• Barker, N. Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat. Rev. Mol. Cell Biol. 15, 19–33 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • van der Flier, L. G. & Clevers, H. Stem cells, self-renewal, and differentiation in the intestinal epithelium. Annu. Rev. Physiol. 71, 241–260 (2009).

    Article 
    PubMed 

    Google Scholar
     

  • Tian, C. M. et al. Stem cell therapy in inflammatory bowel disease: a review of achievements and challenges. J. Inflamm. Res. 16, 2089–2119 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kang, E. J. et al. The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation. Nat. Commun. 15, 2983 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hou, Q. et al. Bacillus subtilis programs the differentiation of intestinal secretory lineages to inhibit Salmonella infection. Cell Rep. 40, 111416 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).

    Article 
    PubMed 

    Google Scholar
     

  • Almeqdadi, M., Mana, M. D., Roper, J. & Yilmaz Ö. H. Gut organoids: mini-tissues in culture to study intestinal physiology and disease. Am. J. Physiol. Cell Physiol. 317, C405–C419 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liao, Y. et al. Fungal symbiont transmitted by free-living mice promotes type 2 immunity. Nature 636, 697–704 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Destruelle, M., Holzer, H. & Klionsky, D. J. Identification and characterization of a novel yeast gene: the YGP1 gene product is a highly glycosylated secreted protein that is synthesized in response to nutrient limitation. Mol. Cell. Biol. 14, 2740–2754 (1994).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hageman, J. H. et al. Intestinal regeneration: regulation by the microenvironment. Dev. Cell 54, 435–446 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Eichele, D. D. & Kharbanda, K. K. Dextran sodium sulfate colitis murine model: an indispensable tool for advancing our understanding of inflammatory bowel diseases pathogenesis. World J. Gastroenterol. 23, 6016–6029 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chassaing, B., Aitken, J. D., Malleshappa, M. & Vijay-Kumar, M. Dextran sulfate sodium (DSS)-induced colitis in mice. Curr. Protoc. Immunol. 104, 15.25.11–15.25.14 (2014).

    Article 

    Google Scholar
     

  • Sonis, S. T. The pathobiology of mucositis. Nat. Rev. Cancer 4, 277–284 (2004).

    Article 
    PubMed 

    Google Scholar
     

  • Longley, D. B., Harkin, D. P. & Johnston, P. G. 5-fluorouracil: mechanisms of action and clinical strategies. Nat. Rev. Cancer 3, 330–338 (2003).

    Article 
    PubMed 

    Google Scholar
     

  • Fink, M. et al. Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signalling to drive regeneration. Nat. Cell Biol. 26, 2084–2098 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Laschinger, M. et al. The CGRP receptor component RAMP1 links sensory innervation with YAP activity in the regenerating liver. FASEB J. 34, 8125–8138 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Moya, I. M. & Halder, G. Hippo-YAP/TAZ signalling in organ regeneration and regenerative medicine. Nat. Rev. Mol. Cell Biol. 20, 211–226 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Amitrano, A. et al. Extracellular fluid viscosity regulates human mesenchymal stem cell lineage and function. Sci. Adv. 11, eadr5023 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kaneda, A. et al. The novel potent TEAD inhibitor, K-975, inhibits YAP1/TAZ-TEAD protein–protein interactions and exerts an anti-tumor effect on malignant pleural mesothelioma. Am. J. Cancer Res. 10, 4399–4415 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sun, L. et al. ENO1 promotes liver carcinogenesis through YAP1-dependent arachidonic acid metabolism. Nat. Chem. Biol. 19, 1492–1503 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Sun, Y. et al. Integrative plasma and fecal metabolomics identify functional metabolites in adenoma-colorectal cancer progression and as early diagnostic biomarkers. Cancer Cell 42, 1386–1400.e8 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Leonard, P. G. et al. SF2312 is a natural phosphonate inhibitor of enolase. Nat. Chem. Biol. 12, 1053–1058 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nash, A. K. et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5, 153 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, F., Aschenbrenner, D., Yoo, J. Y. & Zuo, T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. Lancet Microbe 3, e969–e983 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Huang, H. et al. The mycobiome as integral part of the gut microbiome: crucial role of symbiotic fungi in health and disease. Gut Microbes 16, 2440111 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hiengrach, P., Chindamporn, A. & Leelahavanichkul, A. Kazachstania pintolopesii in blood and intestinal wall of macrophage-depleted mice with cecal ligation and puncture, the control of fungi by macrophages during sepsis. J. Fungi 9, 1164 (2023).

  • Sekeresova Kralova, J. et al. Competitive fungal commensalism mitigates candidiasis pathology. J. Exp. Med. 221, e20231686 (2024).

  • Avershina, E., Qureshi, A. I., Winther-Larsen, H. C. & Rounge, T. B. Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases. Microbiome 13, 66 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Porras, A. M. et al. Geographic differences in gut microbiota composition impact susceptibility to enteric infection. Cell Rep. 36, 109457 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Imbrizi, M., Magro, F. & Coy, C. S. R. Pharmacological therapy in inflammatory bowel diseases: a narrative review of the past 90 years. Pharmaceuticals 16, 1272 (2023).

  • Wynn, T. A. Type 2 cytokines: mechanisms and therapeutic strategies. Nat. Rev. Immunol. 15, 271–282 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Hams, E. et al. IL-25 and type 2 innate lymphoid cells induce pulmonary fibrosis. Proc. Natl Acad. Sci. USA 111, 367–372 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Lin, Z. et al. Cardiac-specific YAP activation improves cardiac function and survival in an experimental murine MI model. Circ. Res. 115, 354–363 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xin, M. et al. Hippo pathway effector Yap promotes cardiac regeneration. Proc. Natl Acad. Sci. USA 110, 13839–13844 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heallen, T. et al. Hippo signaling impedes adult heart regeneration. Development 140, 4683–4690 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhong, Z., Jiao, Z. & Yu, F. X. The Hippo signaling pathway in development and regeneration. Cell Rep. 43, 113926 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Wang, Y. et al. USP10 strikes down β-catenin by dual-wielding deubiquitinase activity and phase separation potential. Cell Chem. Biol. 30, 1436–1452.e10 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Kong, L. et al. The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity 56, 2855 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Kondo, J. et al. LRIG1 regulates ontogeny of smooth muscle-derived subsets of interstitial cells of cajal in mice. Gastroenterology 149, 407–419.e8 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pierce, B. G. et al. ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers. Bioinformatics 30, 1771–1773 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kozakov, D. et al. The ClusPro web server for protein–protein docking. Nat. Protoc. 12, 255–278 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Honorato, R. V. et al. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nat. Protoc. 19, 3219–3241 (2024).

    Article 
    PubMed 

    Google Scholar