IAI.00449-12 google scholar
• Massot, J., Sanchez, O., Couchy, R., Astoin, J., & Parodi, A. L. (1984). Bacterio-pharmacological activity of Saccharomyces boulardii in clindamycin-induced colitis in the hamster. Arzneimittel-Forschung, 34(7), 794-797. google scholar
• Meador, J. P., Caldwell, M. E., Cohen, P. S., & Conway, T. (2014). Escherichia coli pathotypes occupy distinct ni-ches in the mouse intestine. Infection and immunity, 82(5), 1931-1938. https://doi.org/10.1128/IAI.01435-13 google scholar
• Medeiros, A. O., Kohler, L. M., Hamdan, J. S., Missagia, B. S., Barbosa, F. A., & Rosa, C. A. (2008). Diversity and antifungal susceptibility of yeasts from tropical freshwater environments in Southeastern Brazil. Water research, 42(14), 3921-3929. https://doi.org/10.1016/j.watres.2008.05.026 google scholar
• Misic, A. M., Davis, M. F., Tyldsley, A. S., Hodkinson, B. P., Tolomeo, P., Hu, B., Nachamkin, I., Lautenbach, E., Morris, D. O., & Grice, E. A. (2015). The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites. Microbiome, 3, 2. https://doi.org/10.1186/s40168-014-0052-7 google scholar
• Mohamadi, J., Motaghi, M., Panahi, J., Havasian, M. R., Delpisheh, A., Azizian, M., & Pakzad, I. (2014). Anti-fungal resistance in candida isolated from oral and diaper rash candidiasis in neonates. Bioinformati-on, 10(11), 667-670. https://doi.org/10.6026/97320630010667 google scholar
• Mootsikapun P. (2007). Bacteremia in adult patients with acquired immunodeficiency syndrome in the northeast of Thailand. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 11(3), 226-231. https://doi.org/10.1016/j.ijid.2006.02.010 google scholar
• Morschhauser J. (2010). Regulation of white-opaque switching in Candida albicans. Medical microbiology and immunology, 199(3), 165-172. https://doi.org/10.1007/s00430-010-0147-0 google scholar
• Mukherjee, P. K., Chandra, J., Retuerto, M., Tatsuoka, C., Ghannoum, M. A., & McComsey, G. A. (2018). Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection. PloS one, 13(7), e0200285. https://doi.org/10.1371/journal. pone.0200285 google scholar
• Nagata, R., Nagano, H., Ogishima, D., Nakamura, Y., Hiruma, M., & Sugita, T. (2012). Transmission of the major skin microbiota, Malassezia, from mother to neonate. Pediatrics international : official journal of the Japan Pediatric Society, 54(3), 350-355. https://doi.org/10.1111/j.1442-200X.2012.03563.x google scholar
• Nagpal, R., Neth, B. J., Wang, S., Mishra, S. P., Craft, S., & Yadav, H. (2020). Gut mycobiome and its interaction with diet, gut bacteria and alzheimer’s disease markers in subjects with mild cognitive impairment: A pilot study. EBioMedicine, 59, 102950. https://doi.org/10.1016/j.ebiom.2020.102950 google scholar
• Nakagawa, T., Mori, N., Kajiwara, C., Kimura, S., Akasaka, Y., Ishii, Y., Saji, T., & Tateda, K. (2016). Endoge-nous IL-17 as a factor determining the severity of Clostridium difficile infection in mice. Journal of medical microbiology, 65(8), 821-827. https://doi.org/10.1099/jmm.0.000273 google scholar
• Nash, A. K., Auchtung, T. A., Wong, M. C., Smith, D. P., Gesell, J. R., Ross, M. C., Stewart, C. J., Metcalf, G. A., Muzny, D. M., Gibbs, R. A., Ajami, N. J., & Petrosino, J. F. (2017). The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome, 5(1), 153. https://doi.org/10.1186/s40168-017-0373-4 google scholar
• Nauseef, W. M., Root, R. K., & Malech, H. L. (1983). Biochemical and immunologic analysis of hereditary mye-loperoxidase deficiency. The Journal of clinical investigation, 71(5), 1297-1307. https://doi.org/10.1172/ jci110880 google scholar
• Nelson, A., Stewart, C. J., Kennedy, N. A., Lodge, J. K., Tremelling, M., UK IBD Genetics Consortium, Pro-bert, C. S., Parkes, M., Mansfield, J. C., Smith, D. L., Hold, G. L., Lees, C. W., Bridge, S. H., & Lamb, C. A. (2021). The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation. Journal of Crohn’s & colitis, 15(5), 800-812. https://doi.org/10.1093/ecco-jcc/jjaa220 google scholar
• Nerandzic, M. M., Mullane, K., Miller, M. A., Babakhani, F., & Donskey, C. J. (2012). Reduced acquisition and overgrowth of vancomycin-resistant enterococci and Candida species in patients treated with fidaxomicin versus vancomycin for Clostridium difficile infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 55 Suppl 2 (Suppl 2), S121-S126. https://doi.org/10.1093/ cid/cis440 google scholar
• Nielsen, D. S., H0nholt, S., Tano-Debrah, K., & Jespersen, L. (2005). Yeast populations associated with Ghanaian cocoa fermentations analysed using denaturing gradient gel electrophoresis (DGGE). Yeast (Chichester, England), 22(4), 271-284. https://doi.org/10.1002/yea.1207 google scholar
• Nizet, V., & Johnson, R. S. (2009). Interdependence of hypoxic and innate immune responses. Nature reviews. Immunology, 9(9), 609-617. https://doi.org/10.1038/nri2607 google scholar
• Noble, S. M., Gianetti, B. A., & Witchley, J. N. (2017). Candida albicans cell-type switching and functional plasticity in the mammalian host. Nature reviews. Microbiology, 15(2), 96-108. https://doi.org/10.1038/ nrmicro.2016.157 google scholar
• Noverr, M. C., & Huffnagle, G. B. (2004). Regulation of Candida albicans morphogenesis by fatty acid me-tabolites. Infection and immunity, 72(11), 6206-6210. https://doi.org/10.1128/IAI.72.11.6206-6210.2004 google scholar
• Odds, F. C., Davidson, A. D., Jacobsen, M. D., Tavanti, A., Whyte, J. A., Kibbler, C. C., Ellis, D. H., Maiden, M. C., Shaw, D. J., & Gow, N. A. (2006). Candida albicans strain maintenance, replacement, and microvariation demonstrated by multilocus sequence typing. Journal of clinical microbiology, 44(10), 3647-3658. https:// doi.org/10.1128/JCM.00934-06 google scholar
• Ost, K. S., O’Meara, T. R., Stephens, W. Z., Chiaro, T., Zhou, H., Penman, J., Bell, R., Catanzaro, J. R., Song, D., Singh, S., Call, D. H., Hwang-Wong, E., Hanson, K. E., Valentine, J. F., Christensen, K. A., O’Connell, R. M., Cormack, B., İbrahim, A. S., Palm, N. W., Noble, S. M., .. Round, J. L. (2021). Adaptive immunity induces mutualism between commensal eukaryotes. Nature, 596(7870), 114-118. https://doi.org/10.1038/ s41586-021-03722-w google scholar
• Pande, K., Chen, C., & Noble, S. M. (2013). Passage through the mammalian gut triggers a phenotypic switch that promotes Candida albicans commensalism. Nature genetics, 45(9), 1088-1091. https://doi.org/10.1038/ ng.2710 google scholar
• Pappas P. G. (2006). Invasive candidiasis. Infectious disease clinics of North America, 20(3), 485-506. https:// doi.org/10.1016/j.idc.2006.07.004 google scholar
• Pasqualotto, A. C., Nedel, W. L., Machado, T. S., & Severo, L. C. (2006). Risk factors and outcome for no-socomial breakthrough candidaemia. The Journal of infection, 52(3), 216-222. https://doi.org/10.1016/j. jinf.2005.04.020 google scholar
• Peleg, A. Y., Tampakakis, E., Fuchs, B. B., Eliopoulos, G. M., Moellering, R. C., Jr, & Mylonakis, E. (2008). Prokaryote-eukaryote interactions identified by using Caenorhabditis elegans. Proceedings of the Natio-nal Academy of Sciences of the United States of America, 105(38), 14585-14590. https://doi.org/10.1073/ pnas.0805048105 google scholar
• Pennacchia, C., Blaiotta, G., Pepe, O., & Villani, F. (2008). Isolation of Saccharomyces cerevisiae strains from different food matrices and their preliminary selection for a potential use as probiotics. Journal of applied microbiology, 105(6), 1919-1928. https://doi.org/10.1111/j.1365-2672.2008.03968.x google scholar
• Pepin, J., Saheb, N., Coulombe, M. A., Alary, M. E., Corriveau, M. P., Authier, S., Leblanc, M., Rivard, G., Bettez, M., Primeau, V., Nguyen, M., Jacob, C. E., & Lanthier, L. (2005). Emergence of fluoroquinolones as the predominant risk factor for Clostridium difficile-associated diarrhea: a cohort study during an epi-demic in Quebec. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 41(9), 1254-1260. https://doi.org/10.1086/496986 google scholar
• Perez J. C. (2021). Fungi of the human gut microbiota: Roles and significance. International journal of medical microbiology : IJMM, 311(3), 151490. https://doi.org/10.1016/j.ijmm.2021.151490 google scholar
• Perez J. C. (2019). Candida albicans dwelling in the mammalian gut. Current opinion in microbiology, 52, 41-46. https://doi.org/10.1016/j.mib.2019.04.007 google scholar
• Pessione E. (2012). Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows. Frontiers in cellular and infection microbiology, 2, 86. https://doi.org/10.3389/fcimb.2012.00086 google scholar
• Peyssonnaux, C., Datta, V., Cramer, T., Doedens, A., Theodorakis, E. A., Gallo, R. L., Hurtado-Ziola, N., Nizet, V., & Johnson, R. S. (2005). HIF-1alpha expression regulates the bactericidal capacity of phagocytes. The Journal of clinical investigation, 115(7), 1806-1815. https://doi.org/10.1172/JCI23865 google scholar
• Pfaller, M. A., Moet, G. J., Messer, S. A., Jones, R. N., & Castanheira, M. (2011). Geographic variations in species distribution and echinocandin and azole antifungal resistance rates among Candida bloodstream infection isolates: report from the SENTRY Antimicrobial Surveillance Program (2008 to 2009). Journal of clinical microbiology, 49(1), 396-399. https://doi.org/10.1128/JCM.01398-10 google scholar
• Pierce, J. V., Dignard, D., Whiteway, M., & Kumamoto, C. A. (2013). Normal adaptation of Candida albicans to the murine gastrointestinal tract requires Efg1p-dependent regulation of metabolic and host defense genes. Eukaryotic cell, 12(1), 37-49. https://doi.org/10.1128/EC.00236-12 google scholar
• Pulimood, S., Ganesan, L., Alangaden, G., & Chandrasekar, P. (2002). Polymicrobial candidemia. Diagnostic microbiology and infectious disease, 44(4), 353-357. https://doi.org/10.1016/s0732-8893(02)00460-1 google scholar
• Raffatellu, M., George, M. D., Akiyama, Y., Hornsby, M. J., Nuccio, S. P., Paixao, T. A., Butler, B. P., Chu, H., Santos, R. L., Berger, T., Mak, T. W., Tsolis, R. M., Bevins, C. L., Solnick, J. V., Dandekar, S., & Baumler, A. J. (2009). Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell host & microbe, 5(5), 476-486. https://doi.org/10.1016/j. chom.2009.03.011 google scholar
• Raman, A. S., Gehrig, J. L., Venkatesh, S., Chang, H. W., Hibberd, M. C., Subramanian, S., Kang, G., Bessong, P. O., Lima, A. A. M., Kosek, M. N., Petri, W. A., Jr, Rodionov, D. A., Arzamasov, A. A., Leyn, S. A., Osterman, A. L., Huq, S., Mostafa, I., İslam, M., Mahfuz, M., Haque, R., ... Gordon, J. I. (2019). A sparse covarying unit that describes healthy and impaired human gut microbiota development. Science (New York, N.Y.), 365(6449), eaau4735. https://doi.org/10.1126/science.aau4735 google scholar
• Rao, C., Coyte, K. Z., Bainter, W., Geha, R. S., Martin, C. R., & Rakoff-Nahoum, S. (2021). Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature, 591(7851), 633-638. https://doi. org/10.1038/s41586-021-03241-8 google scholar
• Rea, M. C., Sit, C. S., Clayton, E., O’Connor, P. M., Whittal, R. M., Zheng, J., Vederas, J. C., Ross, R. P., & Hill, C. (2010). Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. Proceedings of the National Academy of Sciences of the United States of America, 107(20), 9352-9357. https://doi.org/10.1073/pnas.0913554107 google scholar
• Richard, M. L., & Sokol, H. (2019). The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nature reviews. Gastroenterology & hepatology, 16(6), 331-345. https:// doi.org/10.1038/s41575-019-0121-2 google scholar
• Richard, M. L., Liguori, G., Lamas, B., Brandi, G., da Costa, G., Hoffmann, T. W., Pierluigi Di Simone, M., Calabrese, C., Poggioli, G., Langella, P., Campieri, M., & Sokol, H. (2018). Mucosa-associated microbiota dysbiosis in colitis associated cancer. Gut microbes, 9(2), 131-142. https://doi.org/10.1080/19490976.20 17.1379637 google scholar
• Roilides, E., Farmaki, E., Evdoridou, J., Francesconi, A., Kasai, M., Filioti, J., Tsivitanidou, M., Sofianou, D., Kremenopoulos, G., & Walsh, T. J. (2003). Candida tropicalis in a neonatal intensive care unit: epidemio-logic and molecular analysis of an outbreak of infection with an uncommon neonatal pathogen. Journal of clinical microbiology, 41(2), 735-741. https://doi.org/10.1128/JCM.41.2.735-741.2003 google scholar
• Rosenbach, A., Dignard, D., Pierce, J. V., Whiteway, M., & Kumamoto, C. A. (2010). Adaptations of Candi-da albicans for growth in the mammalian intestinal tract. Eukaryotic cell, 9(7), 1075-1086. https://doi. org/10.1128/EC.00034-10 google scholar
• Roth, S., & Ruland, J. (2013). Caspase recruitment domain-containing protein 9 signaling in innate immunity and inflammation. Trends in immunology, 34(6), 243-250. https://doi.org/10.1016Zj.it.2013.02.006 google scholar
• Rubino, S. J., Geddes, K., & Girardin, S. E. (2012). Innate IL-17 and IL-22 responses to enteric bacterial pat-hogens. Trends in immunology, 33(3), 112-118. https://doi.org/10.1016/j.it.2012.01.003 google scholar
• Ruiz-Herrera, J., Elorza, M. V., Valentm, E., & Sentandreu, R. (2006). Molecular organization of the cell wall of Candida albicans and its relation to pathogenicity. FEMS yeast research, 6(1), 14-29. https://doi.or-g/10.1111/j.1567-1364.2005.00017.x google scholar
• Sassone-Corsi, M., Nuccio, S. P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raf-fatellu, M. (2016). Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Natu-re, 540(7632), 280-283. https://doi.org/10.1038/nature20557 google scholar
• Sawa, N., Wilaipun, P., Kinoshita, S., Zendo, T., Leelawatcharamas, V., Nakayama, J., & Sonomoto, K. (2012). Isolation and characterization of enterocin W, a novel two-peptide lantibiotic produced by Enterococcus faecalis NKR-4-1. Applied and environmental microbiology, 78(3), 900-903. https://doi.org/10.1128/ AEM.06497-11 google scholar
• Schlecht, L. M., Peters, B. M., Krom, B. P., Freiberg, J. A., Hansch, G. M., Filler, S. G., Jabra-Rizk, M. A., & Shirtliff, M. E. (2015). Systemic Staphylococcus aureus infection mediated by Candida albicans hyphal invasion of mucosal tissue. Microbiology (Reading, England), 161(Pt 1), 168-181. https://doi.org/10.1099/ mic.0.083485-0 google scholar
• Severance, E. G., Gressitt, K. L., Stallings, C. R., Katsafanas, E., Schweinfurth, L. A., Savage, C. L., Adamos, M. B., Sweeney, K. M., Origoni, A. E., Khushalani, S., Leweke, F. M., Dickerson, F. B., & Yolken, R. H. (2016). Candida albicans exposures, sex specificity and cognitive deficits in schizophrenia and bipolar disorder. NPJ schizophrenia, 2, 16018. https://doi.org/10.1038/npjschz.2016.18 google scholar
• Severance, E. G., Alaedini, A., Yang, S., Halling, M., Gressitt, K. L., Stallings, C. R., Origoni, A. E., Vaughan, C., Khushalani, S., Leweke, F. M., Dickerson, F. B., & Yolken, R. H. (2012). Gastrointestinal inflammation and associated immune activation in schizophrenia. Schizophrenia research, 138(1), 48-53. https://doi. org/10.1016/j.schres.2012.02.025 google scholar
• Shah, S., Locca, A., Dorsett, Y., Cantoni, C., Ghezzi, L., Lin, Q., Bokoliya, S., Panier, H., Suther, C., Gormley, M., Liu, Y., Evans, E., Mikesell, R., Obert, K., Salter, A., Cross, A. H., Tarr, P. I., Lovett-Racke, A., Piccio, L., & Zhou, Y. (2021). Alterations of the gut mycobiome in patients with MS. EBioMedicine, 71, 103557. https://doi.org/10.1016/j.ebiom.2021.103557 google scholar
• Slutsky, B., Staebell, M., Anderson, J., Risen, L., Pfaller, M., & Soll, D. R. (1987). “White-opaque transition”: a second high-frequency switching system in Candida albicans. Journal of bacteriology, 169(1), 189-197. https://doi.org/10.1128/jb.169.1.189-197.1987 google scholar
• Sohnle, P. G., Hahn, B. L., & Santhanagopalan, V. (1996). Inhibition of Candida albicans growth by calprotectin in the absence of direct contact with the organisms. The Journal of infectious diseases, 174(6), 1369-1372. https://doi.org/10.1093/infdis/174.6.1369 google scholar
• Sokol, H., Leducq, V., Aschard, H., Pham, H. P., Jegou, S., Landman, C., Cohen, D., Liguori, G., Bourrier, A., Nion-Larmurier, I., Cosnes, J., Seksik, P., Langella, P., Skurnik, D., Richard, M. L., & Beaugerie, L. (2017). Fungal microbiota dysbiosis in IBD. Gut, 66(6), 1039-1048. https://doi.org/10.1136/gutjnl-2015-310746 google scholar
• Sonnenburg, J. L., Chen, C. T., & Gordon, J. I. (2006). Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS biology, 4(12), e413. https://doi.org/10.1371/journal.pbio.0040413 google scholar
• Spatz, M., & Richard, M. L. (2020). Overview of the Potential Role of Malassezia in Gut Health and Disea-se. Frontiers in cellular and infection microbiology, 10, 201. https://doi.org/10.3389/fcimb.2020.00201 google scholar
• Stelter, C., Kappeli, R., König, C., Krah, A., Hardt, W. D., Stecher, B., & Bumann, D. (2011). Salmonella-indu-ced mucosal lectin ReglIIp kills competing gut microbiota. PloS one, 6(6), e20749. https://doi.org/10.1371/ journal.pone.0020749 google scholar
• Stoldt, V. R., Sonneborn, A., Leuker, C. E., & Ernst, J. F. (1997). Efg1p, an essential regulator of morphoge-nesis of the human pathogen Candida albicans, is a member of a conserved class of bHLH proteins regu-lating morphogenetic processes in fungi. The EMBO journal, 16(8), 1982-1991. https://doi.org/10.1093/ emboj/16.8.1982 google scholar
• Strati, F., Calabro, A., Donati, C., De Felice, C., Hayek, J., Jousson, O., Leoncini, S., Renzi, D., Rizzetto, L., De Filippo, C., & Cavalieri, D. (2018). Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent traits and capacity to persist within the host. BMC gastroenterology, 18(1), 57. https:// doi.org/10.1186/s12876-018-0785-z google scholar
• Strati, F., Cavalieri, D., Albanese, D., De Felice, C., Donati, C., Hayek, J., Jousson, O., Leoncini, S., Renzi, D., Calabro, A., & De Filippo, C. (2017). New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome, 5(1), 24. https://doi.org/10.1186/s40168-017-0242-1 google scholar
• Strati, F., Cavalieri, D., Albanese, D., De Felice, C., Donati, C., Hayek, J., Jousson, O., Leoncini, S., Pindo, M., Renzi, D., Rizzetto, L., Stefanini, I., Calabro, A., & De Filippo, C. (2016). Altered gut microbiota in Rett syndrome. Microbiome, 4(1), 41. https://doi.org/10.1186/s40168-016-0185-y google scholar
• Strati, F., Di Paola, M., Stefanini, I., Albanese, D., Rizzetto, L., Lionetti, P., Calabro, A., Jousson, O., Donati, C., Cavalieri, D., & De Filippo, C. (2016). Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract. Frontiers in microbiology, 7, 1227. https://doi.org/10.3389/fmicb.2016.01227 google scholar
• Sudbery P. E. (2011). Growth of Candida albicans hyphae. Nature reviews. Microbiology, 9(10), 737-748. https:// doi.org/10.1038/nrmicro2636 google scholar
• Suh, S. O., Nguyen, N. H., & Blackwell, M. (2008). Yeasts isolated from plant-associated beetles and other insects: seven novel Candida species near Candida albicans. FEMS yeast research, 8(1), 88-102. https:// doi.org/10.1111/j.1567-1364.2007.00320.x google scholar
• Sun, S., Sun, L., Wang, K., Qiao, S., Zhao, X., Hu, X., Chen, W., Zhang, S., Li, H., Dai, H., & Liu, H. (2021). The gut commensal fungus, Candida parapsilosis, promotes high fat-diet induced obesity in mice. Commu-nications biology, 4(1), 1220. https://doi.org/10.1038/s42003-021-02753-3 google scholar
• Tao, L., Du, H., Guan, G., Dai, Y., Nobile, C. J., Liang, W., Cao, C., Zhang, Q., Zhong, J., & Huang, G. (2014). Discovery of a “white-gray-opaque” tristable phenotypic switching system in candida albicans: roles of non-genetic diversity in host adaptation. PLoS biology, 12(4), e1001830. https://doi.org/10.1371/journal. pbio.1001830 google scholar
• Thewes, S., Kretschmar, M., Park, H., Schaller, M., Filler, S. G., & Hube, B. (2007). In vivo and ex vivo com-parative transcriptional profiling of invasive and non-invasive Candida albicans isolates identifies genes associated with tissue invasion. Molecular microbiology, 63(6), 1606-1628. https://doi.org/10.1111/j.1365-2958.2007.05614.x google scholar
• Torosantucci, A., Romagnoli, G., Chiani, P., Stringaro, A., Crateri, P., Mariotti, S., Teloni, R., Arancia, G., Cas-sone, A., & Nisini, R. (2004). Candida albicans yeast and germ tube forms interfere differently with human monocyte differentiation into dendritic cells: a novel dimorphism-dependent mechanism to escape the host’s immune response. Infection and immunity, 72(2), 833-843. https://doi.org/10.1128/IAI.72.2.833-843.2004 google scholar
• Trofa, D., Gacser, A., & Nosanchuk, J. D. (2008). Candida parapsilosis, an emerging fungal pathogen. Clinical microbiology reviews, 21(4), 606-625. https://doi.org/10.1128/CMR.00013-08 google scholar
• Uryu, H., Hashimoto, D., Kato, K., Hayase, E., Matsuoka, S., Ogasawara, R., Takahashi, S., Maeda, Y., Iwasaki, H., Miyamoto, T., Saijo, S., Iwakura, Y., Hill, G. R., Akashi, K., & Teshima, T. (2015). a-Mannan indu-ces Th17-mediated pulmonary graft-versus-host disease in mice. Blood, 125(19), 3014-3023. https://doi. org/10.1182/blood-2014-12-615781 google scholar
• van der Velden, W. J., Netea, M. G., de Haan, A. F., Huls, G. A., Donnelly, J. P., & Blijlevens, N. M. (2013). Role of the mycobiome in human acute graft-versus-host disease. Biology of blood and marrow transplan-tation : journal of the American Society for Blood and Marrow Transplantation, 19(2), 329-332. https:// doi.org/10.1016/j.bbmt.2012.11.008 google scholar
• Van Dyken, S. J., Garcia, D., Porter, P., Huang, X., Quinlan, P. J., Blanc, P. D., Corry, D. B., & Locksley, R. M. (2011). Fungal chitin from asthma-associated home environments induces eosinophilic lung infiltrati-on. Journal of immunology (Baltimore, Md. : 1950), 187(5), 2261-2267. https://doi.org/10.4049/jimmu-nol.1100972 google scholar
• van Leeuwen, P. T., van der Peet, J. M., Bikker, F. J., Hoogenkamp, M. A., Oliveira Paiva, A. M., Kostidis, S., Mayboroda, O. A., Smits, W. K., & Krom, B. P. (2016). Interspecies Interactions between Clostridium diffi-cile and Candida albicans. mSphere, 1(6), e00187-16. https://doi.org/10.1128/mSphere.00187-16 google scholar
• van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F., Tijssen, J. G., Speelman, P., Dijkgraaf, M. G., & Keller, J. J. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England journal of medicine, 368(5), 407-415. https://doi.org/10.1056/NEJMoa1205037 google scholar
• Vasquez, A., Jakobsson, T., Ahrne, S., Forsum, U., & Molin, G. (2002). Vaginal lactobacillus flora of he-althy Swedish women. Journal of clinical microbiology, 40(8), 2746-2749. https://doi.org/10.1128/ JCM.40.8.2746-2749.2002 google scholar
• Vautier, S., Drummond, R. A., Chen, K., Murray, G. I., Kadosh, D., Brown, A. J., Gow, N. A., MacCallum, D. M., Kolls, J. K., & Brown, G. D. (2015). Candida albicans colonization and dissemination from the muri-ne gastrointestinal tract: the influence of morphology and Th17 immunity. Cellular microbiology, 17(4), 445-450. https://doi.org/10.1111/cmi.12388 google scholar
• Vermeire, S., Joossens, S., Peeters, M., Monsuur, F., Marien, G., Bossuyt, X., Groenen, P., Vlietinck, R., & Rutgeerts, P. (2001). Comparative study of ASCA (Anti-Saccharomyces cerevisiae antibody) assays in inflammatory bowel disease. Gastroenterology, 120(4), 827-833. https://doi.org/10.1053/gast.2001.22546 google scholar
• Walker, L. A., Maccallum, D. M., Bertram, G., Gow, N. A., Odds, F. C., & Brown, A. J. (2009). Genome-wide analysis of Candida albicans gene expression patterns during infection of the mammalian kidney. Fungal genetics and biology : FG & B, 46(2), 210-219. https://doi.org/10.1016/j.fgb.2008.10.012 google scholar
• Wang, Y., & Xu, X. L. (2008). Bacterial peptidoglycan-derived molecules activate Candida albicans hyphal growth. Communicative & integrative biology, 1(2), 137-139. https://doi.org/10.4161/cib.1.2.6870 google scholar
• Ward, T. L., Dominguez-Bello, M. G., Heisel, T., Al-Ghalith, G., Knights, D., & Gale, C. A. (2018). Development of the Human Mycobiome over the First Month of Life and across Body Sites. mSystems, 3(3), e00140-17. https://doi.org/10.1128/mSystems.00140-17 google scholar
• Wheeler, M. L., Limon, J. J., Bar, A. S., Leal, C. A., Gargus, M., Tang, J., Brown, J., Funari, V. A., Wang, H. L., Crother, T. R., Arditi, M., Underhill, D. M., & Iliev, I. D. (2016). Immunological Consequences of Intestinal Fungal Dysbiosis. Cell host & microbe, 19(6), 865-873. https://doi.org/10.1016/j.chom.2016.05.003 google scholar
• White, S. J., Rosenbach, A., Lephart, P., Nguyen, D., Benjamin, A., Tzipori, S., Whiteway, M., Mecsas, J., & Kumamoto, C. A. (2007). Self-regulation of Candida albicans population size during GI colonization. PLoS pathogens, 3(12), e184. https://doi.org/10.1371/journal.ppat.0030184 google scholar
• Wu, X., Xia, Y., He, F., Zhu, C., & Ren, W. (2021). Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. Microbiome, 9(1), 60. https://doi.org/10.1186/s40168-021-01024-x google scholar
• Xu, J., Zhang, Y., Wang, X., Ren, X., & Liu, Y. (2020). Changes and roles of intestinal fungal microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease. American journal of translational research, 12(7), 3445-3460. google scholar
• Yang, A. M., Inamine, T., Hochrath, K., Chen, P., Wang, L., Llorente, C., Bluemel, S., Hartmann, P., Xu, J., Koyama, Y., Kisseleva, T., Torralba, M. G., Moncera, K., Beeri, K., Chen, C. S., Freese, K., Hellerbrand, C., Lee, S. M., Hoffman, H. M., Mehal, W. Z., ... Schnabl, B. (2017). Intestinal fungi contribute to deve-lopment of alcoholic liver disease. The Journal of clinical investigation, 127(7), 2829-2841. https://doi. org/10.1172/JCI90562 google scholar
• Yang, Y. L., Lin, C. C., Chang, T. P., Lauderdale, T. L., Chen, H. T., Lee, C. F., Hsieh, C. W., Chen, P. C., & Lo, H. J. (2012). Comparison of human and soil Candida tropicalis isolates with reduced susceptibility to fluconazole. PloS one, 7(4), e34609. https://doi.org/10.1371/journal.pone.0034609 google scholar
• Yapar N. (2014). Epidemiology and risk factors for invasive candidiasis. Therapeutics and clinical risk mana-gement, 10, 95-105. https://doi.org/10.2147/TCRM.S40160 google scholar
• Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hi-dalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R., .. Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222-227. https://doi.org/10.1038/ nature11053 google scholar
• Yu, X. Y., Fu, F., Kong, W. N., Xuan, Q. K., Wen, D. H., Chen, X. Q., He, Y. M., He, L. H., Guo, J., Zhou, A. P., Xi, Y. H., Ni, L. J., Yao, Y. F., & Wu, W. J. (2018). Streptococcus agalactiae Inhibits Candida albicans Hy-phal Development and Diminishes Host Vaginal Mucosal TH17 Response. Frontiers in microbiology, 9, 198. https://doi.org/10.3389/fmicb.2018.00198 google scholar
• Zakikhany, K., Naglik, J. R., Schmidt-Westhausen, A., Holland, G., Schaller, M., & Hube, B. (2007). In vivo transcript profiling of Candida albicans identifies a gene essential for interepithelial dissemination. Cellular microbiology, 9(12), 2938-2954. https://doi.org/10.1111/j.1462-5822.2007.01009.x google scholar
• Ze, X., Duncan, S. H., Louis, P., & Flint, H. J. (2012). Ruminococcus bromii is a keystone species for the degra-dation of resistant starch in the human colon. The ISME journal, 6(8), 1535-1543. https://doi.org/10.1038/ ismej.2012.4 google scholar
• Zhai, B., Ola, M., Rolling, T., Tosini, N. L., Joshowitz, S., Littmann, E. R., Amoretti, L. A., Fontana, E., Wright, R. J., Miranda, E., Veelken, C. A., Morjaria, S. M., Peled, J. U., van den Brink, M. R. M., Babady, N. E., Butler, G., Taur, Y., & Hohl, T. M. (2020). High-resolution mycobiota analysis reveals dynamic intesti-nal translocation preceding invasive candidiasis. Nature medicine, 26(1), 59-64. https://doi.org/10.1038/ s41591-019-0709-7 google scholar
• Zhang, F., Aschenbrenner, D., Yoo, J. Y., & Zuo, T. (2022). The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. The Lancet. Microbe, 3(12), e969-e983. https://doi.org/10.1016/S2666-5247(22)00203-8 google scholar
• Zheng, L., Kelly, C. J., & Colgan, S. P. (2015). Physiologic hypoxia and oxygen homeostasis in the healthy intestine. A Review in the Theme: Cellular Responses to Hypoxia. American journal of physiology. Cell physiology, 309(6), C350-C360. https://doi.org/10.1152/ajpcell.00191.2015 google scholar
• Zou, R., Wang, Y., Duan, M., Guo, M., Zhang, Q., & Zheng, H. (2021). Dysbiosis of Gut Fungal Microbiota in Children with Autism Spectrum Disorders. Journal of autism and developmental disorders, 51(1), 267-275. https://doi.org/10.1007/s10803-020-04543-y google scholar
• Zuo, T., Wu, X., Wen, W., & Lan, P. (2021). Gut Microbiome Alterations in COVID-19. Genomics, proteomics & bioinformatics, 19(5), 679-688. https://doi.org/10.1016/j.gpb.2021.09.004 google scholar
• Zuo, T., Zhan, H., Zhang, F., Liu, Q., Tso, E. Y. K., Lui, G. C. Y., Chen, N., Li, A., Lu, W., Chan, F. K. L., Chan, P. K. S., & Ng, S. C. (2020). Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge. Gastroenterology, 159(4), 1302-1310.e5. https://doi.org/10.1053/j. gastro.2020.06.048 google scholar
• Zuo, T., Wong, S. H., Cheung, C. P., Lam, K., Lui, R., Cheung, K., Zhang, F., Tang, W., Ching, J. Y. L., Wu, J. C. Y., Chan, P. K. S., Sung, J. J. Y., Yu, J., Chan, F. K. L., & Ng, S. C. (2018). Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection. Nature commu-nications, 9(1), 3663. https://doi.org/10.1038/s41467-018-06103-6 google scholar