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  • 1.

    Lessa, F. C. et al. Burden of Clostridium difficile infection in the United States. N. Engl. J. Med. 372, 825–834 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 2.

    Rivera-Chávez, F. & Bäumler, A. J. The pyromaniac inside you: Salmonella metabolism in the host gut. Annu. Rev. Microbiol. 69, 31–48 (2015).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • 3.

    Faber, F. et al. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion. Nature 534, 697–699 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 4.

    Lopez, C. A. et al. Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration. Science 353, 1249–1253 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 5.

    Bäumler, A. J. & Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535, 85–93 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 6.

    Rivera-Chávez, F. & Mekalanos, J. J. Cholera toxin promotes pathogen acquisition of host-derived nutrients. Nature 572, 244–248 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 7.

    El Feghaly, R. E. et al. Markers of intestinal inflammation, not bacterial burden, correlate with clinical outcomes in Clostridium difficile infection. Clin. Infect. Dis. 56, 1713–1721 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    Hryckowian, A. J., Pruss, K. M. & Sonnenburg, J. L. The emerging metabolic view of Clostridium difficile pathogenesis. Curr. Opin. Microbiol. 35, 42–47 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 9.

    Yamada, M. & Saier, M. H., Jr. Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon. J. Biol. Chem. 262, 5455–5463 (1987).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 10.

    Svensäter, G., Edwardsson, S. & Kalfas, S. Purification and properties of sorbitol-6-phosphate dehydrogenase from oral streptococci. Oral Microbiol. Immunol. 7, 148–154 (1992).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 11.

    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).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 12.

    Moing, A. Sugar alcohols as carbohydrate reserves in some higher plants. Dev. Crop Sci. 26, 337–358 (2000).

    Article 

    Google Scholar 

  • 13.

    Hryckowian, A. J. et al. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat. Microbiol. 3, 662–669 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 14.

    Collins, J. et al. Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature 553, 291–294 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Kumar, N. et al. Adaptation of host transmission cycle during Clostridium difficile speciation. Nat. Genet. 51, 1315–1320 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Di Rienzi, S. C. & Britton, R. A. Adaptation of the gut microbiota to modern dietary sugars and sweeteners. Adv. Nutr. 11, 616–629 (2020).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 17.

    Tang, W. H., Martin, K. A. & Hwa, J. Aldose reductase, oxidative stress, and diabetic mellitus. Front. Pharmacol. 3, 87 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Pal, P. B., Sonowal, H., Shukla, K., Srivastava, S. K. & Ramana, K. V. Aldose reductase mediates NLRP3 inflammasome-initiated innate immune response in hyperglycemia-induced Thp1 monocytes and male mice. Endocrinology 158, 3661–3675 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Kashima, K., Sato, N., Sato, K., Shimizu, H. & Mori, M. Effect of epalrestat, an aldose reductase inhibitor, on the generation of oxygen-derived free radicals in neutrophils from streptozotocin-induced diabetic rats. Endocrinology 139, 3404–3408 (1998).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 20.

    Antunes, A. et al. Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile. Nucleic Acids Res. 40, 10701–10718 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Shakov, R., Salazar, R. S., Kagunye, S. K., Baddoura, W. J. & DeBari, V. A. Diabetes mellitus as a risk factor for recurrence of Clostridium difficile infection in the acute care hospital setting. Am. J. Infect. Control 39, 194–198 (2011).

    PubMed 
    Article 

    Google Scholar 

  • 22.

    Hassan, S. A., Rahman, R. A., Huda, N., Wan Bebakar, W. M. & Lee, Y. Y. Hospital-acquired Clostridium difficile infection among patients with type 2 diabetes mellitus in acute medical wards. J. R. Coll. Physicians Edinb. 43, 103–107 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 23.

    Ramana, K. V. Aldose reductase: new insights for an old enzyme. Biomol. Concepts 2, 103–114 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 24.

    The Tabula Muris Consortium. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372 (2018).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 25.

    Biton, M. et al. T helper cell cytokines modulate intestinal stem cell renewal and differentiation. Cell 175, 1307–1320.e22 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730.e22 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 27.

    D’Auria, K. M. et al. In vivo physiological and transcriptional profiling reveals host responses to Clostridium difficile toxin A and toxin B. Infect. Immun. 81, 3814–3824 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 28.

    Whitaker, W. R., Shepherd, E. S. & Sonnenburg, J. L. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 169, 538–546.e12 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Tang, J., Du, Y., Petrash, J. M., Sheibani, N. & Kern, T. S. Deletion of aldose reductase from mice inhibits diabetes-induced retinal capillary degeneration and superoxide generation. PLoS ONE 8, e62081 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Ho, H. T. et al. Aldose reductase-deficient mice develop nephrogenic diabetes insipidus. Mol. Cell. Biol. 20, 5840–5846 (2000).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Kuehne, S. A. et al. The role of toxin A and toxin B in Clostridium difficile infection. Nature 467, 711–713 (2010).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 32.

    Kuehne, S. A. et al. Importance of toxin A, toxin B, and CDT in virulence of an epidemic Clostridium difficile strain. J. Infect. Dis. 209, 83–86 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 33.

    Karasawa, T., Ikoma, S., Yamakawa, K. & Nakamura, S. A defined growth medium for Clostridium difficile. Microbiology 141, 371–375 (1995).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 34.

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

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Ng, Y. K. et al. Expanding the repertoire of gene tools for precise manipulation of the Clostridium difficile genome: allelic exchange using pyrE alleles. PLoS ONE 8, e56051 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 36.

    Minton, N. P. et al. A roadmap for gene system development in Clostridium. Anaerobe 41, 104–112 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 37.

    Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 40.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 41.

    Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 42.

    McKenzie, A. T., Katsyv, I., Song, W. M., Wang, M. & Zhang, B. DGCA: A comprehensive R package for differential gene correlation analysis. BMC Syst. Biol. 10, 106 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 43.

    Mi, H. et al. Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat. Protoc. 14, 703–721 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 44.

    R Core Team. R: a language and environment for statistical computing. https://www.r-project.org/ (R Foundation for Statistical Computing, 2020).

  • 45.

    Wickham, H. ggplot2: Elegant Graphics for Data Analysis 2nd edn (Springer, 2016).



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