Gut microbiota and inflammatory bowel disease: the role of antibiotics in disease management

Structure, function and diversity of the healthy human microbiome

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Diet rapidly and reproducibly alters the human gut microbiome

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Human gut microbiome viewed across age and geography

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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

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The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Epidemiology and Natural History of Inflammatory Bowel Diseases

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Ulcerative Colitis Practice Guidelines in Adults: American College of Gastroenterology, Practice Parameters Committee

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Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice

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Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: A double-blind, placebo-controlled trial

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

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Maintaining remission of ulcerative colitis with the probiotic <i>Escherichia coli</i> Nissle 1917 is as effective as with standard mesalazine

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Low counts of Faecalibacterium prausnitzii in colitis microbiota

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Management of Crohn's Disease in Adults

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Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome

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Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial

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The natural history of fistulizing Crohn's disease in Olmsted County, Minnesota

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Inflammatory bowel disease: Epidemiology, pathogenesis, and therapeutic opportunities

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Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis

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Controlled trial of metronidazole treatment for prevention of crohn's recurrence after ileal resection

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VSL#3 Probiotic-Mixture Induces Remission in Patients with Active Ulcerative Colitis

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High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

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Saccharomyces boulardii in Maintenance Treatment of Crohn’s Disease

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Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis

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Ineffectiveness of probiotics in preventing recurrence after curative resection for Crohn's disease: a randomised controlled trial with Lactobacillus GG

Prantera, C. (2002) · Gut · doi:10.1136/gut.51.3.405 · Cited by 566 · see citing works

Double blind, placebo controlled trial of metronidazole in Crohn's disease.

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Effect of a Probiotic Preparation (VSL#3) on Induction and Maintenance of Remission in Children With Ulcerative Colitis

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The Probiotic Preparation, VSL#3 Induces Remission in Patients With Mild-to-Moderately Active Ulcerative Colitis

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An update on the use and investigation of probiotics in health and disease

Sanders, M. E., Guarner, F., Guerrant, R., Holt, P. R., Quigley, E. M., Sartor, R. B., Sherman, P. M., & Mayer, E. A. (2013) · Gut · doi:10.1136/gutjnl-2012-302504 · Cited by 503 · see citing works

Treatment of Relapsing Mild-to-Moderate Ulcerative Colitis With the Probiotic VSL#3 as Adjunctive to a Standard Pharmaceutical Treatment: A Double-Blind, Randomized, Placebo-Controlled Study

Tursi, A., Brandimarte, G., Papa, A., Giglio, A., Elisei, W., Giorgetti, G. M., Forti, G., Morini, S., Hassan, C., Pistoia, M. A., et al. (2010) · American Journal of Gastroenterology · doi:10.1038/ajg.2010.218 · Cited by 489 · see citing works

Antibiotic Exposure and IBD Development Among Children: A Population-Based Cohort Study

Kronman, M. P., Zaoutis, T. E., Haynes, K., Feng, R., & Coffin, S. E. (2012) · PEDIATRICS · doi:10.1542/peds.2011-3886 · Cited by 445 · 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

Ornidazole for prophylaxis of postoperative Crohn’s disease recurrence: A randomized, double-blind, placebo-controlled trial

Rutgeerts, P. J., Assche, G. V., Vermeire, S., D’Haens, G., Baert, F., Noman, M., Aerden, I., Hertogh, G. D., Geboes, K. J., Hiele, M. I., et al. (2005) · Gastroenterology · doi:10.1053/j.gastro.2005.01.010 · Cited by 416 · see citing works

Ineffectiveness of Lactobacillus johnsonii LA1 for prophylaxis of postoperative recurrence in Crohn’s disease: a randomised, double blind, placebo controlled GETAID trial

Marteau, P. R., Lémann, M., Seksik, P., Laharie, D., Colombel, J. F., Bouhnik, Y., Cadiot, G., Soulé, J. C., Bourreille, A., Metman, E.-H., et al. (2005) · Gut · doi:10.1136/gut.2005.076604 · Cited by 412 · see citing works

Smoking Cessation Induces Profound Changes in the Composition of the Intestinal Microbiota in Humans

Biedermann, L., Zeitz, J., Mwinyi, J., Sutter-Minder, E., Rehman, A., Ott, S. J., Steurer-Stey, C. A., Frei, A. L., Frei, P., Scharl, M. M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059260 · Cited by 411 · see citing works

New antibiotics for bad bugs: where are we?

Bassetti, M., Merelli, M., Temperoni, C., & Astilean, A. (2013) · Annals of Clinical Microbiology and Antimicrobials · doi:10.1186/1476-0711-12-22 · Cited by 403 · see citing works

Randomized placebo‐controlled trial assessing the effect of bifidobacteria‐fermented milk on active ulcerative colitis

Kato, K., Mizuno, S., Umesaki, Y., Ishii, Y., Sugitani, M., Imaoka, A., Otsuka, M., Hasunuma, O., Kurihara, R., Iwasaki, A., et al. (2004) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/j.1365-2036.2004.02268.x · Cited by 397 · see citing works

A pilot trial of Saccharomyces boulardii in ulcerative colitis

Guslandi, M., Giollo, P., & Testoni, P. A. (2003) · European Journal of Gastroenterology & Hepatology · doi:10.1097/00042737-200306000-00017 · Cited by 383 · see citing works

Randomized Controlled Trial of the Effect of Bifidobacteria-Fermented Milk on Ulcerative Colitis

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A Randomized, Double-blind Trial of Lactobacillus GG Versus Placebo in Addition to Standard Maintenance Therapy for Children with Crohnʼs Disease

Bousvaros, A., Guandalini, S., Baldassano, R. N., Botelho, C. A., Evans, J., Ferry, G. D., Goldin, B. R., Parker‐Hartigan, L., Kugathasan, S., Levy, J. F., et al. (2005) · Inflammatory Bowel Diseases · doi:10.1097/01.mib.0000175905.00212.2c · Cited by 363 · see citing works

Two-Year Combination Antibiotic Therapy With Clarithromycin, Rifabutin, and Clofazimine for Crohn’s Disease

Selby, W. S., Pavli, P., Crotty, B. J., Florin, T., Radford‐Smith, G. L., Gibson, P. G., Mitchell, B., Connell, W., Read, R. B., Merrett, M. N., et al. (2007) · Gastroenterology · doi:10.1053/j.gastro.2007.03.031 · Cited by 360 · see citing works

Lactobacillus GG in inducing and maintaining remission of Crohn's disease

Schultz, M., Timmer, A., Herfarth, H. H., Sartor, R. B., Vanderhoof, J. A., & Rath, H. C. (2004) · BMC Gastroenterology · doi:10.1186/1471-230x-4-5 · Cited by 349 · see citing works

Review article: the natural history of postoperative C rohn's disease recurrence

Buisson, A., Chevaux, J., Allen, P. B., Bommelaer, G., & Peyrin‐Biroulet, L. (2012) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2012.05002.x · Cited by 343 · see citing works

Surgery in a Population-Based Cohort of Crohn's Disease From Olmsted County, Minnesota (1970–2004)

Peyrin‐Biroulet, L., Harmsen, S. W., Tremaine, W. J., Zinsmeister, A. R., Sandborn, W. J., & Loftus, E. V. (2012) · The American Journal of Gastroenterology · doi:10.1038/ajg.2012.298 · Cited by 314 · see citing works

Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States

Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053838 · Cited by 314 · see citing works

An Evidence-Based Systematic Review on Medical Therapies for Inflammatory Bowel Disease

Talley, N. J., Abreu, M. T., Achkar, J., Bernstein, C. N., Dubinsky, M. C., Hanauer, S. B., Kane, S. V., Sandborn, W. J., Ullman, T. A., & Moayyedi, P. (2011) · The American Journal of Gastroenterology · doi:10.1038/ajg.2011.58 · Cited by 312 · see citing works

Therapy of Metronidazole With Azathioprine to Prevent Postoperative Recurrence of Crohn's Disease: A Controlled Randomized Trial

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Multicenter randomized-controlled clinical trial of probiotics (Lactobacillus johnsonii, LA1) on early endoscopic recurrence of Crohnʼs disease after ileo-caecal resection

Gossum, A. V., Dewit, O., Louis, E. J., Hertogh, G., Baert, F., Fontaine, F., Devos, M., Enslen, M., Paintin, M., & Franchimont, D. P. (2006) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20063 · Cited by 296 · see citing works

Randomised clinical trial: the effectiveness of Lactobacillus reuteri ATCC 55730 rectal enema in children with active distal ulcerative colitis

Oliva, S., Nardo, G. D., Ferrari, F., Mallardo, S., Rossi, P., Patrizi, G., Cucchiara, S., & Stronati, L. (2011) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2011.04939.x · Cited by 280 · see citing works

Ciprofloxacin or metronidazole for the treatment of perianal fistulas in patients with Crohnʼs disease: A randomized, double-blind, placebo-controlled pilot study

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Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease

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Association Between the Use of Antibiotics and New Diagnoses of Crohn's Disease and Ulcerative Colitis

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Microbial ecology and host-microbiota interactions during early life stages

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Clinical and endosonographic effect of ciprofloxacin on the treatment of perianal fistulae in Crohn's disease with infliximab: a double‐blind placebo‐controlled study

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A Controlled Trial Comparing Ciprofloxacin With Mesalazine for The Treatment of Active Crohn's Disease

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The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

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Treatment and prevention of pouchitis after ileal pouch-anal anastomosis for chronic ulcerative colitis

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Low-dose balsalazide plus a high-potency probiotic preparation is more effective than balsalazide alone or mesalazine in the treatment of acute mild-to-moderate ulcerative colitis.

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Long-term treatment of ulcerative colitis with ciprofloxacin: A prospective, double-blind, placebo-controlled study

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Antibiotics and azathioprine for the treatment of perianal fistulas in Crohn's disease

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Combined budesonide and antibiotic therapy for active Crohn's disease: A randomized controlled trial

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Clinical trial: probiotic treatment of acute distal ulcerative colitis with rectally administered Escherichia coli Nissle 1917 (EcN)

Matthes, H., Krummenerl, T., Giensch, M., Wolff, C., & Schulze, J. (2010) · BMC Complementary and Alternative Medicine · doi:10.1186/1472-6882-10-13 · Cited by 207 · see citing works

Association of Repeated Exposure to Antibiotics With the Development of Pediatric Crohn's Disease--A Nationwide, Register-based Finnish Case-Control Study

Virta, L. J., Auvinen, A. P., Helenius, H. Y. M., Huovinen, P., & Kolho, K.-L. (2012) · American Journal of Epidemiology · doi:10.1093/aje/kwr400 · Cited by 197 · see citing works

Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species

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Preliminary Study of Ciprofloxacin in Active Crohn's Disease

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Collateral effects of antibiotics on mammalian gut microbiomes

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High dose probiotic and prebiotic cotherapy for remission induction of active Crohn’s disease

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Rifaximin-Extended Intestinal Release Induces Remission in Patients With Moderately Active Crohn's Disease

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Antibiotic treatment of Crohn's disease: results of a multicentre, double blind, randomized, placebo‐controlled trial with rifaximin

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Development of gut microbiota in infants not exposed to medical interventions

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Letter to the Editor

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Epidemiology and clinical course of Crohn's disease: Results from observational studies

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Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases

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A randomised double-blind placebo-controlled trial with Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis BB-12 for maintenance of remission in ulcerative colitis

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Additional file 7 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697020

Additional file 4 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697011

Additional file 2 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697005

Additional file 5 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697014

Additional file 6 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697017

Additional file 1 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697002

Additional file 3 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

Wu, J., Lv, Y., Hao, P., Zhang, Z., Zheng, Y., Chen, E., & Fan, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26697008

Additional file 8 of Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data

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