Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902 · see citing works

The KEGG resource for deciphering the genome

Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,121 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

An advanced culture method for generating large quantities of highly pure dendritic cells from mouse bone marrow

Lutz, M. B., Kukutsch, N. A., Ogilvie, A. L. J., Rößner, S., Koch, F., Romani, N., & Schuler, G. (1999) · Journal of Immunological Methods · doi:10.1016/s0022-1759(98)00204-x · Cited by 2,972 · see citing works

GO::TermFinder–open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes

Boyle, E. I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J. M., & Sherlock, G. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth456 · Cited by 2,067 · see citing works

Microbial Influences in Inflammatory Bowel Diseases

Sartor, R. B. (2008) · Gastroenterology · doi:10.1053/j.gastro.2007.11.059 · Cited by 1,927 · see citing works

High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease

Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A.-L., Barnich, N., Bringer, M.-A., Swidsinski, A., Beaugerie, L., & Colombel, J.-F. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.04.061 · Cited by 1,566 · see citing works

IL-23 is essential for T cell–mediated colitis and promotes inflammation via IL-17 and IL-6

Yen, D., Cheung, J., Scheerens, H., Poulet, F. M., McClanahan, T. K., McKenzie, B. S., Kleinschek, M. A., Owyang, A. M., Mattson, J. D., Blumenschein, W. M., et al. (2006) · Journal of Clinical Investigation · doi:10.1172/jci21404 · Cited by 1,532 · see citing works

Resident Enteric Bacteria Are Necessary for Development of Spontaneous Colitis and Immune System Activation in Interleukin-10-Deficient Mice

Sellon, R. K., Tonkonogy, S., Schultz, M., Dieleman, L. A., Grenther, W., Balish, E., Rennick, D. M., & Sartor, R. B. (1998) · Infection and Immunity · doi:10.1128/iai.66.11.5224-5231.1998 · Cited by 1,483 · see citing works

Glycan foraging in vivo by an intestine-adapted bacterial symbiont

Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

Camon, E. B. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh021 · Cited by 927 · see citing works

Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease

Darfeuille–Michaud, A., Neut, C., Barnich, N., Lederman, E., Martino, P. D., Desreumaux, P., Gambiez, L. P., Joly, B., Cortot, A., & Colombel, J.-F. (1998) · Gastroenterology · doi:10.1016/s0016-5085(98)70019-8 · Cited by 859 · see citing works

IgA Response to Symbiotic Bacteria as a Mediator of Gut Homeostasis

Peterson, D. A., McNulty, N. P., Guruge, J. L., & Gordon, J. I. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.09.013 · Cited by 828 · see citing works

Factors regulating macrophage production and growth. Purification and some properties of the colony stimulating factor from medium conditioned by mouse L cells.

Stanley, E. R., & Heard, P. M. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)40265-1 · Cited by 740 · see citing works

Spontaneous development of inflammatory bowel disease in T cell receptor mutant mice

Mombaerts, P., Mizoguchi, E., Grusby, M. J., Glimcher, L. H., Bhan, A. K., & Tonegawa, S. (1993) · Cell · doi:10.1016/0092-8674(93)80069-q · Cited by 718 · see citing works

A Small, Stable RNA Induced by Oxidative Stress: Role as a Pleiotropic Regulator and Antimutator

Altuvia, S., Weinstein‐Fischer, D., Zhang, A., Postow, L., & Storz, G. (1997) · Cell · doi:10.1016/s0092-8674(00)80312-8 · Cited by 510 · see citing works

A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem

Hooper, L. V., Xu, J., Falk, P. G., Midtvedt, T., & Gordon, J. I. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9833 · Cited by 500 · see citing works

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Gama‐Castro, S., Jacinto, V. J., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., Contreras‐Moreira, B., Segura-Salazar, J., Muñiz-Rascado, L., Martínez‐Flores, I., Salgado, H., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm994 · Cited by 491 · see citing works

Adherent Invasive Escherichia coli Strains from Patients with Crohn's Disease Survive and Replicate within Macrophages without Inducing Host Cell Death

Glasser, A.-L., Boudeau, J., Barnich, N., Perruchot, M.-H., Colombel, J., & Darfeuille–Michaud, A. (2001) · Infection and Immunity · doi:10.1128/iai.69.9.5529-5537.2001 · Cited by 465 · see citing works

Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria

Kim, S. C., Tonkonogy, S. L., Albright, C. A., Tsang, J., Balish, E., Braun, J., Huycke, M. M., & Sartor, R. B. (2005) · Gastroenterology · doi:10.1053/j.gastro.2005.02.009 · Cited by 433 · see citing works

High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease

Kotłowski, R., Bernstein, C. N., Sepehri, S., & Krause, D. O. (2006) · Gut · doi:10.1136/gut.2006.099796 · Cited by 422 · see citing works

Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens

Rey, F. E., Faith, J. J., Bain, J. R., Muehlbauer, M. J., Stevens, R. D., Newgard, C. B., & Gordon, J. I. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.117713 · Cited by 417 · see citing works

Expression of flagella is coincident with uropathogenic Escherichia coli ascension to the upper urinary tract

Lane, M. C., Alteri, C. J., Smith, S. N., & Mobley, H. L. T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607898104 · Cited by 406 · see citing works

IL-12, but not IFN-gamma, plays a major role in sustaining the chronic phase of colitis in IL-10-deficient mice.

Davidson, N. J., Hudak, S. A., Lesley, R., Menon, S., Leach, M. W., & Rennick, D. M. (1998) · PubMed · Cited by 250 · see citing works

Increases in free radicals and cytoskeletal protein oxidation and nitration in the colon of patients with inflammatory bowel disease

Keshavarzian, A., Banan, A., Farhadi, A., Komanduri, S., Mutlu, E., Zhang, Y., & Fields, J. Z. (2003) · Gut · doi:10.1136/gut.52.5.720 · Cited by 237 · see citing works

Sero-Reactivity to Microbial Components in Crohn's Disease Is Associated with Disease Severity and Progression, but not NOD2/CARD15 Genotype

Arnott, I. D., Landers, C. J., Nimmo, E., Drummond, H. E., Smith, B., Targan, S. R., & Satsangi, J. (2004) · The American Journal of Gastroenterology · doi:10.1111/j.1572-0241.2004.40417.x · Cited by 230 · see citing works

Anti-inflammatory properties of<i>Lactobacillus gasseri</i>expressing manganese superoxide dismutase using the interleukin 10-deficient mouse model of colitis

Carroll, I. M., Andrus, J. M., Bruno-Bárcena, J. M., Klaenhammer, T. R., Hassan, H. M., & Threadgill, D. S. (2007) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00132.2007 · Cited by 208 · see citing works

IL-12, But Not IFN-γ, Plays a Major Role in Sustaining the Chronic Phase of Colitis in IL-10-Deficient Mice

Davidson, N. J., Hudak, S. A., Lesley, R., Menon, S., Leach, M. W., & Rennick, D. M. (1998) · The Journal of Immunology · doi:10.4049/jimmunol.161.6.3143 · Cited by 208 · see citing works

The role of mucosal immunity and host genetics in defining intestinal commensal bacteria

Hansen, J. J., Gulati, A., & Sartor, R. B. (2010) · Current Opinion in Gastroenterology · doi:10.1097/mog.0b013e32833f1195 · Cited by 177 · see citing works

Small heat shock proteins, IbpA and IbpB, are involved in resistances to heat and superoxide stresses inEscherichia coli

Kitagawa, M., Matsumura, Y., & Tsuchido, T. (2000) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2000.tb09009.x · Cited by 169 · see citing works

Dual-association of gnotobiotic Il-10−/− mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis

Kim, S. C., Tonkonogy, S. L., Karrasch, T., Jobin, C., & Sartor, R. B. (2007) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20246 · Cited by 131 · see citing works

Escherichia coli small heat shock proteins, IbpA and IbpB, protect enzymes from inactivation by heat and oxidants

Kitagawa, M., 宮川, 瑞., Matsumura, Y., & Tsuchido, T. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.02958.x · Cited by 119 · see citing works

The Small Heat Shock Protein IbpA of Escherichia coli Cooperates with IbpB in Stabilization of Thermally Aggregated Proteins in a Disaggregation Competent State

Matuszewska, M., Kuczyńska‐Wiśnik, D., Laskowska, E., & Liberek, K. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m412706200 · Cited by 113 · see citing works

Escherichia coli heat-shock proteins IbpA/B are involved in resistance to oxidative stress induced by copper

Matuszewska, E., Kwiatkowska, J., Kuczyńska‐Wiśnik, D., & Laskowska, E. (2008) · Microbiology · doi:10.1099/mic.0.2007/014696-0 · Cited by 67 · see citing works

Escherichia coli heat-shock proteins IbpA and IbpB affect biofilm formation by influencing the level of extracellular indole

Kuczyńska‐Wiśnik, D., Matuszewska, E., & Laskowska, E. (2009) · Microbiology · doi:10.1099/mic.0.032334-0 · Cited by 56 · see citing works

Transcription of the ibpB Heat-Shock Gene Is under Control of ς32- and ς54-Promoters, a Third Regulon of Heat-Shock Response

Kuczyńska‐Wiśnik, D., Laskowska, E., & Taylor, A. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.4926 · Cited by 31 · see citing works

An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits

Liu, Y., Li, J., Sam, L. T., Goh, C.-S., Gerstein, M., & Lussier, Y. A. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020159 · Cited by 30 · see citing works

Adoptive transfer of nontransgenic mesenteric lymph node cells induces colitis in athymic HLA-B27 transgenic nude rats

Hoentjen, F., Tonkonogy, S. L., Liu, B., Sartor, R. B., Taurog, J. D., & Dieleman, L. A. (2006) · Clinical & Experimental Immunology · doi:10.1111/j.1365-2249.2006.03013.x · Cited by 15 · see citing works

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

Intestinal inflammation targets cancer-inducing activity of the microbiota

Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T.-J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012) · Science · doi:10.1126/science.1224820 · Cited by 2,263 · see citing works

The microbiome and cancer

Schwabe, R. F., & Jobin, C. (2013) · Nature Reviews Cancer · doi:10.1038/nrc3610 · Cited by 1,689 · see citing works

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota

Albenberg, L., Esipova, T. V., Judge, C. P., Bittinger, K., Chen, J., Laughlin, A., Grunberg, S., Baldassano, R. N., Lewis, J. D., Li, H., et al. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.07.020 · Cited by 886 · see citing works

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

Sartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808 · see citing works

The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease

Zuo, T., & Ng, S. C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02247 · Cited by 590 · see citing works

Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer

Arthur, J. C., Gharaibeh, R. Z., Mühlbauer, M., Perez-Chanona, E., Uronis, J. M., McCafferty, J., Fodor, A. A., & Jobin, C. (2014) · Nature Communications · doi:10.1038/ncomms5724 · Cited by 392 · see citing works

Therapeutic modulation of intestinal dysbiosis

Walker, A. W., & Lawley, T. D. (2012) · Pharmacological Research · doi:10.1016/j.phrs.2012.09.008 · Cited by 197 · see citing works

The microbial basis of inflammatory bowel diseases

Dalal, S. R., & Chang, E. B. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72330 · Cited by 195 · see citing works

Dysbiosis in intestinal inflammation: Cause or consequence

Buttó, L. F., & Haller, D. (2016) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2016.02.010 · Cited by 189 · see citing works

Role of commensal gut bacteria in inflammatory bowel diseases

Loh, G., & Blaut, M. (2012) · Gut Microbes · doi:10.4161/gmic.22156 · Cited by 177 · see citing works

Human Gut Microbiota: Toward an Ecology of Disease

Selber‐Hnatiw, S., Rukundo, B., Ahmadi, M., Akoubi, H., Al-Bizri, H., Aliu, A. F., Ambeaghen, T. U., Avetisyan, L., Bahar, I., Baird, A., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01265 · Cited by 145 · see citing works

The gut microbiota and inflammatory bowel diseases

Miyoshi, J., & Chang, E. B. (2016) · Translational research · doi:10.1016/j.trsl.2016.06.002 · Cited by 141 · see citing works

Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer

Zhu, W., Miyata, N., Winter, M. G., Arenales, A., Hughes, E. R., Spiga, L., Kim, J., Sifuentes-Dominguez, L., Starokadomskyy, P., Gopal, P., et al. (2019) · The Journal of Experimental Medicine · doi:10.1084/jem.20181939 · Cited by 124 · see citing works

Signaling pathways bridging microbial-triggered inflammation and cancer

Kipanyula, M. J., Etet, P. F. S., Vecchio, L., Farahna, M., Nukenine, E. N., & Kamdje, A. H. N. (2012) · Cellular Signalling · doi:10.1016/j.cellsig.2012.10.014 · Cited by 119 · see citing works

E. coli and colorectal cancer: a complex relationship that deserves a critical mindset

Wassenaar, T. M. (2018) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2018.1481013 · Cited by 119 · see citing works

Microbiota in cancer development and treatment

Raza, M. H., Gul, K., Arshad, A., Riaz, N., Waheed, U., Rauf, A., Aldakheel, F. M., Alduraywish, S. A., Rehman, M. U., Abdullah, M., et al. (2018) · Journal of Cancer Research and Clinical Oncology · doi:10.1007/s00432-018-2816-0 · Cited by 120 · see citing works

Microbial imbalance and intestinal pathologies: connections and contributions

Yang, Y., & Jobin, C. (2014) · Disease Models & Mechanisms · doi:10.1242/dmm.016428 · Cited by 112 · see citing works

Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation

Becattini, S., Sorbara, M. T., Kim, S. G., Littmann, E. R., Dong, Q., Walsh, G., Wright, R. J., Amoretti, L. A., Fontana, E., Hohl, T. M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.003 · Cited by 103 · see citing works

The complex interplay between inflammation, the microbiota and colorectal cancer

Arthur, J. C., & Jobin, C. (2013) · Gut Microbes · doi:10.4161/gmic.24220 · Cited by 95 · see citing works

Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection

Buttó, L. F., Schaubeck, M., & Haller, D. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00555 · Cited by 92 · see citing works

Noninvasive assessment of gut function using transcriptional recording sentinel cells

Schmidt, F., Zimmermann, J., Tanna, T., Farouni, R., Conway, T., Macpherson, A. J., & Platt, R. J. (2022) · Science · doi:10.1126/science.abm6038 · Cited by 92 · see citing works

Dysbiosis of gut microbiota in inflammatory bowel disease: Current therapies and potential for microbiota-modulating therapeutic approaches

Alshehri, D., Saadah, O. I., Mosli, M. H., Edris, S., Al-Hindi, R. R., & Bahieldin, A. (2020) · Biomolecules and Biomedicine · doi:10.17305/bjbms.2020.5016 · Cited by 76 · see citing works

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis

Lengfelder, I., Sava, I. G., Hansen, J. J., Kleigrewe, K., Herzog, J., Neuhaus, K., Hofmann, T. F., Sartor, R. B., & Haller, D. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01420 · Cited by 74 · see citing works

Effect of Vitamin E With Therapeutic Iron Supplementation on Iron Repletion and Gut Microbiome in US Iron Deficient Infants and Toddlers

Tang, M., Frank, D. N., Sherlock, L. G., Ir, D., Robertson, C. E., & Krebs, N. F. (2016) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000001154 · Cited by 74 · see citing works

Role of Carbon Monoxide in Host–Gut Microbiome Communication

Hopper, C., Cruz, L. K. D. L., Lyles, K. V. M., Wareham, L. K., Gilbert, J. A., Eichenbaum, Z., Magierowski, M., Poole, R. K., Wollborn, J., & Wang, B. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.0c00586 · Cited by 72 · see citing works

Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain

Spindler, M. P., Siu, S., Mogno, I., Li, Z., Yang, C., Mehandru, S., Britton, G. J., & Faith, J. J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.08.009 · Cited by 65 · see citing works

Characteristics and pathogenic role of adherent-invasive Escherichia coli in inflammatory bowel disease: Potential impact on clinical outcomes

Lee, J. G., Han, D. S., Jo, S. V., Lee, A. R., Park, C. H., Eun, C. S., & Lee, Y. (2019) · PLoS ONE · doi:10.1371/journal.pone.0216165 · Cited by 60 · see citing works

Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction

Sugihara, K., Kitamoto, S., Saraithong, P., Nagao‐Kitamoto, H., Hoostal, M. J., McCarthy, C., Rosevelt, A., Muraleedharan, C. K., Gillilland, M. G., Imai, J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111093 · Cited by 54 · see citing works

<i>Akkermansia muciniphila</i> strain ATCC BAA-835 does not promote short-term intestinal inflammation in gnotobiotic interleukin-10-deficient mice

Ring, C., Klopfleisch, R., Dahlke, K., Basic, M., Bleich, A., & Blaut, M. (2019) · Gut Microbes · doi:10.1080/19490976.2018.1511663 · Cited by 52 · see citing works

Yersiniabactin-Producing Adherent/Invasive Escherichia coli Promotes Inflammation-Associated Fibrosis in Gnotobiotic Il10 −/− Mice

Ellermann, M., Gharaibeh, R. Z., Fulbright, L. E., Dogan, B., Moore, L. N., Broberg, C. A., Lopez, L. R., Rothemich, A., Herzog, J., Rogala, A. R., et al. (2019) · Infection and Immunity · doi:10.1128/iai.00587-19 · Cited by 54 · see citing works

Metabolic network of the gut microbiota in inflammatory bowel disease

Sugihara, K., & Kamada, N. (2024) · Inflammation and Regeneration · doi:10.1186/s41232-024-00321-w · Cited by 54 · see citing works

Dietary iron variably modulates assembly of the intestinal microbiota in colitis-resistant and colitis-susceptible mice

Ellermann, M., Gharaibeh, R. Z., Maharshak, N., Peréz-Chanona, E., Jobin, C., Carroll, I. M., Arthur, J. C., Plevy, S. E., Fodor, A. A., Brouwer, C., et al. (2019) · Gut Microbes · doi:10.1080/19490976.2019.1599794 · Cited by 52 · see citing works

Adherent-Invasive Escherichia coli Production of Cellulose Influences Iron-Induced Bacterial Aggregation, Phagocytosis, and Induction of Colitis

Ellermann, M., Huh, E. Y., Liu, B., Carroll, I. M., Tamayo, R., & Sartor, R. B. (2015) · Infection and Immunity · doi:10.1128/iai.00904-15 · Cited by 48 · see citing works

Molecular detection of bacterial contamination in gnotobiotic rodent units

Packey, C. D., Shanahan, M. T., Manick, S., Bower, M., Ellermann, M., Tonkonogy, S. L., Carroll, I. M., & Sartor, R. B. (2013) · Gut Microbes · doi:10.4161/gmic.25824 · Cited by 43 · see citing works

The Colitis-Associated Transcriptional Profile of Commensal Bacteroides thetaiotaomicron Enhances Adaptive Immune Responses to a Bacterial Antigen

Hansen, J. J., Huang, Y., Peterson, D. A., Goeser, L. E., Fan, T.-J., Chang, E. B., & Sartor, R. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042645 · Cited by 42 · see citing works

Intestinal Microbiota in Animal Models of Inflammatory Diseases

Hörmannsperger, G., Schaubeck, M., & Haller, D. (2015) · ILAR Journal · doi:10.1093/ilar/ilv019 · Cited by 40 · see citing works

Microbiota — an amplifier of autoimmunity

Vogelzang, A., Guerrini, M. M., Minato, N., & Fagarasan, S. (2018) · Current Opinion in Immunology · doi:10.1016/j.coi.2018.09.003 · Cited by 39 · see citing works

Microbiota, Epithelium, Inflammation, and TGF-β Signaling: An Intricate Interaction in Oncogenesis

Pang, X., Tang, Y.-J., Ren, X., Chen, Q., Tang, Y., & Liang, X. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01353 · Cited by 37 · see citing works

Strategies to Dissect Host-Microbial Immune Interactions That Determine Mucosal Homeostasis vs. Intestinal Inflammation in Gnotobiotic Mice

Rogala, A. R., Oka, A., & Sartor, R. B. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00214 · Cited by 35 · see citing works

What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk

Caffaratti, C., Plazy, C., Méry, G., Tidjani, A.-R., Fiorini, F., Thiroux, S., Toussaint, B., Hannani, D., & Gouëllec, A. L. (2021) · Metabolites · doi:10.3390/metabo11060406 · Cited by 35 · see citing works

The Oncobiome in Gastroenteric and Genitourinary Cancers

D’Antonio, D. L., Marchetti, S., Pignatelli, P., Piattelli, A., & Curia, M. C. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23179664 · Cited by 33 · see citing works

Dysbiotic infection in the stomach

Iizasa, H. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i40.11450 · Cited by 26 · see citing works

Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken

Hussain, H. I., Zahid, I., Seleem, M. N., Huang, D., Sattar, A., Hao, H., & Yuan, Z. (2017) · Scientific Reports · doi:10.1038/s41598-017-07798-1 · Cited by 25 · see citing works

Escherichia coli heme oxygenase modulates host innate immune responses

Maharshak, N., Ryu, H. S., Fan, T., Onyiah, J. C., Schulz, S., Otterbein, S. L., Wong, R. J., Hansen, J. J., Otterbein, L. E., Carroll, I. M., et al. (2015) · Microbiology and Immunology · doi:10.1111/1348-0421.12282 · Cited by 24 · see citing works

Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract

Lindenstrauß, A. G., Ehrmann, M. A., Behr, J., Landstorfer, R., Haller, D., Sartor, R. B., & Vogel, R. F. (2014) · Archives of Microbiology · doi:10.1007/s00203-014-0982-2 · Cited by 24 · see citing works

Inflammation-Induced Acid Tolerance Genes gadAB in Luminal Commensal Escherichia coli Attenuate Experimental Colitis

Tchaptchet, S., Fan, T., Goeser, L. E., Schoenborn, A. A., Gulati, A., Sartor, R. B., & Hansen, J. J. (2013) · Infection and Immunity · doi:10.1128/iai.00355-13 · Cited by 24 · see citing works

A new colitis therapy strategy via the target colonization of magnetic nanoparticle-internalized Roseburia intestinalis

Xiao, M., Shen, Z., Luo, W., Tan, B., Meng, X., Wu, X., Wu, S., Nie, K., Tong, T., Hong, J., et al. (2019) · Biomaterials Science · doi:10.1039/c9bm00980a · Cited by 22 · see citing works

Cytotoxic Escherichia coli strains encoding colibactin colonize laboratory mice

García, A., Mannion, A. J., Feng, Y., Madden, C. M., Bakthavatchalu, V., Shen, Z., Ge, Z., & Fox, J. G. (2016) · Microbes and Infection · doi:10.1016/j.micinf.2016.07.005 · Cited by 22 · see citing works

Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease

Lopez, L. R., Ahn, J.-H., Alves, T., & Arthur, J. C. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.934619 · Cited by 22 · see citing works

Adherent-invasive Escherichia coli in Crohn’s disease: the 25th anniversary

Barnich, N., Arthur, J. C., Buisson, A., Campbell, B. J., Carbonnel, F., Chassaing, B., Coombes, B. K., Denizot, J., Dogan, B., Faith, J. J., et al. (2025) · Gut · doi:10.1136/gutjnl-2025-335331 · Cited by 20 · see citing works

Enterococcus faecalis Gluconate Phosphotransferase System Accelerates Experimental Colitis and Bacterial Killing by Macrophages

Fan, T., Goeser, L. E., Naziripour, A., Redinbo, M. R., & Hansen, J. J. (2019) · Infection and Immunity · doi:10.1128/iai.00080-19 · Cited by 19 · see citing works

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin‐10 signalling

Wu, C., Sartor, R. B., Huang, K., & Tonkonogy, S. L. (2016) · Immunology · doi:10.1111/imm.12612 · Cited by 18 · see citing works

The Yin and Yang of host-commensal mutualism

Tchaptchet, S., & Hansen, J. J. (2011) · Gut Microbes · doi:10.4161/gmic.19089 · Cited by 21 · see citing works

Epithelial-microbial diplomacy: escalating border tensions drive inflammation in inflammatory bowel disease

King, S. J., & McCole, D. F. (2019) · Intestinal Research · doi:10.5217/ir.2018.00170 · Cited by 17 · see citing works

Role of signaling pathways in the interaction between microbial, inflammation and cancer

Kamdje, A. H. N., Simo, R. T., Dongmo, H. P. F., Bidias, A., & Netongo, P. M. (2023) · Holistic Integrative Oncology · doi:10.1007/s44178-023-00064-7 · Cited by 18 · see citing works

Cytotoxic Escherichia coli strains encoding colibactin isolated from immunocompromised mice with urosepsis and meningitis

Bakthavatchalu, V., Wert, K. J., Feng, Y., Mannion, A. J., Ge, Z., García, A., Scott, K. E., Caron, T. J., Madden, C. M., Jacobsen, J. T., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194443 · Cited by 16 · see citing works

From Stress Tolerance to Virulence: Recognizing the Roles of Csps in Pathogenicity and Food Contamination

Cardoza, E., & Singh, H. (2024) · Pathogens · doi:10.3390/pathogens13010069 · Cited by 15 · see citing works

Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

Wang, J., Bleich, R. M., Zarmer, S., Zhang, S., Dogan, B., Simpson, K. W., & Arthur, J. C. (2021) · PLoS ONE · doi:10.1371/journal.pone.0259141 · Cited by 14 · see citing works

Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis

Fan, T., Goeser, L. E., Lü, K., Faith, J. J., & Hansen, J. J. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2021.06.017 · Cited by 15 · see citing works

Environmental Factors Modify the Severity of Acute DSS Colitis in Caspase-11-Deficient Mice

Fan, T., Tchaptchet, S., Arsene, D., Mishima, Y., Liu, B., Sartor, R. B., Carroll, I. M., Miao, E. A., Fodor, A. A., & Hansen, J. J. (2018) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izy244 · Cited by 14 · see citing works

Effect of Dietary Monosaccharides on Pseudomonas aeruginosa Virulence

Nelson, R. K., Poroyko, V. A., Morowitz, M. J., Liu, D., & Alverdy, J. C. (2013) · Surgical Infections · doi:10.1089/sur.2011.063 · Cited by 14 · see citing works

Long-chain unsaturated fatty acids released during immune responses stimulate host-microbe trans-kingdom communication

Czauderna, A., Kulkarni, G. V., Bianchi, N., Cheng, L., Sim, M., Realini, N. R., Gach, J., Caillon, A., Kloehn, J., Lambeau, G. J., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.08.011 · Cited by 16 · see citing works

Small Heat-Shock Proteins, IbpAB, Protect Non-Pathogenic Escherichia coli from Killing by Macrophage-Derived Reactive Oxygen Species

Goeser, L. E., Fan, T.-J., Tchaptchet, S., Stasulli, N. M., Goldman, W. E., Sartor, R. B., & Hansen, J. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0120249 · Cited by 12 · see citing works

Impact of metal exposure on environmentally isolated Serratia marcescens’ growth, oxidative-stress resistance, biofilm formation, and proliferation in eukaryotic co-culture models

Adedoyin, F. T., Sridhar, B. B. M., & Rosenzweig, J. A. (2023) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2023.114677 · Cited by 9 · see citing works

Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation

David, C. N., Czauderna, A., Cheng, L., Lagune, M., Jung, H.-J., Kim, S. G., Pamer, E. G., Prados, J., Chen, L., & Becattini, S. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2340486 · Cited by 10 · see citing works

Mild gut inflammation modulates the proteome of intestinal E scherichia coli

Schumann, S., Alpert, C., Engst, W., Klopfleisch, R., Loh, G., Bleich, A., & Blaut, M. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12192 · Cited by 9 · see citing works

A nadA Mutation Confers Nicotinic Acid Auxotrophy in Pro-carcinogenic Intestinal Escherichia coli NC101

Lopez, L. R., Barlogio, C. J., Broberg, C. A., Wang, J., & Arthur, J. C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.670005 · Cited by 6 · see citing works

The rsmS (ybaM) mutation causes bypass suppression of the RsmAB post-transcriptional virulence regulation system in enterobacterial phytopathogens

Monson, R. E., Apagyi, K., Bowden, S. D., Simpson, N. J. L., Williamson, N. R., Cubitt, M. F., Harris, S., Toth, I. K., & Salmond, G. P. C. (2019) · Scientific Reports · doi:10.1038/s41598-019-40970-3 · Cited by 6 · see citing works

Essential Oil Chemical Composition, Antioxidant and Antibacterial Activities of Eucalyptus largiflorens F. Muell

Bidgoli, R. D., Abdullah, F. O., Budriesi, R., Mattioli, L., Spadoni, G., Mari, M., & Micucci, M. (2023) · Polish Journal of Environmental Studies · doi:10.15244/pjoes/161886 · Cited by 5 · see citing works

Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial bindingPreprint

Jans, M., Kolata, M., Blancke, G., Ciers, M., Dohlman, A. B., Kusakabe, T., Sze, M., Thiran, A., Berx, G., Tejpar, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.16.553526 · Cited by 4 · see citing works

Intestinal Microbiology and Ecology in Crohn’s Disease and Ulcerative Colitis

Buttó, L. F., & Haller, D. (2017) · Springer eBooks · doi:10.1007/978-3-319-33703-6_4 · Cited by 2 · see citing works

Bacterial Infections and Cancer Development

Agassandian, M., & Shurin, G. V. (2015) · Springer eBooks · doi:10.1007/978-3-319-20669-1_4 · Cited by 2 · see citing works

Transcriptomic and proteomic analysis of the effect of hydrogen peroxide on enterohemorrhagic Escherichia coli

Kijewski, A., Anonsen, J. H., Witsø, I. L., Sundaram, A. Y. M., Brynildsrud, O., Anonsen, E. B., & Aspholm, M. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e44064 · Cited by 1 · see citing works

Bacterial Mediated Gastrointestinal Inflammation

Uronis, J. M., & Sun, X. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-481-4_22 · Cited by 1 · see citing works

ДИСБІОЗ СЕЧОСТАТЕВОЇ СИСТЕМИ ЧОЛОВІКІВ ТА ПОРУШЕННЯ ГОРМОНАЛЬНОГО ГОМЕОСТАЗУ (ОГЛЯД ЛІТЕРАТУРИ)

Мельник, О. В., Коваленко, И. В., Nemchenko, O. O., Павляк, У. В., & Shykula, R. G. (2024) · Международная научно-практическая конференция «Актуальные проблемы науки и образования в условиях современных вызовов» · doi:10.36059/978-966-397-371-5-13 · Cited by 1 · see citing works

Role of the Gut Microbiota in Maintaining GI Health: Highlights on Inflammatory Bowel Disease

Gruber, L., & Haller, D. (2014) · Molecular and integrative toxicology · doi:10.1007/978-1-4471-6539-2_13 · Cited by 1 · see citing works

Disruption of Complex Enteric Commensal Microbial Communities and Their Mutualistic Functions with the Host Contributes to the Severity of Common Intestinal Disorders and Serves as a Promising Therapeutic Target

Packey, C. D. (2014) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.13140/rg.2.2.22562.63686

The effects of treadmill and voluntary wheel training on morbidity and inflammation during ulcerative colitis in mice

Cook, M. D. (2013) · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)

The Role of Enterococcus faecalis Sugar Transport in Experimental Colitis

Fan, T. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/rq58-hv96

Body Fluid Microbiome as Cancer Biomarkers

Dakubo, G. D. (2019) · Springer eBooks · doi:10.1007/978-3-030-24725-6_14

The global stress response regulator oxyS in an adherent-invasive Escherichia coli strain attenuates experimental colitis

Arsene, D., Tchaptchet, S., & Hansen, J. J. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2473518

Rôle de l'îlot génomique pks dans la synthèse des sidérophores-microcines chez Escherichia coli

Massip, C. (2019) · theses.fr (ABES) · doi:10.70675/79fd3cdcz6be0z491ez95c5zf2b155b65e97

Développement de biomédicaments vivants ingénierés au métabolisme contrôlé en vue d'une utilisation en tant que thérapie innovante dans le domaine de l'immunothérapie

Caffaratti, C. (2023) · theses.fr (ABES) · doi:10.70675/5872762az54e0z4783za2bfz94f6f9658f84

Mise en évidence d'immunomodulations médiées par les métabolites : de l'identification à l'application en contexte infectieux

Plazy, C. (2022) · doi:10.70675/8ad06787z1f75z4656zb37bz660982e34087

Experimental colitis induces stress responses in commensal Escherichia coli that impair luminal bacterial survival and attenuate inflammation

Hansen, J. J., Fan, T., Tchaptchet, S., & Sartor, R. B. (2011) · Inflammatory Bowel Diseases · doi:10.1097/00054725-201112002-00022

Mo1773 Resilience of the Human Intestinal Microbiota After an Antibiotic Perturbation: Influence of a Probiotic Compared to Placebo

Heinsen, F., Knecht, H., Neulinger, S. C., Friedrichs, A. K., Kuehbacher, T., Baines, J. F., Rosenstiel, P. C., Schreiber, S., & Ott, S. J. (2012) · Gastroenterology · doi:10.1016/s0016-5085(12)62627-4

Mo1772 Crohn's Disease-Associated Enterococcus Faecalis Strain Trigger Differential Host Response in Germfree and Conventional NOD2 Deficient Mice

Sava, I. G., Hrncir, T., Ocvirk, S., & Haller, D. (2012) · Gastroenterology · doi:10.1016/s0016-5085(12)62626-2

Inflammation-Induced Acid Tolerance Genes gadAB in Luminal Commensal Escherichia coli Attenuate Experimental Colitis

Tchaptchet, S., Fan, T., Goeser, L. E., Schoenborn, A. A., Gulati, A., Sartor, R. B., & Hansen, J. J. (2013) · Infection and Immunity · doi:10.1128/iai.00355-13 · Cited by 24 · see citing works

262 Impact of NOD2 on Intestinal Microbiota and Mucosal Homeostasis: Respective Roles of Epithelial and Immune Cells

Nabhani, Z. A., Hugot, J., Montcuquet, N., Roux, K. L., Mauny, P., Roy, M., Dussaillant, M., Cerf–Bensussan, N., Lepage, P., & Barreau, F. (2013) · Gastroenterology · doi:10.1016/s0016-5085(13)60208-5