Brennan, C. A. & Garrett, W. S. Fusobacterium nucleatum—symbiont, opportunist and oncobacterium. Nat. Rev. Microbiol. 17, 156–166 (2019).
Janney, A., Powrie, F. & Mann, E. H. Host-microbiota maladaptation in colorectal most cancers. Nature 585, 509–517 (2020).
O’Keefe, S. J. Eating regimen, microorganisms and their metabolites, and colon most cancers. Nat. Rev. Gastroenterol. Hepatol. 13, 691–706 (2016).
Tilg, H., Adolph, T. E., Gerner, R. R. & Moschen, A. R. The intestinal microbiota in colorectal most cancers. Most cancers Cell 33, 954–964 (2018).
Wong, S. H. & Yu, J. Intestine microbiota in colorectal most cancers: mechanisms of motion and medical functions. Nat. Rev. Gastroenterol. Hepatol. 16, 690–704 (2019).
Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal most cancers attributable to genotoxic pks+ E. coli. Nature 580, 269–273 (2020).
Slowicka, Ok. et al. Zeb2 drives invasive and microbiota-dependent colon carcinoma. Nat. Most cancers 1, 620–634 (2020).
Morgan, E. et al. World burden of colorectal most cancers in 2020 and 2040: incidence and mortality estimates from GLOBOCAN. Intestine 72, 338–344 (2023).
Keum, N. & Giovannucci, E. World burden of colorectal most cancers: rising traits, threat components and prevention methods. Nat. Rev. Gastroenterol. Hepatol. 16, 713–732 (2019).
GBD 2019 Colorectal Most cancers Collaborators. The worldwide, regional, and nationwide burden of colorectal most cancers and its attributable threat components in 195 international locations and territories, 1990–2017: a scientific evaluation for the World Burden of Illness Research 2017. Lancet Gastroenterol. Hepatol. 4, 913–933 (2019).
Zepeda-Rivera, M. et al. A definite Fusobacterium nucleatum clade dominates the colorectal most cancers area of interest. Nature https://doi.org/10.1038/s41586-024-07182-w (2024).
Buc, E. et al. Excessive prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon most cancers. PLoS ONE 8, e56964 (2013).
Arthur, J. C. et al. Microbial genomic evaluation reveals the important function of irritation in bacteria-induced colorectal most cancers. Nat. Commun. 5, 4724 (2014).
Dejea, C. M. et al. Sufferers with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic micro organism. Science 359, 592–597 (2018).
Nougayrede, J. P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848–851 (2006).
Cuevas-Ramos, G. et al. Escherichia coli induces DNA injury in vivo and triggers genomic instability in mammalian cells. Proc. Natl Acad. Sci. USA 107, 11537–11542 (2010).
Rosendahl Huber, A. et al. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal most cancers. Most cancers Cell 42, 487–496 (2024).
Cougnoux, A. et al. Bacterial genotoxin colibactin promotes colon tumour progress by inducing a senescence-associated secretory phenotype. Intestine 63, 1932–1942 (2014).
Brugiroux, S. et al. Genome-guided design of an outlined mouse microbiota that confers colonization resistance in opposition to Salmonella enterica serovar Typhimurium. Nat. Microbiol. 2, 16215 (2016).
Bonnet, M. et al. Colonization of the human intestine by E. coli and colorectal most cancers threat. Clin. Most cancers Res. 20, 859–867 (2014).
Arthur, J. C. et al. Intestinal irritation targets cancer-inducing exercise of the microbiota. Science 338, 120–123 (2012).
Tomkovich, S. et al. Locoregional results of microbiota in a preclinical mannequin of colon carcinogenesis. Most cancers Res. 77, 2620–2632 (2017).
Salesse, L. et al. Colibactin-producing Escherichia coli induce the formation of invasive carcinomas in a power inflammation-associated mouse mannequin. Cancers 13, 2060 (2021).
Lucas, C. et al. Autophagy of intestinal epithelial cells inhibits colorectal carcinogenesis induced by colibactin-producing Escherichia coli in ApcMin/+ mice. Gastroenterology 158, 1373–1388 (2020).
Li, Z. R. et al. Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin. Nat. Chem. Biol. 12, 773–775 (2016).
Wernke, Ok. M. et al. Construction and bioactivity of colibactin. Bioorg. Med. Chem. Lett. 30, 127280 (2020).
Conover, M. S. et al. Irritation-induced adhesin-receptor interplay offers a health benefit to uropathogenic E. coli throughout power an infection. Cell Host Microbe 20, 482–492 (2016).
Jones, C. H. et al. FimH adhesin of kind 1 pili is assembled right into a fibrillar tip construction within the Enterobacteriaceae. Proc. Natl Acad. Sci. USA 92, 2081–2085 (1995).
Kalas, V. et al. Construction-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion throughout urinary tract an infection. Proc. Natl Acad. Sci. USA 115, E2819–E2828 (2018).
Maddirala, A. R. et al. Biphenyl Gal and GalNAc FmlH lectin antagonists of uropathogenic E. coli (UPEC): optimization by iterative rational drug design. J. Med. Chem. 62, 467–479 (2019).
Stentebjerg-Olesen, B., Chakraborty, T. & Klemm, P. Kind 1 fimbriation and part switching in a pure Escherichia coli fimB null pressure, Nissle 1917. J. Bacteriol. 181, 7470–7478 (1999).
Dreux, N. et al. Level mutations in FimH adhesin of Crohn’s disease-associated adherent-invasive Escherichia coli improve intestinal inflammatory response. PLoS Pathog. 9, e1003141 (2013).
Iebba, V. et al. Microevolution in fimH gene of mucosa-associated Escherichia coli strains remoted from pediatric sufferers with inflammatory bowel illness. Infect. Immun. 80, 1408–1417 (2012).
Schwartz, D. J. et al. Positively chosen FimH residues improve virulence throughout urinary tract an infection by altering FimH conformation. Proc. Natl Acad. Sci. USA 110, 15530–15537 (2013).
Reinisch, W. et al. Security, pharmacokinetic, and pharmacodynamic research of sibofimloc, a novel FimH blocker in sufferers with energetic Crohn’s illness. J. Gastroenterol. Hepatol. 37, 832–840 (2022).
Chevalier, G. et al. Blockage of bacterial FimH prevents mucosal irritation related to Crohn’s illness. Microbiome 9, 176 (2021).
Reuter, C., Alzheimer, M., Walles, H. & Oelschlaeger, T. A. An adherent mucus layer attenuates the genotoxic impact of colibactin. Cell Microbiol. https://doi.org/10.1111/cmi.12812 (2018).
Zhao, Z., Xu, S., Zhang, W., Wu, D. & Yang, G. Probiotic Escherichia coli NISSLE 1917 for inflammatory bowel illness functions. Meals Funct. 13, 5914–5924 (2022).
Olier, M. et al. Genotoxicity of Escherichia coli Nissle 1917 pressure can’t be dissociated from its probiotic exercise. Intestine Microbes 3, 501–509 (2012).
Giaffer, M. H., Holdsworth, C. D. & Duerden, B. I. Virulence properties of Escherichia coli strains remoted from sufferers with inflammatory bowel illness. Intestine 33, 646–650 (1992).
Darfeuille-Michaud, A. et al. Presence of adherent Escherichia coli strains in ileal mucosa of sufferers with Crohn’s illness. Gastroenterology 115, 1405–1413 (1998).
Harnack, C. et al. Quick-term mucosal disruption permits colibactin-producing E. coli to trigger long-term perturbation of colonic homeostasis. Intestine Microbes 15, 2233689 (2023).
van der Publish, S. et al. Structural weakening of the colonic mucus barrier is an early occasion in ulcerative colitis pathogenesis. Intestine 68, 2142–2151 (2019).
Desai, M. S. et al. A dietary fiber-deprived intestine microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353 (2016).
Dalmasso, G. et al. Colibactin-producing Escherichia coli improve resistance to chemotherapeutic medication by selling epithelial to mesenchymal transition and most cancers stem cell emergence. Intestine Microbes 16, 2310215 (2024).
de Oliveira Alves, N. et al. The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal most cancers development and chemoresistance. Intestine Microbes 16, 2320291 (2024).
Volpe, M. R. et al. A small molecule inhibitor prevents intestine bacterial genotoxin manufacturing. Nat. Chem. Biol. 19, 159–167 (2023).
Blanco-Miguez, A. et al. Focused depletion of pks+ micro organism from a fecal microbiota utilizing particular antibodies. mSystems 8, e0007923 (2023).
Gencay, Y. E. et al. Engineered phage with antibacterial CRISPR-Cas selectively scale back E. coli burden in mice. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01759-y (2023).
Spaulding, C. N. et al. Selective depletion of uropathogenic E. coli from the intestine by a FimH antagonist. Nature 546, 528–532 (2017).
Greene, S. E., Hibbing, M. E., Janetka, J., Chen, S. L. & Hultgren, S. J. Human urine decreases perform and expression of kind 1 pili in uropathogenic Escherichia coli. mBio 6, e00820 (2015).
Datsenko, Ok. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli Ok-12 utilizing PCR merchandise. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Ramesh, P., Kirov, A. B., Huels, D. J. & Medema, J. P. Isolation, propagation, and clonogenicity of intestinal stem cells. Strategies Mol. Biol. 2002, 61–73 (2019).
Ewels, P., Magnusson, M., Lundin, S. & Kaller, M. MultiQC: summarize evaluation outcomes for a number of instruments and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
Andrews, S. FastQC: a high quality management device for prime throughput sequence knowledge (2010).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a versatile trimmer for Illumina sequence knowledge. Bioinformatics 30, 2114–2120 (2014).
Dobin, A. et al. STAR: ultrafast common RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Liao, Y., Smyth, G. Ok. & Shi, W. The Subread aligner: quick, correct and scalable learn mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).
Love MI, A. S., Kim, V. & Huber, W. RNA-seq workflow: gene-level exploratory evaluation and differential expression. F1000Research 4, 1070 (2016).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq knowledge with DESeq2. Genome Biol. 15, 550 (2014).
Korotkevich, G. et al. Quick gene set enrichment evaluation. Preprint at bioRxiv https://doi.org/10.1101/060012 (2019).
Stephens, M. False discovery charges: a brand new deal. Biostatistics 18, 275–294 (2017).
Hanzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation evaluation for microarray and RNA-seq knowledge. BMC Bioinform. 14, 7 (2013).
Kolde, R. Pheatmap: fairly heatmaps (2012).
Thakur, S. D., Obradovic, M., Dillon, J. R., Ng, S. H. & Wilson, H. L. Improvement of circulate cytometry based mostly adherence assay for Neisseria gonorrhoeae utilizing 5′-carboxyfluorosceinsuccidyl ester. BMC Microbiol. 19, 67 (2019).
Martin, H. M. et al. Enhanced Escherichia coli adherence and invasion in Crohn’s illness and colon most cancers. Gastroenterology 127, 80–93 (2004).
Wirth, T. et al. Intercourse and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60, 1136–1151 (2006).
Vizcaino, M. I., Engel, P., Trautman, E. & Crawford, J. M. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules. J. Am. Chem. Soc. 136, 9244–9247 (2014).