{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T13:57:02Z","timestamp":1775224622987,"version":"3.50.1"},"reference-count":120,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Ulcerative colitis (UC) is a chronic inflammatory bowel disease closely associated with dysbiosis of the gut microbiome, encompassing not only bacterial communities but also fungal populations. Despite the growing recognition of the gut microbiome\u2019s role in UC pathogenesis, the contribution of intestinal fungi has only recently garnered significant attention. In this review, we comprehensively examine the characteristics of intestinal fungi in both healthy individuals and UC patients, elucidating their role in disease pathogenesis and their interactions with bacterial communities. Additionally, we explore the impact of intestinal fungi on disease severity and therapeutic responses in UC. Furthermore, we evaluate the therapeutic potential of antifungal agents, probiotics, and fecal microbiota transplantation (FMT) in UC management, emphasizing the critical role of fungi in these treatment modalities. Future research should prioritize elucidating the multifunctional roles of fungi in UC pathogenesis and their implications for treatment strategies. Moreover, the identification of fungal biomarkers associated with FMT efficacy could pave the way for precision medicine approaches in FMT, offering novel insights into personalized therapeutic interventions for UC.<\/jats:p>","DOI":"10.3390\/microorganisms13040794","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T08:48:00Z","timestamp":1743410880000},"page":"794","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The Role of Intestinal Fungi in the Pathogenesis and Treatment of Ulcerative Colitis"],"prefix":"10.3390","volume":"13","author":[{"given":"Yujing","family":"Zhang","sequence":"first","affiliation":[{"name":"Microbiota Laboratory, Clinical Division of Microbiota, Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China"},{"name":"Medical School of Chinese PLA, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Wang","sequence":"additional","affiliation":[{"name":"Microbiota Laboratory, Clinical Division of Microbiota, Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China"},{"name":"Medical School of Chinese PLA, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lihua","family":"Peng","sequence":"additional","affiliation":[{"name":"Microbiota Laboratory, Clinical Division of Microbiota, Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.cgh.2019.07.005","article-title":"Ulcerative Colitis and Crohn\u2019s Disease Have Similar Burden and Goals for Treatment","volume":"18","author":"Ananthakrishnan","year":"2020","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1001\/jama.2023.15389","article-title":"Ulcerative Colitis in Adults","volume":"330","author":"Gros","year":"2023","journal-title":"JAMA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2652","DOI":"10.1056\/NEJMra2002697","article-title":"Pathophysiology of Inflammatory Bowel Diseases","volume":"383","author":"Chang","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1053\/j.gastro.2018.12.001","article-title":"Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis","volume":"156","author":"Paramsothy","year":"2019","journal-title":"Gastroenterology"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1053\/j.gastro.2019.11.294","article-title":"Differences in Gut Microbiota in Patients with vs. Without Inflammatory Bowel Diseases: A Systematic Review","volume":"158","author":"Pittayanon","year":"2020","journal-title":"Gastroenterology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1016\/j.immuni.2019.05.023","article-title":"Gut Mycobiota in Immunity and Inflammatory Disease","volume":"50","author":"Li","year":"2019","journal-title":"Immunity"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1053\/j.gastro.2020.06.100","article-title":"Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases","volume":"160","author":"Iliev","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","article-title":"Fungal microbiota dysbiosis in IBD","volume":"66","author":"Sokol","year":"2017","journal-title":"Gut"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1016\/j.cgh.2023.09.023","article-title":"Dynamics of the Gut Mycobiome in Patients with Ulcerative Colitis","volume":"22","author":"Jangi","year":"2023","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1093\/ecco-jcc\/jjaa252","article-title":"Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease","volume":"15","author":"Eberl","year":"2021","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41575-023-00816-w","article-title":"Commensal fungi in intestinal health and disease","volume":"20","author":"Ost","year":"2023","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19490976.2020.1854640","article-title":"Efficacy and safety of fecal microbiota transplantation for the treatment of diseases other than Clostridium difficile infection: A systematic review and meta-analysis","volume":"12","author":"Green","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S2468-1253(21)00400-3","article-title":"Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): A randomised, double-blind, placebo-controlled trial","volume":"7","author":"Haifer","year":"2022","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1016\/S0140-6736(17)30182-4","article-title":"Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: A randomised placebo-controlled trial","volume":"389","author":"Paramsothy","year":"2017","journal-title":"Lancet"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1053\/j.gastro.2015.03.045","article-title":"Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients with Ulcerative Colitis","volume":"149","author":"Rossen","year":"2015","journal-title":"Gastroenterology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.chom.2020.03.006","article-title":"Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis","volume":"27","author":"Leonardi","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/s41467-020-20240-x","article-title":"Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Chen, Q., Fan, Y., Zhang, B., Yan, C., Chen, Z., Wang, L., Hu, Y., Huang, Q., Su, J., and Ren, J. (2022). Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis. Front. Cell Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.1086885"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1007\/s00248-017-1105-9","article-title":"Fungi in Gastrointestinal Tracts of Human and Mice: From Community to Functions","volume":"75","author":"Li","year":"2018","journal-title":"Microb. Ecol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.cell.2022.01.017","article-title":"Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity","volume":"185","author":"Leonardi","year":"2022","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e867","DOI":"10.1016\/S2666-5247(22)00184-7","article-title":"The association between early-life gut microbiota and childhood respiratory diseases: A systematic review","volume":"3","author":"Alcazar","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"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., and Gibbs, R.A. (2017). The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome, 5.","DOI":"10.1186\/s40168-017-0373-4"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3685","DOI":"10.1016\/j.csbj.2022.07.010","article-title":"FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling","volume":"20","author":"Xie","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Lai, S., Yan, Y., Pu, Y., Lin, S., Qiu, J.G., Jiang, B.H., Keller, M.I., Wang, M., Bork, P., and Chen, W.H. (2023). Enterotypes of the human gut mycobiome. Microbiome, 11.","DOI":"10.1186\/s40168-023-01586-y"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e969","DOI":"10.1016\/S2666-5247(22)00203-8","article-title":"The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly","volume":"3","author":"Zhang","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nri3684","article-title":"The mycobiota: Interactions between commensal fungi and the host immune system","volume":"14","author":"Underhill","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1136\/gutjnl-2021-326298","article-title":"Mapping the human gut mycobiome in middle-aged and elderly adults: Multiomics insights and implications for host metabolic health","volume":"71","author":"Shuai","year":"2022","journal-title":"Gut"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1111\/1755-0998.13097","article-title":"Exploring the accuracy of amplicon-based internal transcribed spacer markers for a fungal community","volume":"20","author":"Li","year":"2019","journal-title":"Mol. Ecol. Resour."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Blakeley-Ruiz, J.A., Erickson, A.R., Cantarel, B.L., Xiong, W., Adams, R., Jansson, J.K., Fraser, C.M., and Hettich, R.L. (2019). Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn\u2019s remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Microbiome, 7.","DOI":"10.1186\/s40168-019-0631-8"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e0098622","DOI":"10.1128\/msystems.00986-22","article-title":"Host Factors Associated with Gut Mycobiome Structure","volume":"8","author":"Handschuh","year":"2023","journal-title":"mSystems"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1053\/j.gastro.2020.09.057","article-title":"The Healthy Microbiome-What Is the Definition of a Healthy Gut Microbiome?","volume":"160","author":"Shanahan","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Xie, Z., Canalda-Baltrons, A., d\u2019Enfert, C., and Manichanh, C. (2023). Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients. Microbiome, 11.","DOI":"10.1186\/s40168-023-01693-w"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Wu, X., Xia, Y., He, F., Zhu, C., and Ren, W. (2021). Intestinal mycobiota in health and diseases: From a disrupted equilibrium to clinical opportunities. Microbiome, 9.","DOI":"10.1186\/s40168-021-01024-x"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Kostovcikova, K., Coufal, S., Galanova, N., Fajstova, A., Hudcovic, T., Kostovcik, M., Prochazkova, P., Jiraskova Zakostelska, Z., Cermakova, M., and Sediva, B. (2019). Diet Rich in Animal Protein Promotes Pro-inflammatory Macrophage Response and Exacerbates Colitis in Mice. Front. Immunol., 10.","DOI":"10.3389\/fimmu.2019.00919"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1093\/ibd\/izac156","article-title":"Mycobiome and Inflammatory Bowel Disease: Role in Disease Pathogenesis, Current Approaches and Novel Nutritional-based Therapies","volume":"29","author":"Hsu","year":"2023","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1053\/j.gastro.2020.09.014","article-title":"Population-Level Configurations of Gut Mycobiome Across 6 Ethnicities in Urban and Rural China","volume":"160","author":"Sun","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"Arumugam","year":"2011","journal-title":"Nature"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41579-018-0036-x","article-title":"Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier","volume":"16","author":"Martens","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1080\/19490976.2020.1735606","article-title":"Interactions of commensal and pathogenic microorganisms with the mucus layer in the colon","volume":"11","author":"Cai","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1136\/gutjnl-2012-303207","article-title":"Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis","volume":"63","author":"Johansson","year":"2014","journal-title":"Gut"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1136\/gut.35.3.353","article-title":"Thickness of adherent mucus gel on colonic mucosa in humans and its relevance to colitis","volume":"35","author":"Pullan","year":"1994","journal-title":"Gut"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1826","DOI":"10.1002\/eji.201847586","article-title":"Intestinal epithelial cells and T cells differentially recognize and respond to Candida albicans yeast and hypha","volume":"48","author":"Schirbel","year":"2018","journal-title":"Eur. J. Immunol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/s41586-021-03722-w","article-title":"Adaptive immunity induces mutualism between commensal eukaryotes","volume":"596","author":"Ost","year":"2021","journal-title":"Nature"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1038\/s41564-021-00983-z","article-title":"Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn\u2019s disease","volume":"6","author":"Doron","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/nm.3871","article-title":"Activation of HIF-1alpha and LL-37 by commensal bacteria inhibits Candida albicans colonization","volume":"21","author":"Fan","year":"2015","journal-title":"Nat. Med."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.cell.2020.08.048","article-title":"Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption","volume":"183","author":"Chikina","year":"2020","journal-title":"Cell"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1053\/j.gastro.2016.10.012","article-title":"Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches","volume":"152","author":"Sartor","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1126\/science.1221789","article-title":"Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis","volume":"336","author":"Iliev","year":"2012","journal-title":"Science"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Seiwert, N., Heylmann, D., Hasselwander, S., and Fahrer, J. (2020). Mechanism of colorectal carcinogenesis triggered by heme iron from red meat. Biochim. Biophys. Acta (BBA)\u2014Rev. Cancer, 1873.","DOI":"10.1016\/j.bbcan.2019.188334"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e20192195","DOI":"10.1084\/jem.20192195","article-title":"The role of IL-22 in intestinal health and disease","volume":"217","author":"Keir","year":"2020","journal-title":"J. Exp. Med."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/s41579-022-00796-9","article-title":"Architecture of the dynamic fungal cell wall","volume":"21","author":"Gow","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Cortes, J.C.G., Curto, M.A., Carvalho, V.S.D., Perez, P., and Ribas, J.C. (2019). The fungal cell wall as a target for the development of new antifungal therapies. Biotechnol. Adv., 37.","DOI":"10.1016\/j.biotechadv.2019.02.008"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nri.2017.55","article-title":"Fungal dysbiosis: Immunity and interactions at mucosal barriers","volume":"17","author":"Iliev","year":"2017","journal-title":"Nat. Rev. Immunol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Wang, T., Pan, D., Zhou, Z., You, Y., Jiang, C., Zhao, X., and Lin, X. (2016). Dectin-3 Deficiency Promotes Colitis Development due to Impaired Antifungal Innate Immune Responses in the Gut. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1005662"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.it.2013.02.006","article-title":"Caspase recruitment domain-containing protein 9 signaling in innate immunity and inflammation","volume":"34","author":"Roth","year":"2013","journal-title":"Trends Immunol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Levitz, S.M. (2010). Innate recognition of fungal cell walls. PLoS Pathog., 6.","DOI":"10.1371\/journal.ppat.1000758"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"a019612","DOI":"10.1101\/cshperspect.a019612","article-title":"Adaptive Immunity to Fungi","volume":"5","author":"Verma","year":"2014","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.immuni.2018.08.024","article-title":"SYK-CARD9 Signaling Axis Promotes Gut Fungi-Mediated Inflammasome Activation to Restrict Colitis and Colon Cancer","volume":"49","author":"Malik","year":"2018","journal-title":"Immunity"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1126\/science.aao1503","article-title":"CX3CR1(+) mononuclear phagocytes control immunity to intestinal fungi","volume":"359","author":"Leonardi","year":"2018","journal-title":"Science"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/s41575-023-00755-6","article-title":"Human intestinal B cells in inflammatory diseases","volume":"20","author":"Spencer","year":"2023","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/mi.2009.17","article-title":"Balancing inflammation and tolerance in vivo through dendritic cells by the commensal Candida albicans","volume":"2","author":"Bonifazi","year":"2009","journal-title":"Mucosal Immunol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"4260","DOI":"10.1038\/s41467-018-06607-1","article-title":"The fungal peptide toxin Candidalysin activates the NLRP3 inflammasome and causes cytolysis in mononuclear phagocytes","volume":"9","author":"Kasper","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Ballou, E.R., Avelar, G.M., Childers, D.S., Mackie, J., Bain, J.M., Wagener, J., Kastora, S.L., Panea, M.D., Hardison, S.E., and Walker, L.A. (2016). Lactate signalling regulates fungal beta-glucan masking and immune evasion. Nat. Microbiol., 2.","DOI":"10.1038\/nmicrobiol.2016.238"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1038\/s41586-022-04502-w","article-title":"Immune regulation by fungal strain diversity in inflammatory bowel disease","volume":"603","author":"Li","year":"2022","journal-title":"Nature"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Tan, T.G., Lim, Y.S., Tan, A., Leong, R., and Pavelka, N. (2019). Fungal Symbionts Produce Prostaglandin E(2) to Promote Their Intestinal Colonization. Front. Cell Infect. Microbiol., 9.","DOI":"10.3389\/fcimb.2019.00359"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1128\/CMR.16.3.517-533.2003","article-title":"Production of eicosanoids and other oxylipins by pathogenic eukaryotic microbes","volume":"16","author":"Noverr","year":"2003","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"eaaf9044","DOI":"10.1126\/scitranslmed.aaf9044","article-title":"A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice","volume":"9","author":"Chiaro","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nm.4102","article-title":"CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands","volume":"22","author":"Lamas","year":"2016","journal-title":"Nat. Med."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/ni1408","article-title":"Dectin-1 is required for beta-glucan recognition and control of fungal infection","volume":"8","author":"Taylor","year":"2007","journal-title":"Nat. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.chom.2015.07.003","article-title":"Inhibition of Dectin-1 Signaling Ameliorates Colitis by Inducing Lactobacillus-Mediated Regulatory T Cell Expansion in the Intestine","volume":"18","author":"Tang","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Wang, Y., Spatz, M., Da Costa, G., Michaudel, C., Lapiere, A., Danne, C., Agus, A., Michel, M.L., Netea, M.G., and Langella, P. (2022). Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice. Microbiome, 10.","DOI":"10.1186\/s40168-022-01273-4"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1136\/gutjnl-2022-326917","article-title":"CARD9 in neutrophils protects from colitis and controls mitochondrial metabolism and cell survival","volume":"72","author":"Danne","year":"2023","journal-title":"Gut"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Jacobsen, I.D., Dollive, S., Chen, Y.-Y., Grunberg, S., Bittinger, K., Hoffmann, C., Vandivier, L., Cuff, C., Lewis, J.D., and Wu, G.D. (2013). Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0071806"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"4996","DOI":"10.1128\/IAI.72.9.4996-5003.2004","article-title":"Role of antibiotics and fungal microbiota in driving pulmonary allergic responses","volume":"72","author":"Noverr","year":"2004","journal-title":"Infect. Immun."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Sovran, B., Planchais, J., Jegou, S., Straube, M., Lamas, B., Natividad, J.M., Agus, A., Dupraz, L., Glodt, J., and Da Costa, G. (2018). Enterobacteriaceae are essential for the modulation of colitis severity by fungi. Microbiome, 6.","DOI":"10.1186\/s40168-018-0538-9"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e01250-16","DOI":"10.1128\/mBio.01250-16","article-title":"Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn\u2019s Disease","volume":"7","author":"Hoarau","year":"2016","journal-title":"mBio"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.jaci.2022.11.007","article-title":"Dietary fiber and SCFAs in the regulation of mucosal immunity","volume":"151","author":"Tan","year":"2023","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1080\/19490976.2015.1134082","article-title":"Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism","volume":"7","author":"Morrison","year":"2016","journal-title":"Gut Microbes"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Zeise, K.D., Woods, R.J., and Huffnagle, G.B. (2021). Interplay between Candida albicans and Lactic Acid Bacteria in the Gastrointestinal Tract: Impact on Colonization Resistance, Microbial Carriage, Opportunistic Infection, and Host Immunity. Clin. Microbiol. Rev., 34.","DOI":"10.1128\/CMR.00323-20"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Seelbinder, B., Chen, J., Brunke, S., Vazquez-Uribe, R., Santhaman, R., Meyer, A.C., de Oliveira Lino, F.S., Chan, K.F., Loos, D., and Imamovic, L. (2020). Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome, 8.","DOI":"10.1186\/s40168-020-00899-6"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/nature13995","article-title":"Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism","volume":"517","author":"Cuskin","year":"2015","journal-title":"Nature"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1016\/j.chom.2020.04.018","article-title":"Candida in IBD: Friend or Foe?","volume":"27","author":"Fritsch","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1038\/s41467-020-16431-1","article-title":"Intestinal fungi are causally implicated in microbiome assembly and immune development in mice","volume":"11","author":"Pettersen","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"3192","DOI":"10.1038\/s41467-022-30661-5","article-title":"Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity","volume":"13","author":"Last","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"e2100433","DOI":"10.1002\/mnfr.202100433","article-title":"Faecalibacterium prausnitzii Attenuates DSS-Induced Colitis by Inhibiting the Colonization and Pathogenicity of Candida albicans","volume":"65","author":"Mao","year":"2021","journal-title":"Mol. Nutr. Food Res."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.chom.2008.05.014","article-title":"Bacterial peptidoglycan triggers Candida albicans hyphal growth by directly activating the adenylyl cyclase Cyr1p","volume":"4","author":"Xu","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"6151","DOI":"10.1038\/s41467-021-26390-w","article-title":"A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase","volume":"12","author":"MacAlpine","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"4507","DOI":"10.1073\/pnas.1620432114","article-title":"Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans","volume":"114","author":"Graham","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1093\/ibd\/izad082","article-title":"Alterations in the Fungal Microbiome in Ulcerative Colitis","volume":"29","author":"Hsia","year":"2023","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1080\/19490976.2019.1662712","article-title":"Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34","volume":"11","author":"Panpetch","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1126\/science.abd0919","article-title":"Debaryomyces is enriched in Crohn\u2019s disease intestinal tissue and impairs healing in mice","volume":"371","author":"Jain","year":"2021","journal-title":"Science"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Alsharif, I.A., Fayed, H.M., Abdel-Rahman, R.F., Abd-Elsalam, R.M., and Ogaly, H.A. (2022). Miconazole Mitigates Acetic Acid-Induced Experimental Colitis in Rats: Insight into Inflammation, Oxidative Stress and Keap1\/Nrf-2 Signaling Crosstalk. Biology, 11.","DOI":"10.3390\/biology11020303"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"3663","DOI":"10.1038\/s41467-018-06103-6","article-title":"Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection","volume":"9","author":"Zuo","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1016\/j.chom.2016.05.003","article-title":"Immunological Consequences of Intestinal Fungal Dysbiosis","volume":"19","author":"Wheeler","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1097\/MCG.0000000000001609","article-title":"Oral Fluconazole Therapy in Patients With Active Ulcerative Colitis Who Have Detectable Candida in the Stool: A Double-Blind Randomized Placebo-controlled Trial","volume":"56","author":"Jena","year":"2022","journal-title":"J. Clin. Gastroenterol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","article-title":"Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic","volume":"11","author":"Hill","year":"2014","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1136\/gut.2004.044834","article-title":"Synbiotic therapy (Bifidobacterium longum\/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: A randomised controlled pilot trial","volume":"54","author":"Furrie","year":"2005","journal-title":"Gut"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1111\/1751-7915.13661","article-title":"Modulation of gut mucosal microbiota as a mechanism of probiotics-based adjunctive therapy for ulcerative colitis","volume":"13","author":"Chen","year":"2020","journal-title":"Microb. Biotechnol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1002\/jcp.25911","article-title":"Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review","volume":"233","year":"2018","journal-title":"J. Cell Physiol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"121699","DOI":"10.1016\/j.lfs.2023.121699","article-title":"Bifidobacterium and Lactobacillus improve inflammatory bowel disease in zebrafish of different ages by regulating the intestinal mucosal barrier and microbiota","volume":"324","author":"Ni","year":"2023","journal-title":"Life Sci."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1136\/gut.2005.078303","article-title":"Bacterial and fungal microbiota in relation to probiotic therapy (VSL#3) in pouchitis","volume":"55","author":"Kuhbacher","year":"2006","journal-title":"Gut"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1053\/gast.2001.27224","article-title":"Probiotic bacteria enhance murine and human intestinal epithelial barrier function","volume":"121","author":"Madsen","year":"2001","journal-title":"Gastroenterology"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1080\/19490976.2020.1734423","article-title":"Lactobacillus reuteri maintains intestinal epithelial regeneration and repairs damaged intestinal mucosa","volume":"11","author":"Wu","year":"2020","journal-title":"Gut Microbes"},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Itapary Dos Santos, C., Ramos Franca, Y., Duarte Lima Campos, C., Quaresma Bomfim, M.R., Oliveira Melo, B., Assuncao Holanda, R., Santos, V.L., Gomes Monteiro, S., Buozzi Moffa, E., and Souza Monteiro, A. (2019). Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates. Pathogens, 8.","DOI":"10.3390\/pathogens8030150"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1016\/j.chom.2017.10.013","article-title":"Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria","volume":"22","author":"Jiang","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1111\/j.1365-2036.2007.03442.x","article-title":"Review article: Yeast as probiotics\u2014Saccharomyces boulardii","volume":"26","author":"Czerucka","year":"2007","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Hu, Q., Yu, L., Zhai, Q., Zhao, J., and Tian, F. (2023). Anti-Inflammatory, Barrier Maintenance, and Gut Microbiome Modulation Effects of Saccharomyces cerevisiae QHNLD8L1 on DSS-Induced Ulcerative Colitis in Mice. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24076721"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"8386","DOI":"10.1039\/D1FO01314A","article-title":"Probiotic yeast BR14 ameliorates DSS-induced colitis by restoring the gut barrier and adjusting the intestinal microbiota","volume":"12","author":"Mu","year":"2021","journal-title":"Food Funct."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Xu, X., Wu, J., Jin, Y., Huang, K., Zhang, Y., and Liang, Z. (2023). Both Saccharomyces boulardii and Its Postbiotics Alleviate Dextran Sulfate Sodium-Induced Colitis in Mice, Association with Modulating Inflammation and Intestinal Microbiota. Nutrients, 15.","DOI":"10.3390\/nu15061484"},{"key":"ref_111","doi-asserted-by":"crossref","unstructured":"Gao, H., Li, Y., Xu, J., Zuo, X., Yue, T., Xu, H., Sun, J., Wang, M., Ye, T., and Yu, Y. (2023). Saccharomyces boulardii protects against murine experimental colitis by reshaping the gut microbiome and its metabolic profile. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1204122"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1039\/D1FO02752B","article-title":"Saccharomyces boulardii alleviates DSS-induced intestinal barrier dysfunction and inflammation in humanized mice","volume":"13","author":"Li","year":"2022","journal-title":"Food Funct."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1097\/CM9.0000000000000364","article-title":"Protective effect of Saccharomyces boulardii on intestinal mucosal barrier of dextran sodium sulfate-induced colitis in mice","volume":"132","author":"Dong","year":"2019","journal-title":"Chin. Med. J."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1111\/j.1365-2036.2009.04102.x","article-title":"Review article: Anti-inflammatory mechanisms of action of Saccharomyces boulardii","volume":"30","author":"Pothoulakis","year":"2009","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1038\/s41591-021-01390-x","article-title":"Self-tunable engineered yeast probiotics for the treatment of inflammatory bowel disease","volume":"27","author":"Scott","year":"2021","journal-title":"Nat. Med."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"3432","DOI":"10.1038\/s41467-022-31171-0","article-title":"Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery","volume":"13","author":"Zhou","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nrgastro.2011.244","article-title":"Fecal microbiota transplantation and emerging applications","volume":"9","author":"Borody","year":"2011","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/S2468-1253(21)00303-4","article-title":"Roles of the gut virome and mycobiome in faecal microbiota transplantation","volume":"7","author":"Lam","year":"2022","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"e00905-20","DOI":"10.1128\/mSystems.00905-20","article-title":"Long-Term Bacterial and Fungal Dynamics following Oral Lyophilized Fecal Microbiota Transplantation in Clostridioides difficile Infection","volume":"6","author":"Haifer","year":"2021","journal-title":"mSystems"},{"key":"ref_120","doi-asserted-by":"crossref","unstructured":"van Thiel, I.A.M., Rahman, S., Hakvoort, T.B.M., Davids, M., Verseijden, C., van Hamersveld, P.H.P., B\u00e9nard, M.V., Lodders, M.H., Boekhout, T., and van den Wijngaard, R.M. (2022). Fecal Filobasidium Is Associated with Clinical Remission and Endoscopic Response following Fecal Microbiota Transplantation in Mild-to-Moderate Ulcerative Colitis. Microorganisms, 10.","DOI":"10.3390\/microorganisms10040737"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/4\/794\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:06:21Z","timestamp":1760029581000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/4\/794"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,31]]},"references-count":120,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["microorganisms13040794"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms13040794","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,31]]}}}