Molecular analysis of the intestinal microflora in IBD

Diversity of the Human Intestinal Microbial Flora

Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works

The gut microbiota as an environmental factor that regulates fat storage

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works

Bacterial evolution

Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · see citing works

Microbial diversity in the deep sea and the underexplored “rare biosphere”

Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. B. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,683 · see citing works

Molecular Analysis of Commensal Host-Microbial Relationships in the Intestine

Hooper, L. V., Wong, M. H., Thelin, A., Hansson, L., Falk, P. G., & Gordon, J. I. (2001) · Science · doi:10.1126/science.291.5505.881 · Cited by 2,202 · see citing works

Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology

Muyzer, G., & Smalla, K. (1998) · Antonie van Leeuwenhoek · doi:10.1023/a:1000669317571 · Cited by 2,051 · see citing works

The control and consequences of bacterial fermentation in the human colon

Cummings, J. H., & Macfarlane, G. T. (1991) · Journal of Applied Bacteriology · doi:10.1111/j.1365-2672.1991.tb02739.x · Cited by 1,499 · see citing works

Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut

Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.11.4799-4807.1999 · Cited by 1,490 · see citing works

Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria

Zoetendal, E. G., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3854-3859.1998 · Cited by 1,360 · see citing works

Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells

Stappenbeck, T. S., Hooper, L. V., & Gordon, J. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202604299 · Cited by 1,095 · see citing works

Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes

Franks, A. H., Harmsen, H. J. M., Raangs, G. C., Jansen, G. J., Schut, F., & Welling, G. W. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.9.3336-3345.1998 · Cited by 1,055 · see citing works

Immunity, Inflammation, and Allergy in the Gut

MacDonald, T. T., & Monteleone, G. (2005) · Science · doi:10.1126/science.1106442 · Cited by 1,035 · see citing works

At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies

Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., & Weightman, A. J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.7724-7736.2005 · Cited by 799 · see citing works

Detection of Lactobacillus, Pediococcus, Leuconostoc , and Weissella Species in Human Feces by Using Group-Specific PCR Primers and Denaturing Gradient Gel Electrophoresis

Walter, J., Hertel, C., Tannock, G. W., Lis, C. M., Munro, K., & Hammes, W. P. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.6.2578-2585.2001 · Cited by 782 · see citing works

New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras

Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., & Weightman, A. J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.00556-06 · Cited by 674 · see citing works

Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization

Sghir, A., Gramet, G., Suau, A., Rochet, V., Pochart, P., & Dore, J. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.5.2263-2266.2000 · Cited by 521 · 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

Effects of Dietary Fat Source and Subtherapeutic Levels of Antibiotic on the Bacterial Community in the Ileum of Broiler Chickens at Various Ages

Knarreborg, A., Simon, M. A., Engberg, R. M., Jensen, B. B., & Tannock, G. W. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.12.5918-5924.2002 · Cited by 361 · see citing works

Colonic Microbiota Signatures across Five Northern European Countries

Lay, C., Rigottier‐Gois, L., Holmstrøm, K., Rajilić-Stojanović, M. D., Vaughan, E. E., de Vos, W. M., Collins, M. D., Thiel, R., Namsolleck, P., Blaut, M., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.7.4153-4155.2005 · Cited by 296 · see citing works

The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients

Bibiloni, R., Mangold, M., Madsen, K. L., Fedorak, R. N., & Tannock, G. W. (2006) · Journal of Medical Microbiology · doi:10.1099/jmm.0.46498-0 · Cited by 226 · see citing works

Reduction of Colitis by Prebiotics in HLA-B27 Transgenic Rats Is Associated with Microflora Changes and Immunomodulation

Hoentjen, F., Welling, G. W., Harmsen, H. J. M., Zhang, X., Snart, J., Tannock, G. W., Lien, K. A., Churchill, T. A., Lupicki, M., & Dieleman, L. A. (2005) · Inflammatory Bowel Diseases · doi:10.1097/01.mib.0000183421.02316.d5 · Cited by 218 · see citing works

Identification, Detection, and Enumeration of Human Bifidobacterium Species by PCR Targeting the Transaldolase Gene

Requena, T., Burton, J. P., Matsuki, T., Munro, K., Simon, M. A., Tanaka, R., Watanabe, K., & Tannock, G. W. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.5.2420-2427.2002 · Cited by 188 · see citing works

Supplementation of the Diet with High-Viscosity Beta-Glucan Results in Enrichment for Lactobacilli in the Rat Cecum

Snart, J., Bibiloni, R., Grayson, T., Lay, C., Zhang, H., Allison, G. E., Laverdiere, J. K., Temelli, F., Vasanthan, T., Bell, R. C., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.3.1925-1931.2006 · Cited by 174 · see citing works

Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota

Lay, C., Sutren, M., Rochet, V., Saunier, K., Dore, J. M., & Rigottier‐Gois, L. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00763.x · Cited by 166 · see citing works

Impact of Consumption of Oligosaccharide-Containing Biscuits on the Fecal Microbiota of Humans

Tannock, G. W., Munro, K., Bibiloni, R., Simon, M. A., Hargreaves, P., Gopal, P. K., Harmsen, H. J. M., & Welling, G. W. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.4.2129-2136.2004 · Cited by 144 · see citing works

Detection and Identification of Lactobacillus Species in Crops of Broilers of Different Ages by Using PCR-Denaturing Gradient Gel Electrophoresis and Amplified Ribosomal DNA Restriction Analysis

Guan, L. L., Hagen, K. E., Tannock, G. W., Korver, D. R., Fasenko, G. M., & Allison, G. E. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.11.6750-6757.2003 · Cited by 127 · see citing works

Effects of Feeding a Probiotic Preparation (SIM) Containing Inulin on the Severity of Colitis and on the Composition of the Intestinal Microflora in HLA-B27 Transgenic Rats

Schultz, M., Munro, K., Tannock, G. W., Melchner, I., Göttl, C., Schwietz, H., Schölmerich, J., & Rath, H. C. (2004) · Clinical and Vaccine Immunology · doi:10.1128/cdli.11.3.581-587.2004 · Cited by 83 · see citing works

Analysis of the large bowel microbiota of colitic mice using PCR/DGGE

Bibiloni, R., Simon, M. A., Albright, C. A., Sartor, B. R., & Tannock, G. W. (2005) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.2005.01720.x · Cited by 61 · see citing works

Bifidobacterium animalis causes extensive duodenitis and mild colonic inflammation in monoassociated interleukin-10-deficient mice

Moran, J. P., Walter, J., Tannock, G. W., Tonkonogy, S. L., & Sartor, R. B. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20900 · Cited by 53 · see citing works

Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent?

Bibiloni, R., Tandon, P., Vargas-Voracka, F., Barreto‐Zúñiga, R., Lupian-Sanchez, A., Rico-Hinojosa, M. Á., Guban, J., Fedorak, R. N., & Tannock, G. W. (2007) · Journal of Medical Microbiology · doi:10.1099/jmm.0.47321-0 · Cited by 24 · see citing works

The COX-2 Story: Is Any Drug Completely “Safe?”

DuBois, R. N. (2006) · Gastroenterology · doi:10.1053/j.gastro.2005.11.045 · Cited by 8 · see citing works

Probiotics and the gut microbiota in intestinal health and disease

Gareau, M. G., Sherman, P. M., & Walker, W. A. (2010) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2010.117 · Cited by 907 · see citing works

Microbial Ecology along the Gastrointestinal Tract

Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017) · Microbes and Environments · doi:10.1264/jsme2.me17017 · Cited by 586 · see citing works

Microbial Translocation Across the GI Tract

Brenchley, J. M., & Douek, D. C. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-075001 · Cited by 496 · see citing works

Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis

Bajer, L., Kverka, M., Kostovčík, M., Mačinga, P., Dvořák, J., Stehlíková, Z., Březina, J., Wohl, P., Špičák, J., & Drastich, P. (2017) · World Journal of Gastroenterology · doi:10.3748/wjg.v23.i25.4548 · Cited by 360 · see citing works

Impact of intestinal microbiota on intestinal luminal metabolome

Matsumoto, M., Kibe, R., Ooga, T., Aiba, Y., Kurihara, S., Sawaki, E., Koga, Y., & Benno, Y. (2012) · Scientific Reports · doi:10.1038/srep00233 · Cited by 334 · see citing works

Mucosal bacterial microflora and mucus layer thickness inadolescents with inflammatory bowel disease

Fyderek, K., Strus, M., Kowalska‐Duplaga, K., Gosiewski, T., Wędrychowicz, A., Jedynak‐Wąsowicz, U., Sładek, M., Pieczarkowski, S., Adamski, P., Kochan, P., et al. (2009) · World Journal of Gastroenterology · doi:10.3748/wjg.15.5287 · Cited by 149 · see citing works

The struggle within: Microbial influences on colorectal cancer

Arthur, J. C., & Jobin, C. (2010) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21354 · Cited by 121 · see citing works

Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study

Matsumoto, M., Ooga, T., Kibe, R., Aiba, Y., Koga, Y., & Benno, Y. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169207 · Cited by 80 · see citing works

Mucosal immunity in human and simian immunodeficiency lentivirus infections

Brenchley, J. M. (2013) · Mucosal Immunology · doi:10.1038/mi.2013.15 · Cited by 70 · see citing works

Relationship between intestinal microbiota and colorectal cancer

Çıpe, G., İdiz, U. O., Fırat, Y. D., & Bektaşoğlu, H. K. (2015) · World Journal of Gastrointestinal Oncology · doi:10.4251/wjgo.v7.i10.233 · Cited by 60 · see citing works

A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice

Shi, Y., Zhao, X., Zhao, J., Zhang, H., Zhai, Q., Narbad, A., & Chen, W. (2018) · Journal of Applied Microbiology · doi:10.1111/jam.13687 · Cited by 61 · see citing works

Regulation of the Polymeric Immunoglobulin Receptor in Intestinal Epithelial Cells byEnterobacteriaceae: Implications for Mucosal Homeostasis

Bruno, M. E. C., Rogier, E. W., Frantz, A. L., Stefka, A. T., Thompson, S. N., & Kaetzel, C. S. (2010) · Immunological Investigations · doi:10.3109/08820131003622809 · Cited by 57 · see citing works

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis

Du, Z., Hudcovic, T., Mrázek, J., Kozáková, H., Šrůtková, D., Schwarzer, M., Tlaskalová‐Hogenová, H., Kostovčík, M., & Kverka, M. (2015) · Gut Pathogens · doi:10.1186/s13099-015-0080-2 · Cited by 54 · see citing works

Gut Barrier Damage and Gut Translocation of Pathogen Molecules in Lupus, an Impact of Innate Immunity (Macrophages and Neutrophils) in Autoimmune Disease

Charoensappakit, A., Sae‐khow, K., & Leelahavanichkul, A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23158223 · Cited by 50 · see citing works

The Bowel Microbiota and Inflammatory Bowel Diseases

Tannock, G. W. (2010) · International Journal of Inflammation · doi:10.4061/2010/954051 · Cited by 49 · see citing works

Evaluation of the detection of Toll-like receptors (TLRs) in cancer development and progression in patients with colorectal cancer

Messaritakis, I., Stogiannitsi, M., Koulouridi, A., Sfakianaki, M., Voutsina, A., Sotiriou, A., Athanasakis, E., Xynos, E., Mavroudis, D., Tzardi, M. N., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0197327 · Cited by 48 · see citing works

Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response

Coufal, Š., Galanová, N., Bajer, L., Gajdárová, Z., Schierová, D., Zakostelska, Z. J., Kostovcikova, K., Jackova, Z., Stehlíková, Z., Drastich, P., et al. (2019) · Cells · doi:10.3390/cells8070719 · Cited by 47 · see citing works

Polymicrobial challenges to Koch’s postulates: Ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes

Nelson, A., Soyza, A. D., Perry, J. D., Sutcliffe, I. C., & Cummings, S. P. (2012) · Innate Immunity · doi:10.1177/1753425912439910 · Cited by 47 · see citing works

Application of a single‐colony coculture technique to the isolation of hitherto unculturable gut bacteria

Tanaka, Y., & Benno, Y. (2014) · Microbiology and Immunology · doi:10.1111/1348-0421.12220 · Cited by 40 · see citing works

L. pseudomesenteroides and L. johnsonii isolated from yaks in Tibet modulate gut microbiota in mice to ameliorate enteroinvasive Escherichia coli-induced diarrhea

Wang, Y., Li, J., Liu, J., Mehmood, K., Wangdui, B., Shi, H., Luo, X., Zhang, H., & Li, J. (2019) · Microbial Pathogenesis · doi:10.1016/j.micpath.2019.04.020 · Cited by 33 · see citing works

Two faces of microbiota in inflammatory and autoimmune diseases: triggers and drugs

Kverka, M., & Tlaskalová‐Hogenová, H. (2012) · Apmis · doi:10.1111/apm.12007 · Cited by 30 · see citing works

Intestinal bacteria detected in cancer and adjacent tissue from patients with colorectal cancer

Liu, C., Yuan-Lian, Z., Shang, Y., Wu, B., Yang, E., Luo, Y., & Li, X. (2018) · Oncology Letters · doi:10.3892/ol.2018.9714 · Cited by 30 · see citing works

Emerging drugs for the treatment of ulcerative colitis

Pastorelli, L., Pizarro, T. T., Cominelli, F., & Vecchi, M. L. (2009) · Expert Opinion on Emerging Drugs · doi:10.1517/14728210903146882 · Cited by 26 · see citing works

Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis

Mohamed, S. S., Abdeltawab, N. F., Wadie, W., Ahmed, L. A., Ammar, R. M., Rabini, S., Abdel-Aziz, H., & Khayyal, M. T. (2021) · BMC Complementary Medicine and Therapies · doi:10.1186/s12906-021-03337-8 · Cited by 20 · see citing works

Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes

Matsumoto, W., Takemura, M., Nanaura, H., Ami, Y., Maoka, T., Shindo, K., Kurihara, S., & Misawa, N. (2024) · Engineering Microbiology · doi:10.1016/j.engmic.2024.100147 · Cited by 8 · see citing works

Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota

Shimizu, H., & Benno, Y. (2015) · Microbiology and Immunology · doi:10.1111/1348-0421.12332 · Cited by 7 · see citing works

Isoxanthohumol, a hop-derived flavonoid, alters the metabolomics profile of mouse feces

FUKIZAWA, S., YAMASHITA, M., Fujisaka, S., Tobe, K., Nonaka, Y., & Murayama, N. (2020) · Bioscience of Microbiota Food and Health · doi:10.12938/bmfh.2019-045 · Cited by 7 · see citing works

Probiotics, with special emphasis on their role in the management of irritable bowel syndrome

Stevenson, C., & Blaauw, R. (2011) · South African Journal of Clinical Nutrition · doi:10.1080/16070658.2011.11734353 · Cited by 5 · see citing works

Effect of Dahuang Danpi Decoction on Lactobacillus bulgaricus growth and metabolism

Li, C., Zhang, J., Xu, H. X., Chen, Y., Gao, S., Guo, S.-N., Huang, B., Gao, R., Long, Z., & Jiang, M. (2019) · Medicine · doi:10.1097/md.0000000000013941 · Cited by 4 · see citing works

Intestinal Inflammation and Cancer of the Gastrointestinal Tract

Neurath, M. F., Fichtner‐Feigl, S., & Kesselring, R. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-415847-4.00091-4 · Cited by 2 · see citing works

Probiotics, with special emphasis on their role in the management of irritable bowel syndrome

Stevenson, C., & Blaauw, R. (2012) · Pharmacy management

Additional file 1 of Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis

Mohamed, S. S., Abdeltawab, N. F., Wadie, W., Ahmed, L. A., Ammar, R. M., Rabini, S., Abdel-Aziz, H., & Khayyal, M. T. (2021) · Figshare · doi:10.6084/m9.figshare.14752070

L'initiation précoce du traitement antirétroviral conserve la fonction immunitaire dans l'intestin de patients infectés par le VIH

Kök, A. (2014) · theses.fr (ABES) · doi:10.70675/3fffcbc1ze90bz448dz80b2z11e3e0cb54c7

Functional Impacts of the Intestinal Microbiome in the Pathogenesis of Inflammatory Bowel Disease

Li, J. S. Y., Butcher, J., Mack, D. R., & Stintzi, A. (2014) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000215 · Cited by 150 · see citing works

Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease

Bekkers, M., Stojkovic, B., & Kaiko, G. E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222011243 · Cited by 14 · see citing works

Microbes in the Pathogenesis of Inflammatory Bowel Disease: A Review

Jatwani, S., Malhotra, B. K., Crout, T. M., & Majithia, V. (2019) · Springer eBooks · doi:10.1007/978-3-030-23311-2_37

Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments

Tamburini, S., & Clemente, J. C. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.07.001 · Cited by 5 · see citing works

Gardening Effect of Host Genetics on Human Intestinal Mucosal Microbiome and Its Link to Inflammatory Bowel Disease

Tong, M. (2014) · eScholarship (California Digital Library)