Scallan, E. et al. Foodborne illness acquired in the United States—major pathogens. Emerg. Infect. Dis. 17, 7–15 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Hohmann, E. L. Nontyphoidal salmonellosis. Clin. Infect. Dis. 32, 263–269 (2001).

Article  PubMed  CAS  Google Scholar 

Parry, C. M. et al. A retrospective study of secondary bacteraemia in hospitalised adults with community acquired non-typhoidal Salmonella gastroenteritis. BMC Infect. Dis. 13, 107 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Ng, K. M. et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96–99 (2013).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Faber, F. et al. Respiration of microbiota-derived 1,2-propanediol drives salmonella expansion during colitis. PLoS Pathog. 13, e1006129 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Winter, S. E. et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467, 426–429 (2010).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Thiennimitr, P. et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc. Natl Acad. Sci. USA 108, 17480–17485 (2011).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ott, S. J. et al. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand. J. Gastroenterol. 43, 831–841 (2008).

Article  PubMed  CAS  Google Scholar 

Dollive, S. et al. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS ONE 8, e71806 (2013).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Eriksson, M. et al. The C-type lectin receptor SIGNR3 binds to fungi present in commensal microbiota and influences immune regulation in experimental colitis. Front. Immunol. 4, 196 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Foster, M. L., Dowd, S. E., Stephenson, C., Steiner, J. M. & Suchodolski, J. S. Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs. Vet. Med. Int. 2013, 658373 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Hoffmann, C. et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE 8, e66019 (2013).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Frykman, P. K. et al. Characterization of bacterial and fungal microbiome in children with hirschsprung disease with and without a history of enterocolitis: a multicenter study. PLoS ONE 10, e0124172 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Donovan, P. D., Gonzalez, G., Higgins, D. G., Butler, G. & Ito, K. Identification of fungi in shotgun metagenomics datasets. PLoS ONE 13, e0192898 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Sokol, H. et al. Fungal microbiota dysbiosis in IBD. Gut 66, 1039–1048 (2017).

Article  PubMed  CAS  Google Scholar 

Wheeler, M. L. et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe 19, 865–873 (2016).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Skalski, J. H. et al. Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. PLoS Pathog. 14, e1007260 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Yang, A. M. et al. Intestinal fungi contribute to development of alcoholic liver disease. J. Clin. Investig. 127, 2829–2841 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Bacher, P. et al. Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. Cell 176, 1340–1355.e15 (2019).

Article  PubMed  CAS  Google Scholar 

Zhu, F. et al. Autoreactive T cells and chronic fungal infection drive esophageal carcinogenesis. Cell Host Microbe 21, 478–493.e7 (2017).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Aykut, B. et al. The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature 574, 264–267 (2019).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zhai, B. et al. High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis. Nat. Med. 26, 59–64 (2020).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Rolling, T. et al. Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species. Nat. Microbiol. 6, 1505–1515 (2021).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Deriu, E. et al. Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14, 26–37 (2013).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Andrews, S. C., Robinson, A. K. & Rodríguez-Quiñones, F. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215–237 (2003).

Article  PubMed  CAS  Google Scholar 

Holden, V. I. & Bachman, M. A. Diverging roles of bacterial siderophores during infection. Metallomics 7, 986–995 (2015).

Article  PubMed  CAS  Google Scholar 

Flo, T. H. et al. Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron. Nature 432, 917–921 (2004).

Article  PubMed  CAS  Google Scholar 

Berger, T. et al. Lipocalin 2-deficient mice exhibit increased sensitivity to Escherichia coli infection but not to ischemia–reperfusion injury. Proc. Natl Acad. Sci. USA 103, 1834–1839 (2006).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Crosa, J. H. & Walsh, C. T. Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol. Mol. Biol. Rev. 66, 223–249 (2002).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bachman, M. A., Miller, V. L. & Weiser, J. N. Mucosal lipocalin 2 has pro-inflammatory and iron-sequestering effects in response to bacterial enterobactin. PLoS Pathog. 5, e1000622 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Raffatellu, M. et al. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell Host Microbe 5, 476–486 (2009).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Holmes, M. A., Paulsene, W., Jide, X., Ratledge, C. & Strong, R. K. Siderocalin (Lcn 2) also binds carboxymycobactins, potentially defending against mycobacterial infections through iron sequestration. Structure 13, 29–41 (2005).

Article  PubMed  CAS  Google Scholar 

Hantke, K. Identification of an iron uptake system specific for coprogen and rhodotorulic acid in Escherichia coli K12. Mol. Genet. Genom. 191, 301–306 (1983).

Article  CAS  Google Scholar 

Rabsch, W. Characterization of the catecholate indicator strain S. typhimurium TA2700 as an ent fhuC double mutant. FEMS Microbiol. Lett. 163, 79–84 (1998).

Article  PubMed  CAS  Google Scholar 

Kingsley, R. A. et al. Ferrioxamine-mediated iron(III) utilization by Salmonella enterica. Appl. Environ. Microbiol. 65, 1610–1618 (1999).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Luckey, M., Pollack, J. R., Wayne, R., Ames, B. N. & Neilands, J. B. Iron uptake in Salmonella typhimurium: utilization of exogenous siderochromes as iron carriers. J. Bacteriol. 111, 731–738 (1972).

Article  PubMed  PubMed Central  CAS