Theriot, C. M. et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat. Commun. 5, 3114 (2014).
Dubois, T. et al. A microbiota-generated bile salt induces biofilm formation in Clostridium difficile. npj Biofilms Microbiomes 5, 1–12 (2019).
VanInsberghe, D. et al. Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms. Nat. Microbiol. 5, 642–650 (2020).
Smits, W. K., Lyras, D., Lacy, D. B., Wilcox, M. H. & Kuijper, E. J. Clostridium difficile infection. Nat. Rev. Dis. Primers 2, 16020 (2016).
Bloom, P. P. & Young, V. B. Microbiome therapeutics for the treatment of recurrent Clostridioides difficile infection. Expert Opin. Biol. Ther. 23, 89–101 (2023).
McDonald, L. C. et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin. Infect. Dis. 66, e1–e48 (2018).
Carter, G. P. et al. Defining the roles of TcdA and TcdB in localized gastrointestinal disease, systemic organ damage, and the host response during Clostridium difficile infections. mBio 6, e00551-15 (2015).
Chen, P. et al. Structural basis for recognition of frizzled proteins by Clostridium difficile toxin B. Science 360, 664–669 (2018).
Chen, P. et al. Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection. Nat. Commun. 12, 3748 (2021).
Kordus, S. L., Thomas, A. K. & Lacy, D. B. Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics. Nat. Rev. Microbiol. 20, 285–298 (2022).
Chen, P. et al. Structure of the full-length Clostridium difficile toxin B. Nat. Struct. Mol. Biol. 26, 712–719 (2019).
Kinsolving, J. et al. Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD7. Cell Rep. 43, 113727 (2024).
Tam, J. et al. Small molecule inhibitors of Clostridium difficile toxin B-induced cellular damage. Chem. Biol. 22, 175–185 (2015).
Ridlon, J. M. & Gaskins, H. R. Another renaissance for bile acid gastrointestinal microbiology. Nat. Rev. Gastroenterol. Hepatol. https://doi.org/10.1038/s41575-024-00896-2 (2024).
Monte, M. J., Marin, J. J., Antelo, A. & Vazquez-Tato, J. Bile acids: chemistry, physiology, and pathophysiology. World J. Gastroenterol. 15, 804–816 (2009).
Hofmann, A. F. The enterohepatic circulation of bile acids in mammals: form and functions. Front. Biosci. 14, 2584–2598 (2009).
Tam, J. et al. Intestinal bile acids directly modulate the structure and function of C. difficile TcdB toxin. Proc. Natl Acad. Sci. USA 117, 6792–6800 (2020).
Chandrasekaran, R. & Lacy, D. B. The role of toxins in Clostridium difficile infection. FEMS Microbiol. Rev. 41, 723–750 (2017).
Zhou, Y. et al. Structural dynamics of the CROPs domain control stability and toxicity of Paeniclostridium sordellii lethal toxin. Nat. Commun. 14, 8426 (2023).
Yang, X., Stein, K. R. & Hang, H. C. Anti-infective bile acids bind and inactivate a Salmonella virulence regulator. Nat. Chem. Biol. 19, 91–100 (2023).
Aminzadeh, A., Larsen, C. E., Boesen, T. & Jørgensen, R. High-resolution structure of native toxin A from Clostridioides difficile. EMBO Rep. 23, e53597 (2022).
Stoltz, K. L. et al. Synthesis and biological evaluation of bile acid analogues inhibitory to Clostridium difficile spore germination. J. Med. Chem. 60, 3451–3471 (2017).
Nakhi, A. et al. Structural modifications that increase gut restriction of bile acid derivatives. RSC Med. Chem. 12, 394–405 (2021).
Winston, J. A., Thanissery, R., Montgomery, S. A. & Theriot, C. M. Cefoperazone-treated mouse model of clinically-relevant Clostridium difficile strain R20291. J. Vis. Exp. https://doi.org/10.3791/54850 (2016).
Madhurima, K., Nandi, B. & Sekhar, A. Metamorphic proteins: the Janus proteins of structural biology. Open Biol. 11, 210012 (2021).
Zhou, R. et al. Molecular basis of TMPRSS2 recognition by Paeniclostridium sordellii hemorrhagic toxin. Nat. Commun. 15, 1976 (2024).
von Eichel-Streiber, C., Sauerborn, M. & Kuramitsu, H. K. Evidence for a modular structure of the homologous repetitive C-terminal carbohydrate-binding sites of Clostridium difficile toxins and Streptococcus mutans glucosyltransferases. J. Bacteriol. 174, 6707–6710 (1992).
Shen, A. et al. Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins. Nat. Struct. Mol. Biol. 18, 364–371 (2011).
Icho, S. et al. Intestinal bile acids provide a surmountable barrier against C. difficile TcdB-induced disease pathogenesis. Proc. Natl Acad. Sci. USA 120, e2301252120 (2023).
Poley, J. R. & Hofmann, A. F. Role of fat maldigestion in pathogenesis of steatorrhea in ileal resection. Fat digestion after two sequential test meals with and without cholestyramine. Gastroenterology 71, 38–44 (1976).
Hamilton, J. P. et al. Human cecal bile acids: concentration and spectrum. Am. J. Physiol. Gastrointest. Liver Physiol. 293, G256–G263 (2007).
Wahlström, A., Sayin, S. I., Marschall, H.-U. & Bäckhed, F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 24, 41–50 (2016).
Fiorucci, S., Biagioli, M., Zampella, A. & Distrutti, E. Bile acids activated receptors regulate innate immunity. Front Immunol. 9, 1853 (2018).
Biagioli, M. et al. The bile acid receptor GPBAR1 regulates the M1/M2 phenotype of intestinal macrophages and activation of GPBAR1 rescues mice from murine colitis. J. Immunol. 199, 718–733 (2017).
Džunková, M. et al. The monoclonal antitoxin antibodies (actoxumab–bezlotoxumab) treatment facilitates normalization of the gut microbiota of mice with Clostridium difficile infection. Front. Cell. Infect. Microbiol. 6, 119 (2016).
Thanissery, R., Winston, J. A. & Theriot, C. M. Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids. Anaerobe 45, 86–100 (2017).
Kisthardt, S. C., Thanissery, R., Pike, C. M., Foley, M. H. & Theriot, C. M. The microbial-derived bile acid lithocholate and its epimers inhibit Clostridioides difficile growth and pathogenicity while sparing members of the gut microbiota. J. Bacteriol. 205, e00180-23 (2023).
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Marr, C. R., Benlekbir, S. & Rubinstein, J. L. Fabrication of carbon films with ∼500 nm holes for cryo-EM with a direct detector device. J. Struct. Biol. 185, 42–47 (2014).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153 (2019).
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Meng, E.C. et al. UCSF ChimeraX: tools for structure building and analysis. Prot. Sci. https://doi.org/10.1002/pro.4792 (2023).
Varadi, M. et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52, D368–D375 (2024).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. 60, 2126–2132 (2004).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D. 74, 519–530 (2018).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D. 74, 531–544 (2018).
Sorg, J. A. & Sonenshein, A. L. Chenodeoxycholate is an inhibitor of Clostridium difficile spore germination. J. Bacteriol. 191, 1115–1117 (2009).
Sorg, J. A. & Sonenshein, A. L. Bile salts and glycine as cogerminants for Clostridium difficile spores. J. Bacteriol. 190, 2505–2512 (2008).
Theriot, C. M., Bowman, A. A. & Young, V. B. Antibiotic-induced alterations of the gut microbiota alter secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the large intestine. mSphere 1, e00045-15 (2016).