Ost, K. S. et al. Adaptive immunity induces mutualism between commensal eukaryotes. Nature 596, 114–118 (2021).
Google Scholar
Tso, G. H. W. et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science 362, 589–595 (2018).
Google Scholar
Witchley, J. N. et al. Candida albicans morphogenesis programs control the balance between gut commensalism and invasive infection. Cell Host Microbe 25, 432–443.e436 (2019).
Google Scholar
Moyes, D. L. et al. Candidalysin is a fungal peptide toxin critical for mucosal infection. Nature 532, 64–68 (2016).
Google Scholar
Li, X. V. et al. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 603, 672–678 (2022).
Google Scholar
Doron, I. et al. Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease. Nat Microbiol 6, 1493–1504 (2021).
Google Scholar
Rao, C. et al. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature 591, 633–638 (2021).
Google Scholar
Iliev, I. D. & Cadwell, K. Effects of intestinal fungi and viruses on immune responses and inflammatory bowel diseases. Gastroenterology 160, 1050–1066 (2021).
Google Scholar
Swidergall, M. & LeibundGut-Landmann, S. Immunosurveillance of Candida albicans commensalism by the adaptive immune system. Mucosal Immunol. 15, 829–836 (2022).
Google Scholar
Shao, T. Y., Haslam, D. B., Bennett, R. J. & Way, S. S. Friendly fungi: symbiosis with commensal Candida albicans. Trends Immunol. 43, 706–717 (2022).
Google Scholar
Li, Q. et al. Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J. Clin. Gastroenterol. 48, 513–523 (2014).
Google Scholar
Sokol, H. et al. Fungal microbiota dysbiosis in IBD. Gut 66, 1039–1048 (2017).
Google Scholar
Bacher, P. et al. Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. Cell 176, 1340–1355.e1315 (2019).
Google Scholar
Shao, T. Y. et al. Commensal Candida albicans positively calibrates systemic Th17 immunological responses. Cell Host Microbe 25, 404–417.e406 (2019).
Google Scholar
Yeung, F. et al. Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host Microbe 27, 809–822.e806 (2020).
Google Scholar
Zhai, B. et al. High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis. Nat. Med. 26, 59–64 (2020).
Google Scholar
Pappas, P. G., Lionakis, M. S., Arendrup, M. C., Ostrosky-Zeichner, L. & Kullberg, B. J. Invasive candidiasis. Nat. Rev. Dis. Primers 4, 18026 (2018).
Google Scholar
Koh, A. Y., Kohler, J. R., Coggshall, K. T., Van Rooijen, N. & Pier, G. B. Mucosal damage and neutropenia are required for Candida albicans dissemination. PLoS Pathog. 4, e35 (2008).
Google Scholar
Noble, S. M., Gianetti, B. A. & Witchley, J. N. Candida albicans cell-type switching and functional plasticity in the mammalian host. Nat. Rev. Microbiol. 15, 96–108 (2017).
Google Scholar
Kadosh, D. Morphogenesis in Candida albicans: Cellular and Molecular Biology (ed. Prasad, R.) 41–62 (Springer, 2017).
Saville, S. P., Lazzell, A. L., Monteagudo, C. & Lopez-Ribot, J. L. Engineered control of cell morphology in vivo reveals distinct roles for yeast and filamentous forms of Candida albicans during infection. Eukaryot. Cell 2, 1053–1060 (2003).
Google Scholar
Lo, H. J. et al. Nonfilamentous C. albicans mutants are avirulent. Cell 90, 939–949 (1997).
Google Scholar
Carlisle, P. L. et al. Expression levels of a filament-specific transcriptional regulator are sufficient to determine Candida albicans morphology and virulence. Proc. Natl Acad. Sci. USA 106, 599–604 (2009).
Google Scholar
Bohm, L. et al. The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice. PLoS Pathog. 13, e1006699 (2017).
Google Scholar
Liang, S. H. et al. Hemizygosity enables a mutational transition governing fungal virulence and commensalism. Cell Host Microbe 25, 418–431.e416 (2019).
Google Scholar
Mogavero, S. et al. Candidalysin delivery to the invasion pocket is critical for host epithelial damage induced by Candida albicans. Cell Microbiol. 23, e13378 (2021).
Google Scholar
Naglik, J. R., Gaffen, S. L. & Hube, B. Candidalysin: discovery and function in Candida albicans infections. Curr. Opin. Microbiol. 52, 100–109 (2019).
Google Scholar
Stoldt, V. R., Sonneborn, A., Leuker, C. E. & Ernst, J. F. Efg1p, an essential regulator of morphogenesis of the human pathogen Candida albicans, is a member of a conserved class of bHLH proteins regulating morphogenetic processes in fungi. EMBO J. 16, 1982–1991 (1997).
Google Scholar
Braun, B. R. & Johnson, A. D. TUP1, CPH1 and EFG1 make independent contributions to filamentation in Candida albicans. Genetics 155, 57–67 (2000).
Google Scholar
Wakade, R. S., Huang, M., Mitchell, A. P., Wellington, M. & Krysan, D. J. Intravital imaging of Candida albicans identifies differential in vitro and in vivo filamentation phenotypes for transcription factor deletion mutants. mSphere 6, e0043621 (2021).
Google Scholar
Fan, D. et al. Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat. Med. 21, 808–814 (2015).
Google Scholar
Yamaguchi, N. et al. Gastric colonization of Candida albicans differs in mice fed commercial and purified diets. J. Nutr. 135, 109–115 (2005).
Google Scholar
McDonough, L. D. et al. Candida albicans isolates 529L and CHN1 exhibit stable colonization of the murine gastrointestinal tract. mBio 12, e0287821 (2021).
Google Scholar
Braun, B. R., Kadosh, D. & Johnson, A. D. NRG1, a repressor of filamentous growth in C. albicans, is down-regulated during filament induction. EMBO J. 20, 4753–4761 (2001).
Google Scholar
Murad, A. M. et al. NRG1 represses yeast-hypha morphogenesis and hypha-specific gene expression in Candida albicans. EMBO J. 20, 4742–4752 (2001).
Google Scholar
Wakade, R. S., Kramara, J., Wellington, M. & Krysan, D. J. Candida albicans filamentation does not require the cAMP–PKA pathway in vivo. mBio 13, e0085122 (2022).
Google Scholar
Vautier, S. et al. Candida albicans colonization and dissemination from the murine gastrointestinal tract: the influence of morphology and Th17 immunity. Cell Microbiol 17, 445–450 (2015).
Google Scholar
Miller, B. M., Liou, M. J., Lee, J. Y. & Baumler, A. J. The longitudinal and cross-sectional heterogeneity of the intestinal microbiota. Curr. Opin. Microbiol. 63, 221–230 (2021).
Google Scholar
Brugiroux, S. et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol 2, 16215 (2016).
Google Scholar
Trexler, P. C., & Orcutt, R.P. Chapter Sixteen: Development of Gnotobiotics and Contamination Control in Laboratory Animal Science. In: 50 Years of Laboratory Animal Science. Memphis, TN: Am Assoc Lab Anim Sci, 121–128 (2000).
Caballero, S. et al. Cooperating commensals restore colonization resistance to vancomycin-resistant Enterococcus faecium. Cell Host Microbe 21, 592–602.e594 (2017).
Google Scholar
Dambuza, I. M. & Brown, G. D. Managing the mycobiota with IgA. Nat. Microbiol. 6, 1471–1472 (2021).
Google Scholar
Kasper, L. et al. The fungal peptide toxin candidalysin activates the NLRP3 inflammasome and causes cytolysis in mononuclear phagocytes. Nat. Commun. 9, 4260 (2018).
Google Scholar
Swidergall, M. et al. Candidalysin is required for neutrophil recruitment and virulence during systemic Candida albicans infection. J. Infect. Dis. 220, 1477–1488 (2019).
Google Scholar
White, S. J. et al. Self-regulation of Candida albicans population size during GI colonization. PLoS Pathog. 3, e184 (2007).
Google Scholar
Hoyer, L. L., Payne, T. L., Bell, M., Myers, A. M. & Scherer, S. Candida albicans ALS3 and insights into the nature of the ALS gene family. Curr. Genet. 33, 451–459 (1998).
Google Scholar
Phan, Q. T. et al. Als3 is a Candida albicans invasin that binds to cadherins and induces endocytosis by host cells. PLoS Biol. 5, e64 (2007).
Google Scholar
Almeida, R. S. et al. The hyphal-associated adhesin and invasin Als3 of Candida albicans mediates iron acquisition from host ferritin. PLoS Pathog. 4, e1000217 (2008).
Google Scholar
Martchenko, M., Alarco, A. M., Harcus, D. & Whiteway, M. Superoxide dismutases in Candida albicans: transcriptional regulation and functional characterization of the hyphal-induced SOD5 gene. Mol. Biol. Cell 15, 456–467 (2004).
Google Scholar
Fradin, C. et al. Granulocytes govern the transcriptional response, morphology and proliferation of Candida albicans in human blood. Mol. Microbiol. 56, 397–415 (2005).
Google Scholar
Hube, B. Fungal adaptation to the host environment. Curr. Opin. Microbiol. 12, 347–349 (2009).
Google Scholar
Dewhirst, F. E. et al. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl. Environ. Microbiol. 65, 3287–3292 (1999).
Google Scholar
Guthrie, C. & Fink, G. R. Guide to Yeast Genetics and Molecular Biology (Academic Press, 1991).
Liu, H., Kohler, J. & Fink, G. R. Suppression of hyphal formation in Candida albicans by mutation of a STE12 homolog. Science 266, 1723–1726 (1994).
Google Scholar
Park, S. O., Frazer, C. & Bennett, R. J. An adjuvant-based approach enables the use of dominant HYG and KAN selectable markers in Candida albicans. mSphere 7, e0034722 (2022).
Google Scholar
Reuss, O., Vik, A., Kolter, R. & Morschhauser, J. The SAT1 flipper, an optimized tool for gene disruption in Candida albicans. Gene 341, 119–127 (2004).
Google Scholar
Noble, S. M. & Johnson, A. D. Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen Candida albicans. Eukaryot. Cell 4, 298–309 (2005).
Google Scholar
Mancera, E. et al. Genetic modification of closely related Candida species. Front. Microbiol. 10, 357 (2019).
Google Scholar
Gerami-Nejad, M., Zacchi, L. F., McClellan, M., Matter, K. & Berman, J. Shuttle vectors for facile gap repair cloning and integration into a neutral locus in Candida albicans. Microbiology 159, 565–579 (2013).
Google Scholar
Hollomon, J. M. et al. The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway. PLoS Genet. 18, e1009622 (2022).
Google Scholar
Dallari, S. et al. Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome. Cell Host Microbe 29, 1014–1029.e1018 (2021).
Google Scholar
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
Google Scholar
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Google Scholar
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Google Scholar
Bokulich, N. A. et al. q2-longitudinal: longitudinal and paired-sample analyses of microbiome data. mSystems 3, e00219–18 (2018).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Google Scholar
Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27, 325–349 (1957).
Google Scholar
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).
Google Scholar
Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Google Scholar
Benjaminii, Y. & Hichberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
Google Scholar
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).
Google Scholar
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).
Google Scholar
Mogavero, S. & Hube, B. Candida albicans interaction with oral epithelial cells: adhesion, invasion, and damage assays. Methods Mol. Biol. 2260, 133–143 (2021).
Google Scholar
Gerwien, F. et al. A novel hybrid iron regulation network combines features from pathogenic and nonpathogenic yeasts. mBio 7, e01782-16 (2016).
Google Scholar
Ramirez-Zavala, B. et al. The Snf1-activating kinase Sak1 is a key regulator of metabolic adaptation and in vivo fitness of Candida albicans. Mol. Microbiol. 104, 989–1007 (2017).
Google Scholar
Miramon, P. et al. A family of glutathione peroxidases contributes to oxidative stress resistance in Candida albicans. Med. Mycol. 52, 223–239 (2014).
Google Scholar
Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021).
Google Scholar