- 1.
Almeida, A.; Mitchell, A.L.; Boland, M.; et al. A new genomic blueprint of the human gut microbiota. Nature 2019, 568, 499–504.
- 2.
Leviatan, S.; Shoer, S.; Rothschild, D.; et al. An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species. Nat. Commun. 2022, 13, 3863.
- 3.
Yan, Q.; Li, S.; Yan, Q.; et al. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024, 187, 2969–2989.
- 4.
Garcia-Bonete, M.J.; Rajan, A.; Suriano, F.; et al. The underrated gut microbiota helminths, bacteriophages, fungi, and archaea. Life 2023, 13, 1765.
- 5.
Fan, Y.; Pedersen, O. Gut microbiota in human metabolic health and disease. Nat. Rev. Microbiol. 2021, 19, 55–71.
- 6.
Woźniak, D.; Cichy, W.; Przysławski, J.; et al. The role of microbiota and enteroendocrine cells in maintaining homeostasis in the human digestive tract. Adv. Med. Sci. 2021, 66, 284–292.
- 7.
Chu, J.; Feng, S.; Guo, C.; et al. Immunological mechanisms of inflammatory diseases caused by gut microbiota dysbiosis: A review. Biomed. Pharmacother. 2023, 164, 114985.
- 8.
Colella, M.; Charitos, I.A.; Ballini, A.; et al. Microbiota revolution: How gut microbes regulate our lives. World J. Gastroenterol. 2023, 29, 4368.
- 9.
Zhou Y.-D.; Liang F.-X.; Tian H.-R.; et al. Mechanisms of gut microbiota-immune-host interaction on glucose regulation in type 2 diabetes. Front. Microbiol. 2023, 14, 1121695.
- 10.
Fujisaka, S.; Watanabe, Y.; Tobe, K. The gut microbiome: A core regulator of metabolism. J. Endocrinol. 2023, 256, e220111.
- 11.
Kim, S.; Seo S.-U.; Kweon M.-N. Gut microbiota-derived metabolites tune host homeostasis fate. In Seminars in Immunopathology; Springer: Berlin/Heidelberg, Germany, 2024; p. 2.
- 12.
Chen, L.; Zhang, L.; Hua, H.; et al. Interactions between toll-like receptors signaling pathway and gut microbiota in host homeostasis. Immun. Inflamm. Dis. 2024, 12, e1356.
- 13.
Huseyin, C.E.; O’Toole, P.W.; Cotter, P.D.; et al. Forgotten fungi—The gut mycobiome in human health and disease. FEMS Microbiol. Rev. 2017, 41, 479–511.
- 14.
Di Paola, M.; Rizzetto, L.; Stefanini, I.; et al. Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn’s disease patients and their interactions with the gut microbiome. J. Transl. Autoimmun. 2020, 3, 100036.
- 15.
Peroumal, D.; Sahu, S.R.; Kumari, P.; et al. Commensal fungus Candida albicans maintains a long-term mutualistic relationship with the host to modulate gut microbiota and metabolism. Microbiol. Spectr. 2022, 10, e02462-22.
- 16.
Wang, X.; Wu, S.; Li, L.; et al. Candida albicans overgrowth disrupts the gut microbiota in mice bearing oral cancer. Mycology 2024, 15, 57–69.
- 17.
Pérez, J.C. Fungi of the human gut microbiota: Roles and significance. Int. J. Med. Microbiol. 2021, 311, 151490.
- 18.
Richard, M.L.; Sokol, H. The gut mycobiota: Insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat. Rev. Gastroenterol. Hepatol. 2019, 16, 331–345.
- 19.
Zhai, B.; Liao, C.; Jaggavarapu, S.; et al. Antifungal heteroresistance causes prophylaxis failure and facilitates breakthrough Candida parapsilosis infections. Nat. Med. 2024, 30, 3163–3172.
- 20.
Bayoumy, A.B.; Mulder, C.J.J.; Mol, J.J.; et al. Gut fermentation syndrome: A systematic review of case reports. United Eur. Gastroenterol. J. 2021, 9, 332–342.
- 21.
Demir, M.; Lang, S.; Hartmann, P.; et al. The fecal mycobiome in non-alcoholic fatty liver disease. J. Hepatol. 2022, 76, 788–799.
- 22.
Hallen-Adams, H.E.; Suhr M.J. Fungi in the healthy human gastrointestinal tract. Virulence 2017, 8, 352–358.
- 23.
Liu, T.; Asif, I.M.; Chen, Y.; et al. The Relationship between Diet, Gut Mycobiome, and Functional Gastrointestinal Disorders: Evidence, Doubts, and Prospects. Mol. Nutr. Food Res. 2024, 68, e2300382.
- 24.
Kumamoto, C.A.; Gresnigt, M.S.; Hube, B. The gut, the bad and the harmless: Candida albicans as a commensal and opportunistic pathogen in the intestine. Curr. Opin. Microbiol. 2020, 56, 7–15.
- 25.
d’Enfert, C.; Kaune, A.K.; Alaban, L.R.; et al. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: Current knowledge and new perspectives. FEMS Microbiol. Rev. 2021, 45, fuaa060.
- 26.
Boutin, R.C.T.; Sbihi, H.; McLaughlin, R.J.; et al. Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. mBio 2021, 12, e0339620.
- 27.
Maas, E.; Penders, J. Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals. J. Fungi 2023, 9, 139.
- 28.
Termén, S.; Tollin, M.; Rodriguez, E.; et al. PU.1 and bacterial metabolites regulate the human gene CAMP encoding antimicrobial peptide LL-37 in colon epithelial cells. Mol. Immunol. 2008, 45, 3947–3955.
- 29.
Islam, K.B.; Fukiya, S.; Hagio, M.; et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 2011, 141, 1773–1781.
- 30.
Tang, W.H.W.; Li, D.Y.; Hazen S.L. Dietary metabolism, the gut microbiome, and heart failure. Nat. Rev. Cardiol. 2019, 16, 137–154.
- 31.
Qu, R.; Zhang, Y.; Ma, Y.; et al. Role of the Gut Microbiota and Its Metabolites in Tumorigenesis or Development of Colorectal Cancer. Adv. Sci. 2023, 10, e2205563.
- 32.
Chen, J.; Vitetta, L. Intestinal dysbiosis in celiac disease: Decreased butyrate production may facilitate the onset of the disease. Proc. Natl. Acad. Sci. USA 2021, 118, e2113655118.
- 33.
Waclawiková B.; Codutti, A.; Alim, K.; et al. Gut microbiota-motility interregulation: Insights from in vivo, ex vivo and in silico studies. Gut Microbes 2022, 14, 1997296.
- 34.
Wang, J.; Zhu, N.; Su, X.; et al. Gut-Microbiota-Derived Metabolites Maintain Gut and Systemic Immune Homeostasis. Cells 2023, 12, 793.
- 35.
Gao, B.; Chi, L.; Zhu, Y. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021, 11, 530.
- 36.
Li, X.V.; Leonardi, I. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 2022, 603, 672–678. Erratum in Nature 2022, 608, E21.
- 37.
Gasch, A.P.; Yu, F.B.; Hose, J.; et al. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol. 2017, 15, e2004050.
- 38.
Nadal-Ribelles, M.; Islam, S.; Wei, W. Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nat. Microbiol. 2019, 4, 683–692.
- 39.
Saint, M.; Bertaux, F. Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation. Nat. Microbiol. 2019, 4, 480–491.
- 40.
Chetty, A.; Blekhman, R. Multi-omic approaches for host-microbiome data integration. Gut Microbes. 2024, 16, 2297860.
- 41.
Ost, K.S.; Round J.L. Commensal fungi in intestinal health and disease. Nat. Rev. Gastroenterol. Hepatol. 2023, 20, 723–734.