BPG is committed to discovery and dissemination of knowledge
Cited by in CrossRef
For: Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol 2014; 5(3): 213-227 [PMID: 25133024 DOI: 10.4291/wjgp.v5.i3.213]
URL: https://www.wjgnet.com/2150-5330/full/v5/i3/213.htm
Number Citing Articles
1
Magdalena Pilarczyk-Zurek, Magdalena Strus, Pawel Adamski, Piotr B. Heczko. The dual role of Escherichia coli in the course of ulcerative colitis. BMC Gastroenterology 2016; 16(1) doi: 10.1186/s12876-016-0540-2
2
Jean-Félix Sicard, Philippe Vogeleer, Guillaume Le Bihan, Yaindrys Rodriguez Olivera, Francis Beaudry, Mario Jacques, Josée Harel. N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli. Gut Pathogens 2018; 10(1) doi: 10.1186/s13099-018-0252-y
3
Geeta Kulkarni, Bo Shen. Atlas of Endoscopy Imaging in Inflammatory Bowel Disease. 2026;  doi: 10.1016/B978-0-443-29172-2.00002-8
4
Qi Zhang, Xueqing Duan, Rui Chen, Zhixuan Duan, Chen Zhu, Qi Yu, Weiyi Tian. Effects of Cortex meliae on the Intestinal Flora in Rats. Journal of Biobased Materials and Bioenergy 2023; 17(6) doi: 10.1166/jbmb.2023.2323
5
Laurel K. Mydock-McGrane, Zachary T. Cusumano, James W. Janetka. Mannose-derived FimH antagonists: a promising anti-virulence therapeutic strategy for urinary tract infections and Crohn’s disease. Expert Opinion on Therapeutic Patents 2016; 26(2) doi: 10.1517/13543776.2016.1131266
6
Alejandro Cabezas-Cruz, Luis G. Bermúdez-Humarán. Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications . Computational and Structural Biotechnology Journal 2024; 23 doi: 10.1016/j.csbj.2023.11.027
7
Ram Hari Dahal, Yoon-Jung Choi, Shukho Kim, Jungmin Kim. Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns. Antibiotics 2023; 12(1) doi: 10.3390/antibiotics12010154
8
Olga V. Pobeguts, Maria A. Galyamina, Elena V. Mikhalchik, Sergey I. Kovalchuk, Igor P. Smirnov, Alena V. Lee, Lyubov Yu. Filatova, Kirill V. Sikamov, Oleg M. Panasenko, Alexey Yu. Gorbachev. The Role of Propionate-Induced Rearrangement of Membrane Proteins in the Formation of the Virulent Phenotype of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli. International Journal of Molecular Sciences 2024; 25(18) doi: 10.3390/ijms251810118
9
Luis Cabrera-Sosa, Theresa J. Ochoa. Hunter's Tropical Medicine and Emerging Infectious Diseases. 2020;  doi: 10.1016/B978-0-323-55512-8.00046-6
10
Claudia F. Martinez de la Peña, Glen D. Armstrong, Margarita M. P. Arenas-Hernández, Roberto J. Cieza. Escherichia coli in the Americas. 2016;  doi: 10.1007/978-3-319-45092-6_12
11
Grégoire Chevalier, Arnaud Laveissière, Guillaume Desachy, Nicolas Barnich, Adeline Sivignon, Marc Maresca, Cendrine Nicoletti, Eric Di Pasquale, Margarita Martinez-Medina, Kenneth William Simpson, Vijay Yajnik, Harry Sokol, Temitayo Adegbamigbe, Tariq Ahmad, Ian Arnott, Yoram Bouhnik, Franck Carbonnel, Jean-Frédéric Colombel, Glen Doherty, J. R. Fraser Cummings, Xavier Hébuterne, Hans Herfarth, David Kevans, Guillaume Pineton de Chambrun, Maria Nachury, Stéphane Nancey, Xavier Roblin, Mark A. W. Tremelling, Jonathan Plassais, Francesco Strozzi, Alessandra Cervino, Rachel Morra, Christophe Bonny. Blockage of bacterial FimH prevents mucosal inflammation associated with Crohn’s disease. Microbiome 2021; 9(1) doi: 10.1186/s40168-021-01135-5
12
Cherrie L. Small, Lydia Xing, Joseph B. McPhee, Hong T. Law, Brian K. Coombes, Andreas J Baumler. Acute Infectious Gastroenteritis Potentiates a Crohn's Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period. PLOS Pathogens 2016; 12(10) doi: 10.1371/journal.ppat.1005907
13
Yun Ji, Xiaoxiao Fan, Yunchang Zhang, Ju Li, Zhaolai Dai, Zhenlong Wu. Glycine regulates mucosal immunity and the intestinal microbial composition in weaned piglets. Amino Acids 2022; 54(3) doi: 10.1007/s00726-021-02976-y
14
Aarti Yadav, S. Hamsa, Ruby Tiwari, Asha Bharti, Tejpal Dhewa, Rekha Mehrotra, Preeti Verma. Nutritional Science and Technology. 2023;  doi: 10.1002/9781394229116.ch3
15
Shahanavaj Khan. Potential role of Escherichia coli DNA mismatch repair proteins in colon cancer. Critical Reviews in Oncology/Hematology 2015; 96(3) doi: 10.1016/j.critrevonc.2015.05.002
16
Qiwen Xie, Huan Xu, Xiaoming Yang, Ying Chen, Zhenjiang Zech Xu. Natural carrier-free self-assembled binary polyphenol nanoparticles remodel the gut microenvironment for inflammatory bowel disease prevention. Materials Today Bio 2026; 38 doi: 10.1016/j.mtbio.2026.103063
17
Youlian Zhou, Yan He, Le Liu, Wanyan Zhou, Pu Wang, Han Hu, Yuqiang Nie, Ye Chen. Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases. Frontiers in Nutrition 2021; 8 doi: 10.3389/fnut.2021.615064
18
Yongjia Gong, Guojun Wu, Stephanie Tavarez, Cuiping Zhao, Liping Zhao, Shreya Ghosh, Katrine Whiteson. Dietary fiber fermentation restores microbiome resilience to oxygen stress in a host-independent ex vivo model . mBio 2026; 17(4) doi: 10.1128/mbio.03934-25
19
R. B. Gorodnichev, D. V. Rakitina, A. I. Manolov, Yu. P. Baykova, P. L. Scherbakov, G. B. Smirnov, E. N. Ilina. FEATURES OF ESCHERICHIA COLI CLINICAL STRAINS, ISOLATED FROM THE PATIENTS WITH CROHN’S DISEASE. Journal of microbiology, epidemiology and immunobiology 2017; 94(6) doi: 10.36233/0372-9311-2017-6-42-49
20
Methods for Monitoring Mitochondrial Functions During Pathogen Infection. Methods in Cell Biology 2025; 194 doi: 10.1016/bs.mcb.2024.08.011
21
Johanne Ahrenfeldt, Madina Waisi, Isabella C. Loft, Philip T. L. C. Clausen, Rosa Allesøe, Judit Szarvas, Rene S. Hendriksen, Frank M. Aarestrup, Ole Lund. Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering. Scientific Reports 2020; 10(1) doi: 10.1038/s41598-020-59292-w
22
Razie Kamali Dolatabadi, Hossein Fazeli, Mohammad Hassan Emami, Vajihe Karbasizade, Fatemeh Maghool, Alireza Fahim, Hojatollah Rahimi. Phenotypicand Genotypic Characterization of Clinical Isolates of Intracellular Adherent–Invasive Escherichia coli Among Different Stages, Family History, and Treated Colorectal Cancer Patients in Iran. Frontiers in Cellular and Infection Microbiology 2022; 12 doi: 10.3389/fcimb.2022.938477
23
Mostafa Vaghari-Tabari, Forough Alemi, Maryam Zokaei, Soheila Moein, Durdi Qujeq, Bahman Yousefi, Payam Farzami, Seyed Soheil Hosseininasab. Polyphenols and inflammatory bowel disease: Natural products with therapeutic effects?. Critical Reviews in Food Science and Nutrition 2024; 64(13) doi: 10.1080/10408398.2022.2139222
24
Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ramón Gómez-Moreno, Juan M. Cruz, Dayanara M. Velázquez-Morales, Igor B. Rogozin, Abel Baerga-Ortiz. The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. Frontiers in Genetics 2018; 9 doi: 10.3389/fgene.2018.00116
25
Lucie Gibold, Estelle Garenaux, Guillaume Dalmasso, Camille Gallucci, David Cia, Benoit Mottet-Auselo, Tiphanie Faïs, Arlette Darfeuille-Michaud, Hang Thi Thu Nguyen, Nicolas Barnich, Richard Bonnet, Julien Delmas. The Vat-AIEC protease promotes crossing of the intestinal mucus layer by Crohn's disease-associatedEscherichia coli. Cellular Microbiology 2016; 18(5) doi: 10.1111/cmi.12539
26
Asuka Yasueda, Tsunekazu Mizushima, Riichiro Nezu, Ryoko Sumi, Mamoru Tanaka, Junichi Nishimura, Yasuyuki Kai, Masaki Hirota, Hideki Osawa, Kiyokazu Nakajima, Masaki Mori, Toshinori Ito. The effect of Clostridium butyricum MIYAIRI on the prevention of pouchitis and alteration of the microbiota profile in patients with ulcerative colitis. Surgery Today 2016; 46(8) doi: 10.1007/s00595-015-1261-9
27
Nour Eissa, Hatem Kittana, João Carlos Gomes-Neto, Hayam Hussein. Mucosal immunity and gut microbiota in dogs with chronic enteropathy. Research in Veterinary Science 2019; 122 doi: 10.1016/j.rvsc.2018.11.019
28
Michael J. Ormsby, Michael Logan, Síle A. Johnson, Anne McIntosh, Ghaith Fallata, Rodanthi Papadopoulou, Eleftheria Papachristou, Georgina L. Hold, Richard Hansen, Umer Z. Ijaz, Richard K. Russell, Konstantinos Gerasimidis, Daniel M. Wall. Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli. EBioMedicine 2019; 43 doi: 10.1016/j.ebiom.2019.03.071
29
J. Vila, E. Sáez-López, J. R. Johnson, U. Römling, U. Dobrindt, R. Cantón, C. G. Giske, T. Naas, A. Carattoli, M. Martínez-Medina, J. Bosch, P. Retamar, J. Rodríguez-Baño, F. Baquero, S. M. Soto, Kenn Gerdes. Escherichia coli: an old friend with new tidings. FEMS Microbiology Reviews 2016; 40(4) doi: 10.1093/femsre/fuw005
30
Carolina Palmela, Caroline Chevarin, Zhilu Xu, Joana Torres, Gwladys Sevrin, Robert Hirten, Nicolas Barnich, Siew C Ng, Jean-Frederic Colombel. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 2018; 67(3) doi: 10.1136/gutjnl-2017-314903
31
Ronald D. Hills Jr., Benjamin A. Pontefract, Hillary R. Mishcon, Cody A. Black, Steven C. Sutton, Cory R. Theberge. Gut Microbiome: Profound Implications for Diet and Disease. Kompass Nutrition & Dietetics 2022;  doi: 10.1159/000523712
32
Indah Salsabila, Khairan Khairan, Pati Kemala, Ghifari Maulana Idroes, Nadia Isnaini, Nur Balqis Maulydia, Mohamed El-Shazly, Rinaldi Idroes. Hybrid Handwash with Silver Nanoparticles from Calotropis gigantea Leaves and Patchouli Oil: Development and Properties. Malacca Pharmaceutics 2024; 2(2) doi: 10.60084/mp.v2i2.206
33
Jody Andersen, Gui-Xin He, Prathusha Kakarla, Ranjana KC, Sanath Kumar, Wazir Lakra, Mun Mukherjee, Indrika Ranaweera, Ugina Shrestha, Thuy Tran, Manuel Varela. Multidrug Efflux Pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus Bacterial Food Pathogens. International Journal of Environmental Research and Public Health 2015; 12(2) doi: 10.3390/ijerph120201487
34
Husamettin Aygun, Murat Karamese, Cem Ozic, Fikret Uyar. The Effects of Mucosal Media on some Pathogenic Traits of Crohn's Disease-Associated Escherichia Coli LF82 . Future Microbiology 2018; 13(2) doi: 10.2217/fmb-2017-0133
35
Ervine Chastine Marind, Fiona McCullough. Gut Health Responses to Nutritional Interventions in Paediatric Crohn’s Disease, Including the Potential Outcomes of Mucosal Barrier Preservation: A Systematic Review. Nutrients 2026; 18(7) doi: 10.3390/nu18071146
36
Mireia López-Siles, Carla Camprubí-Font, Eva M. Gómez del Pulgar, Miriam Sabat Mir, David Busquets, Yolanda Sanz, Margarita Martinez-Medina. Prevalence, Abundance, and Virulence of Adherent-Invasive Escherichia coli in Ulcerative Colitis, Colorectal Cancer, and Coeliac Disease. Frontiers in Immunology 2022; 13 doi: 10.3389/fimmu.2022.748839
37
Qi Zhao, Miaoli Shao, Lisha Ma, Renfang Zhou. Insights into Modeling Inflammatory Bowel Disease from Stem Cell Derived Intestinal Organoids. Stem Cell Reviews and Reports 2025; 21(5) doi: 10.1007/s12015-025-10887-8
38
Theresa J. Ochoa, Alejandro Llanos-Chea. Feigin and Cherry's Textbook of Pediatric Infectious Diseases. 2025;  doi: 10.1016/B978-0-323-82763-8.00046-7
39
Michael A. Polewski, Daniel Esquivel-Alvarado, Nicholas S. Wedde, Christian G. Kruger, Jess D. Reed. Isolation and Characterization of Blueberry Polyphenolic Components and Their Effects on Gut Barrier Dysfunction. Journal of Agricultural and Food Chemistry 2020; 68(10) doi: 10.1021/acs.jafc.9b01689
40
Zeus Saldaña-Ahuactzi, Jorge Soria-Bustos, Verónica I. Martínez-Santos, Jorge A. Yañez-Santos, Ygnacio Martínez-Laguna, María Lilia Cedillo-Ramirez, José L. Puente, Jorge A. Girón. The Fis Nucleoid Protein Negatively Regulates the Phase Variation fimS Switch of the Type 1 Pilus Operon in Enteropathogenic Escherichia coli. Frontiers in Microbiology 2022; 13 doi: 10.3389/fmicb.2022.882563
41
Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Qiyun Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon Sanders, Paul L. Beck, Weizhong Li, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Emma Allen-Vercoe, Bernhard O. Palsson, Larry Smarr. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology 2018; 9 doi: 10.3389/fmicb.2018.02559
42
Lacey R. Lopez, Cassandra J. Barlogio, Christopher A. Broberg, Jeremy Wang, Janelle C. Arthur. A nadA Mutation Confers Nicotinic Acid Auxotrophy in Pro-carcinogenic Intestinal Escherichia coli NC101. Frontiers in Microbiology 2021; 12 doi: 10.3389/fmicb.2021.670005
43
Maitham Abbas Khajah. The potential role of fecal microbiota transplantation in the treatment of inflammatory Bowel disease. Scandinavian Journal of Gastroenterology 2017; 52(11) doi: 10.1080/00365521.2017.1347812
44
Souhir Badi, Rim Werheni Ammeri, Mohamed Salah Abbassi, Mejdi Snousssi, Paola Cremosini, Mario Luini, Bianca Castiglioni, Abdennaceur Hassen. Study of the diversity of 16S–23S rDNA internal transcribed spacer (ITS) typing of Escherichia coli strains isolated from various biotopes in Tunisia. Archives of Microbiology 2022; 204(1) doi: 10.1007/s00203-021-02684-x
45
Qianjin Lu, Yue Xin. The Rose and Mackay Textbook of Autoimmune Diseases. 2024;  doi: 10.1016/B978-0-443-23947-2.00008-4
46
A. Butera, M. Di Paola, L. Pavarini, F. Strati, M. Pindo, M. Sanchez, D. Cavalieri, M. Boirivant, C. De Filippo. Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells. Scientific Reports 2018; 8(1) doi: 10.1038/s41598-018-32583-z
47
Charles O Elson. Adherent invasive Escherichia coli in Crohn’s disease: guilt by association?. Gut 2023; 72(1) doi: 10.1136/gutjnl-2022-327342
48
Mariam Moshkovskaya, Tatyana Vakhrusheva, Daria Rakitina, Julia Baykova, Oleg Panasenko, Lilia Basyreva, Sergey Gusev, Alexander Gusev, Elena Mikhalchik, Natalia Smolina, Gennadiy Dobretsov, Petr Scherbakov, Asfold Parfenov, Nina Fadeeva, Olga Pobeguts, Vadim Govorun. Neutrophil activation by Escherichia coli isolates from human intestine: effects of bacterial hydroperoxidase activity and surface hydrophobicity. FEBS Open Bio 2020; 10(3) doi: 10.1002/2211-5463.12796
49
Yongshun Ma, Yao Zhang, Houxiang Jiang, Shixin Xiang, Yueshui Zhao, Mintao Xiao, Fukuan Du, Huijiao Ji, Parham Jabbarzadeh Kaboli, Xu Wu, Mingxing Li, Qinglian Wen, Jing Shen, Zhongming Yang, Jing Li, Zhangang Xiao. Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer. Frontiers in Cellular and Infection Microbiology 2021; 11 doi: 10.3389/fcimb.2021.599734
50
Filippo Vaccari, Leilei Zhang, Gianluca Giuberti, Alfina Grasso, Francesca Bandini, Pascual García-Pérez, Chiara Copat, Luigi Lucini, Margherita Dall’Asta, Margherita Ferrante, Edoardo Puglisi. The impact of metallic nanoparticles on gut fermentation processes: An integrated metabolomics and metagenomics approach following an in vitro digestion and fecal fermentation model. Journal of Hazardous Materials 2023; 453 doi: 10.1016/j.jhazmat.2023.131331
51
Bahareh Vakili, Parisa Shoaei, Zahra Esfandiari, Seyed Davar Siadat. Effect of Microbiota on Health and Disease. 2022;  doi: 10.5772/intechopen.105842
52
Tomas Hudcovic, Petra Petr Hermanova, Hana Kozakova, Oldrich Benada, Olga Kofronova, Martin Schwarzer, Dagmar Srutkova. Priority order of neonatal colonization by a probiotic or pathogenic Escherichia coli strain dictates the host response to experimental colitis. Frontiers in Microbiology 2024; 15 doi: 10.3389/fmicb.2024.1393732
53
Suprabhat Mukherjee, Nikhilesh Joardar, Subhasree Sengupta, Santi P. Sinha Babu. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. The Journal of Nutritional Biochemistry 2018; 61 doi: 10.1016/j.jnutbio.2018.07.010
54
Xiao-Pei Peng, Wei Ding, Jian-Min Ma, Jie Zhang, Jian Sun, Yun Cao, Li-Hui Lei, Jinshan Zhao, Yun-Fu Li. Effect of Escherichia Coli Infection on Metabolism of Dietary Protein in Intestine. Current Protein & Peptide Science 2020; 21(8) doi: 10.2174/1389203720666191113144049
55
Mireia Lopez-Siles, Xavier Aldeguer, Miriam Sabat-Mir, Mariona Serra-Pagès, Sylvia H Duncan, Harry J Flint, L Jesús Garcia-Gil, Margarita Martinez-Medina. Evaluation of bacterial biomarkers to aid in challenging inflammatory bowel diseases diagnostics and subtype classification. World Journal of Gastrointestinal Pathophysiology 2020; 11(3): 64-77 doi: 10.4291/wjgp.v11.i3.64
56
A. V. Zhestkov, Yu. A. Khalitova, Yu. V. Myakisheva. The role of the microbiota of the gastrointestinal tract in the pathogenesis of inflammatory bowel diseases. Astrakhan medical journal 2023; 18(3) doi: 10.17021/1992-6499-2023-3-33-42
57
Zeshan Hassan, Ammara Hassan, Muhaiman Riaz, Azhar Abbas Khan, Sami Ul-Allah, Umbreen Shehzad, Muhammad Khurshid, Ali Bakhsh, Jawad Munawar Shah, Zahid Manzoor. Increased health risk assessment in different vegetables grown under untreated sewerage irrigation regime due to higher heavy metals accumulation. Environmental Science and Pollution Research 2023; 30(36) doi: 10.1007/s11356-023-28413-z
58
Terence Van Raay, Emma Allen-Vercoe. Bugs as Drugs. 2018;  doi: 10.1128/9781555819705.ch4
59
Nazanin Arjomand Fard, Heather Armstrong, Troy Perry, Eytan Wine. Appendix and Ulcerative Colitis: a Key to Explaining the Pathogenesis and Directing Novel Therapies?. Inflammatory Bowel Diseases 2023; 29(1) doi: 10.1093/ibd/izac106
60
Behnoush Asgari, Georgia Bradford, Eva Hatje, Anna Kuballa, Mohammad Katouli. Limosilactobacillus reuteri M4-100 Mitigates the Pathogenicity of Escherichia coli Strain HMLN-1 in an Intestinal Epithelial Model and Modulates Host Cell Gene Expression. Microorganisms 2025; 13(6) doi: 10.3390/microorganisms13061428
61
Wenyu Zhang, Xianzong Ma, Wenqing Tian, Yongsheng Teng, Meihua Ji. Cellular senescence defining the disease characteristics of Crohn’s disease. Frontiers in Immunology 2025; 16 doi: 10.3389/fimmu.2025.1616531
62
Jessica K. Jarett, Dawn D. Kingsbury, Katherine E. Dahlhausen, Holly H. Ganz. Best Practices for Microbiome Study Design in Companion Animal Research. Frontiers in Veterinary Science 2021; 8 doi: 10.3389/fvets.2021.644836
63
Qianyu Li, Siyu Zhou, Yanna Wang, Jing Cong. Changes of intestinal microbiota and microbiota-based treatments in IBD. Archives of Microbiology 2022; 204(7) doi: 10.1007/s00203-022-03069-4
64
Rodrick J. Chiodini, Scot E. Dowd, William M. Chamberlin, Susan Galandiuk, Brian Davis, Angela Glassing, Hauke Smidt. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum. PLOS ONE 2015; 10(7) doi: 10.1371/journal.pone.0134382
65
Nehal M. El-Deeb, Tamer A.E. Ahmed, Amal D. Premarathna, Vitalijs Rjabovs, Rando Tuvikene, Riadh Hammami, Martine Boulianne, Maxwell T. Hincke. An innovative green approach to optimize the extraction of functional ingredients from Ulva lactuca and Ascophyllum nodosum: Safety studies. Food Hydrocolloids 2026; 170 doi: 10.1016/j.foodhyd.2025.111657
66
Lauren C. Chartier, Gordon S. Howarth, Suzanne Mashtoub. Combined Nutraceuticals: A Novel Approach to Colitis-Associated Colorectal Cancer?. Nutrition and Cancer 2019; 71(2) doi: 10.1080/01635581.2019.1578391
67
Dongyue Li, Youlin Yang, Xunhai Yin, Yang Liu, Hongyu Xu, Yu Ni, Ping Hang, Sijia Niu, Huichao Zhang, Wenbo Ding, Hongyu Kuang. Glucagon-like peptide (GLP) -2 improved colonizing bacteria and reduced severity of ulcerative colitis by enhancing the diversity and abundance of intestinal mucosa. Bioengineered 2021; 12(1) doi: 10.1080/21655979.2021.1958600
68
Zelin Guan, Peilin Niu, Qichao Tan, Yidong Wang, Shujing Deng, Danyang Wang, Kai Dong, Jianfeng Xing, Cuiyu You. Therapeutic systems based on natural gut microbiota modulators: the latest advances in the treatment of inflammatory bowel disease. Materials Advances 2025; 6(5) doi: 10.1039/D4MA00896K
69
70
Ashley Gilliland, Jocelyn J. Chan, Travis J. De Wolfe, Hyungjun Yang, Bruce A. Vallance. Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. Gastroenterology 2024; 166(1) doi: 10.1053/j.gastro.2023.09.019
71
Pauline D. Scanlan, Fernando Baquero, Bruce R. Levin. Short-sighted evolution of virulence for invasive gut microbes: From hypothesis to tests. Proceedings of the National Academy of Sciences 2024; 121(49) doi: 10.1073/pnas.2409905121
72
Jefferson J. Feng, Nikhil R. Maddirala, Ashley Saint Fleur, Fenfen Zhou, Di Yu, Feng Wei, Yongrong Zhang. Gut Microbiome and Immune System Crosstalk in Chronic Inflammatory Diseases: A Narrative Review of Mechanisms and Therapeutic Opportunities. Microorganisms 2025; 13(11) doi: 10.3390/microorganisms13112516
73
Muhammad Ahmed Mushtaq, Peter Schierack, Muhammad Yousaf, Fariha Fatima, Tayyaba Qamar, Mashkoor Mohsin, Muhammad Moman Khan. Integrated poultry production as a reservoir of tet(X4) and mcr-1.1 encoding Escherichia coli in Pakistan .  Microbial Genomics 2026; 12(8) doi: 10.1099/mgen.0.001800
74
Shiying Zhang, Belgin Dogan, Cindy Guo, Deepali Herlekar, Katrina Stewart, Ellen J. Scherl, Kenneth W. Simpson. Short Chain Fatty Acids Modulate the Growth and Virulence of Pathosymbiont Escherichia coli and Host Response. Antibiotics 2020; 9(8) doi: 10.3390/antibiotics9080462
75
Aida Mayorgas, Isabella Dotti, Marta Martínez-Picola, Miriam Esteller, Queralt Bonet-Rossinyol, Elena Ricart, Azucena Salas, Margarita Martínez-Medina. A Novel Strategy to Study the Invasive Capability of Adherent-Invasive Escherichia coli by Using Human Primary Organoid-Derived Epithelial Monolayers. Frontiers in Immunology 2021; 12 doi: 10.3389/fimmu.2021.646906
76
Zhaohua Shen, Changxin Zhu, Yongsheng Quan, Wei Yuan, Shuai Wu, Zhenyu Yang, Weiwei Luo, Bei Tan, Xiaoyan Wang. Update on intestinal microbiota in Crohn's disease 2017: Mechanisms, clinical application, adverse reactions, and outlook. Journal of Gastroenterology and Hepatology 2017; 32(11) doi: 10.1111/jgh.13861
77
Jeffrey B Blumberg, Arpita Basu, Christian G Krueger, Mary Ann Lila, Catherine C Neto, Janet A Novotny, Jess D Reed, Ana Rodriguez-Mateos, Cheryl D Toner. Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015. Advances in Nutrition 2016; 7(4) doi: 10.3945/an.116.012583
78
Jun-Hwan Yoo, Mark Donowitz. Intestinal enteroids/organoids: A novel platform for drug discovery in inflammatory bowel diseases. World Journal of Gastroenterology 2019; 25(30): 4125-4147 doi: 10.3748/wjg.v25.i30.4125
79
Lina Y Alkaissi, Martin E Winberg, Stéphanie D S Heil, Staffan Haapaniemi, Pär Myrelid, Eduard F Stange, Johan D Söderholm, Åsa V Keita. Antagonism of Adherent Invasive E. coli LF82 With Human α-defensin 5 in the Follicle-associated Epithelium of Patients With Ileal Crohn’s Disease. Inflammatory Bowel Diseases 2021; 27(7) doi: 10.1093/ibd/izaa315
80
Jaekoo Lee, Jaehyun Jo, Jungho Wan, Hanseul Seo, Seung-Won Han, Yoon-Jung Shin, Dong-Hyun Kim. In Vitro Evaluation of Probiotic Properties and Anti-Pathogenic Effects of Lactobacillus and Bifidobacterium Strains as Potential Probiotics. Foods 2024; 13(14) doi: 10.3390/foods13142301
81
Ronald Hills, Benjamin Pontefract, Hillary Mishcon, Cody Black, Steven Sutton, Cory Theberge. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients 2019; 11(7) doi: 10.3390/nu11071613
82
Andrew Brantley Hall, Moran Yassour, Jenny Sauk, Ashley Garner, Xiaofang Jiang, Timothy Arthur, Georgia K. Lagoudas, Tommi Vatanen, Nadine Fornelos, Robin Wilson, Madeline Bertha, Melissa Cohen, John Garber, Hamed Khalili, Dirk Gevers, Ashwin N. Ananthakrishnan, Subra Kugathasan, Eric S. Lander, Paul Blainey, Hera Vlamakis, Ramnik J. Xavier, Curtis Huttenhower. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Medicine 2017; 9(1) doi: 10.1186/s13073-017-0490-5
83
Qi Yin, Samriddhi Gupta, Efrat Muller, Alexandre Almeida. The human gut microbiome in enteric infections: from association to translation. Gut Microbes 2026; 18(1) doi: 10.1080/19490976.2026.2612836
84
Kostas Koutsoumanis, Ana Allende, Avelino Alvarez‐Ordóñez, Sara Bover‐Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Luisa Peixe, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Claire Jenkins, Sara Monteiro Pires, Stefano Morabito, Taina Niskanen, Flemming Scheutz, Maria Teresa da Silva Felício, Winy Messens, Declan Bolton. Pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA Journal 2020; 18(1) doi: 10.2903/j.efsa.2020.5967
85
Ying Chen, Wenda Zhou, Terrence Roh, Mary K. Estes, David L. Kaplan, Shree Ram Singh. In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses. PLOS ONE 2017; 12(11) doi: 10.1371/journal.pone.0187880
86
Jia-hua Kuang, Yan-yan Huang, Jin-shuang Hu, Jia-jia Yu, Qin-yu Zhou, Dong-mei Liu. Exopolysaccharides from Bacillus amyloliquefaciens DMBA-K4 ameliorate dextran sodium sulfate-induced colitis via gut microbiota modulation. Journal of Functional Foods 2020; 75 doi: 10.1016/j.jff.2020.104212
87
Roghayeh Shahbazi, Hamed Yasavoli-Sharahi, Jean-François Mallet, Farzaneh Sharifzad, Nawal Alsadi, Cyrille Cuenin, Vincent Cahais, Felicia Fei-Lei Chung, Zdenko Herceg, Chantal Matar. Novel Probiotic Bacterium Rouxiella badensis subsp. acadiensis (Canan SV-53) Modulates Gut Immunity through Epigenetic Mechanisms. Microorganisms 2023; 11(10) doi: 10.3390/microorganisms11102456
88
Julia Manasson, Nan Shen, Helga R. Garcia Ferrer, Carles Ubeda, Isa Iraheta, Adriana Heguy, Joan M. Von Feldt, Luis R. Espinoza, Abraham Garcia Kutzbach, Leopoldo N. Segal, Alexis Ogdie, Jose C. Clemente, Jose U. Scher. Gut Microbiota Perturbations in Reactive Arthritis and Postinfectious Spondyloarthritis. Arthritis & Rheumatology 2018; 70(2) doi: 10.1002/art.40359
89
Mauricio Javier Olivares-Morales, Marjorie Katherine De La Fuente, Karen Dubois-Camacho, Daniela Parada, David Diaz-Jiménez, Alejandro Torres-Riquelme, Xiaojiang Xu, Nayaret Chamorro-Veloso, Rodrigo Naves, Maria-Julieta Gonzalez, Rodrigo Quera, Carolina Figueroa, John Anthony Cidlowski, Roberto Mauricio Vidal, Marcela Alejandra Hermoso. Glucocorticoids Impair Phagocytosis and Inflammatory Response Against Crohn’s Disease-Associated Adherent-Invasive Escherichia coli. Frontiers in Immunology 2018; 9 doi: 10.3389/fimmu.2018.01026
90
91
Melanie Schirmer, Ashley Garner, Hera Vlamakis, Ramnik J. Xavier. Microbial genes and pathways in inflammatory bowel disease. Nature Reviews Microbiology 2019; 17(8) doi: 10.1038/s41579-019-0213-6
92
Shuiqing Hu, Lan Peng, Youn-Tae Kwak, Erin McElvania Tekippe, Chandrashekhar Pasare, James S. Malter, Lora V. Hooper, Md. Hasan Zaki. The DNA Sensor AIM2 Maintains Intestinal Homeostasis via Regulation of Epithelial Antimicrobial Host Defense. Cell Reports 2015; 13(9) doi: 10.1016/j.celrep.2015.10.040
93
Nicolas Dufour, Laurent Debarbieux. La phagothérapie. médecine/sciences 2017; 33(4) doi: 10.1051/medsci/20173304011
94
Isa Seida, Zeynep Betul Balcioglu, Kamyar Neyestani, Naim Mahroum. Infection and Autoimmunity. 2024;  doi: 10.1016/B978-0-323-99130-8.00011-8
95
G. R. Bicbavova, M. A. Livzan, M. Yu. Lozinskaya. Pathogenetic factors of ulcerative colitis: mainstream for 2020. Bulletin of Siberian Medicine 2021; 20(2) doi: 10.20538/1682-0363-2021-2-130-138
96
Alessandra Graziottin, Sybil Lizanne R. Bravo, Ryan B. Capitulo, Agnes L. Soriano-Estrella, Mariles H. Nazal. Urogenital health and intimate hygiene practices among Filipino women of all ages: Key issues and insights. Philippine Journal of Obstetrics and Gynecology 2024; 48(3) doi: 10.4103/pjog.pjog_22_24
97
Ankan Dinda, Sirsha Banik, Prithwiraj Kirtania, Priyanka Bhowmik. Advances in Probiotic Delivery Systems. 2025;  doi: 10.1016/B978-0-443-27594-4.00015-2
98
Rajalaksmy A. Ramachandran, Christopher Lupfer, Hasan Zaki. Nitric Oxide and Other Small Signalling Molecules. Advances in Microbial Physiology 2018; 72 doi: 10.1016/bs.ampbs.2018.01.004
99
Héloïse Rytter, Hannah Sturgeon, Benoit Chassaing. Diet–pathobiont interplay in health and inflammatory bowel disease. Trends in Microbiology 2025; 33(9) doi: 10.1016/j.tim.2025.04.003
100
Yage Bu, Lingli Feng, Di Xu, Shuai Zhang, Liang Liang, Jinglei Si, Yujie Lu, Qiaoling Liu, Gang Yan, Yubin Wang, Ganqiu Lan, Jing Liang. Changes in Gut Microbiota Associated with Parity in Large White Sows. Animals 2023; 14(1) doi: 10.3390/ani14010112
101
Pierre Lapaquette, Jean Guzzo, Lionel Bretillon, Marie-Agnès Bringer, Dmitri V. Krysko. Cellular and Molecular Connections between Autophagy and Inflammation. Mediators of Inflammation 2015; 2015(1) doi: 10.1155/2015/398483
102
Aina E. Fossum Moen, Jonas Christoffer Lindstrøm, Tone Møller Tannæs, Simen Vatn, Petr Ricanek, Morten H. Vatn, Jørgen Jahnsen, Anna B. Frengen, Fredrik A. Dahl, Panpan You, Janne Sølvernes, Gunn S. Ekeland, Trond E. Detlie, Christine Olbjørn, Kate R. O’Leary, Nicholas T. Ventham, Nicholas A. Kennedy, Rahul Kalla, Alex Adams, Hazel E. Drummond, Ray Boyapati, Elaine R. Nimmo, David C. Wilson, Jack Satsangi, Simon C. Heath, Marta Gut, Angelika Merkel, Monica Bayes, Ivo G. Gut, Åsa V. Keita, Johan D. Söderholm, Henrik Hjortswang, Adam Carstens, Daniel Bergemalm, Jonas Halfvarson, Erik Andersson, Mårten Lindqvist, Dirk Repsilber, Marieke Pierik, Daisy Jonkers, Fernando Gomollón, Mauro D’Amato, Leif Törkvist, Fredrik Hjelm, Mats Gullberg, Niklas Nordberg, Anette Ocklind, Erik Pettersson, Daniel Ekman, Mikael Sundell, Eddie Modig, Ferdinando Bonfiglio, Anne-Clémence Veillard, Renaud Schoemans, Dominique Poncelet, Céline Sabatel, Torbjørn Lindahl, Ewa Ciemniejewska, Christina Casén, Charles Lees, Colin L. Noble, Ian Arnott, Gwo-Tzer Ho, Alan G. Shand. The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients. Scientific Reports 2018; 8(1) doi: 10.1038/s41598-018-35243-4
103
104
Ali Shawki, Declan F. McCole. Mechanisms of Intestinal Epithelial Barrier Dysfunction by Adherent-Invasive Escherichia coli. Cellular and Molecular Gastroenterology and Hepatology 2017; 3(1) doi: 10.1016/j.jcmgh.2016.10.004
105
Laurel Mydock-McGrane, Zachary Cusumano, Zhenfu Han, Jana Binkley, Maria Kostakioti, Thomas Hannan, Jerome S. Pinkner, Roger Klein, Vasilios Kalas, Jan Crowley, Nigam P. Rath, Scott J. Hultgren, James W. Janetka. Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections. Journal of Medicinal Chemistry 2016; 59(20) doi: 10.1021/acs.jmedchem.6b00948
106
Laila Aldars-García, Alicia C. Marin, María Chaparro, Javier P. Gisbert. The Interplay between Immune System and Microbiota in Inflammatory Bowel Disease: A Narrative Review. International Journal of Molecular Sciences 2021; 22(6) doi: 10.3390/ijms22063076
107
Amr El-Sayed, Lotfi Aleya, Mohamed Kamel. Epigenetics and the role of nutraceuticals in health and disease. Environmental Science and Pollution Research 2023; 30(11) doi: 10.1007/s11356-023-25236-w
108
Wen Zeng, Dong He, Yifan Xing, Junyu Liu, Nan Su, Chong Zhang, Yi Wang, Xinhui Xing. Internal connections between dietary intake and gut microbiota homeostasis in disease progression of ulcerative colitis: a review. Food Science and Human Wellness 2021; 10(2) doi: 10.1016/j.fshw.2021.02.016
109
Emerging Therapeutic Targets and Drug Delivery Approaches in IBD. Advances in Pharmacology 2024; 101 doi: 10.1016/bs.apha.2024.10.011
110
111
Sergio Andreu-Sánchez, Aitor Blanco-Míguez, Daoming Wang, Davide Golzato, Paolo Manghi, Vitor Heidrich, Gloria Fackelmann, Daria V. Zhernakova, Alexander Kurilshikov, Mireia Valles-Colomer, Rinse K. Weersma, Alexandra Zhernakova, Jingyuan Fu, Nicola Segata. Global genetic diversity of human gut microbiome species is related to geographic location and host health. Cell 2025; 188(15) doi: 10.1016/j.cell.2025.04.014
112
Manoj Kumar, Mathieu Garand, Souhaila Al Khodor. Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine. Journal of Translational Medicine 2019; 17(1) doi: 10.1186/s12967-019-02174-1
113
Guojun Wu, Naisi Zhao, Chenhong Zhang, Yan Y. Lam, Liping Zhao. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Medicine 2021; 13(1) doi: 10.1186/s13073-021-00840-y
114
Yaping Sun, Xindi Zhang, Yanli Zhang, Yanpo Si, Bing Cao, Zengfu Shan. Research Progress of Intestinal Flora and Related Diseases. Chinese medicine and natural products 2023; 3(03) doi: 10.1055/s-0043-1774414
115
Shahanavaj Khan, Ahamad Imran, Abdul Malik, Anis Ahmad Chaudhary, Abdur Rub, Arif Tasleem Jan, Jakeera Begum Syed, Christian Rolfo. Bacterial imbalance and gut pathologies: Association and contribution of E. coli in inflammatory bowel disease . Critical Reviews in Clinical Laboratory Sciences 2019; 56(1) doi: 10.1080/10408363.2018.1517144
116
Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand V. Sastry, Erol Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Systems Biology 2018; 12(1) doi: 10.1186/s12918-018-0587-5
117
Arie Levine, Michal Kori, Jarek Kierkus, Rotem Sigall Boneh, Malgorzata Sladek, Johanna C Escher, Eytan Wine, Baruch Yerushalmi, Jorge Amil Dias, Ron Shaoul, Gigi Veereman Wauters, Mona Boaz, Guila Abitbol, Athos Bousvaros, Dan Turner. Azithromycin and metronidazole versus metronidazole-based therapy for the induction of remission in mild to moderate paediatric Crohn’s disease : a randomised controlled trial. Gut 2019; 68(2) doi: 10.1136/gutjnl-2017-315199
118
Marie-Paule Vasson, Carla Domingues-Faria, Nicolas Goncalves-Mendes, Lamia Slimani, Jérémie Talvas, Ahmad Khalil. Des cibles tissulaires multiples pour la vitamine D. Pratiques en nutrition 2015; 11(41) doi: 10.1016/j.pranut.2014.12.004
119
Adrian Szczepaniak, Jakub Fichna. Organometallic Compounds and Metal Complexes in Current and Future Treatments of Inflammatory Bowel Disease and Colorectal Cancer—a Critical Review. Biomolecules 2019; 9(9) doi: 10.3390/biom9090398
120
Rachel M. Bleich, Chuang Li, Shan Sun, Ju-Hyun Ahn, Belgin Dogan, Cassandra J. Barlogio, Christopher A. Broberg, Adrienne R. Franks, Emily Bulik-Sullivan, Ian M. Carroll, Kenneth W. Simpson, Anthony A. Fodor, Janelle C. Arthur. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. Microbiome 2023; 11(1) doi: 10.1186/s40168-023-01710-y
121
Himani Pandey, Dheeraj Jain, Daryl W. T. Tang, Sunny H. Wong, Devi Lal. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intestinal Research 2024; 22(1) doi: 10.5217/ir.2023.00080
122
M.J. Żórawski, D. Dudzik, D. Musiałowska. Genetic similarities of Escherichia coli isolated from hospitalized patients. Progress in Health Sciences 2017; 7(1) doi: 10.5604/01.3001.0010.1874
123
Belgin Dogan, Jing Fu, Shiying Zhang, Ellen J. Scherl, Kenneth W. Simpson. Rifaximin decreases virulence of Crohn’s disease-associated Escherichia coli and epithelial inflammatory responses. The Journal of Antibiotics 2018; 71(5) doi: 10.1038/s41429-017-0022-y
124
D. J. Astley, N. Masters, A. Kuballa, M. Katouli. Commonality of adherent-invasive Escherichia coli isolated from patients with extraintestinal infections, healthy individuals and the environment. European Journal of Clinical Microbiology & Infectious Diseases 2021; 40(1) doi: 10.1007/s10096-020-04066-5
125
Youn Hee Cho, Michael J Renouf, Oluwafikemi Omotoso, Joseph B McPhee. Inflammatory bowel disease-associated adherent-invasive Escherichia coli have elevated host-defense peptide resistance. FEMS Microbiology Letters 2022; 369(1) doi: 10.1093/femsle/fnac098
126
Priyankar Dey. Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts. Frontiers in Immunology 2025; 16 doi: 10.3389/fimmu.2025.1674913
127
Waleska Saitz, David Montero, Mirka Pardo, Daniela Araya, Marjorie De la Fuente, Marcela Hermoso, Mauricio Farfán, Daniel Ginard, Ramon Rosselló-Móra, Dave Rasko, Felipe Del Canto, Roberto Vidal. Characterization of Adherent-Invasive Escherichia coli (AIEC) Outer Membrane Proteins Provides Potential Molecular Markers to Screen Putative AIEC Strains. International Journal of Molecular Sciences 2022; 23(16) doi: 10.3390/ijms23169005
128
Ellen Cristina Souza de Oliveira, Ana Elisa Valencise Quaglio, Daniéla Oliveira Magro, Luiz Claudio Di Stasi, Ligia Yukie Sassaki. Intestinal Microbiota and miRNA in IBD: A Narrative Review about Discoveries and Perspectives for the Future. International Journal of Molecular Sciences 2023; 24(8) doi: 10.3390/ijms24087176
129
Allison Agus, Damien Richard, Tiphanie Faïs, Emilie Vazeille, Mélissa Chervy, Virginie Bonnin, Guillaume Dalmasso, Jérémy Denizot, Elisabeth Billard, Richard Bonnet, Anthony Buisson, Nicolas Barnich, Julien Delmas. Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect . Gut Microbes 2021; 13(1) doi: 10.1080/19490976.2020.1839318
130
G. R. Bikbavova, M. A. Livzan. Modulation of instinal microbiom in the formation and progression of ulterative colitis.. Annals of the Russian academy of medical sciences 2020; 75(6) doi: 10.15690/vramn1238
131
Wenxiu Liu, Qian Wang, Yanrui Bai, Han Xiao, Zhunduo Li, Yan Wang, Qi Wang, Jing Yang, Hui Sun. Potential Application of Intestinal Organoids in Intestinal Diseases. Stem Cell Reviews and Reports 2024; 20(1) doi: 10.1007/s12015-023-10651-w
132
Jeannette S. Messer, Eugene B. Chang. Physiology of the Gastrointestinal Tract. 2018;  doi: 10.1016/B978-0-12-809954-4.00036-0
133
Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet. Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts. Scientific Reports 2019; 9(1) doi: 10.1038/s41598-019-38628-1
134
Manoj Kumar, Noora Almohannadi, Souhaila Al Khodor. Decoding the power of the microbiome in human health. Frontiers in Cellular and Infection Microbiology 2026; 16 doi: 10.3389/fcimb.2026.1877371
135
Gwladys Sevrin, Sébastien Massier, Benoit Chassaing, Allison Agus, Julien Delmas, Jérémy Denizot, Elisabeth Billard, Nicolas Barnich. Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability. Gut Microbes 2020; 11(3) doi: 10.1080/19490976.2017.1421886
136
L. Cochran, S. Hill, U. Lotti, K. Allenspach, D. Palma, M. Forman, A. T. Gary, B. Dogan, S. P. McDonough, K. W. Simpson. Clinical characteristics and long‐term outcome of E. coli‐associated granulomatous ileocolitis in dogs: five cases (2010‐2014). Journal of Small Animal Practice 2021; 62(7) doi: 10.1111/jsap.13313
137
Pritha Chatterjee, Marianne R. Spalinger, Charly Acevedo, Alina N. Santos, Casey M. Gries, Salomon M. Manz, Vinicius Canale, Ali Shawki, Anica Sayoc-Becerra, Hillmin Lei, Meli’sa S. Crawford, Lars Eckmann, James Borneman, Declan F. McCole. Intestinal epithelial PTPN2 limits pathobiont colonization by immune-directed antimicrobial responses. Gut Microbes 2025; 17(1) doi: 10.1080/19490976.2025.2559029
138
Yu-Yang Tsai, Julia Ienes Lima, Sonsiray Alvarez Narvaez, Catherine M. Logue, Jasna Kovac. Whole-genome analysis of five Escherichia coli strains isolated from focal duodenal necrosis in laying hens reveals genetic similarities to the E. coli O25:H4 ST131 strain . Microbiology Spectrum 2025; 13(5) doi: 10.1128/spectrum.02110-24
139
Vivien Deloule, Claire Boisset, Dalil Hannani, Antonia Suau, Audrey Le Gouellec, Jadwiga Chroboczek, Cyrille Botté, Yoshiki Yamaryo-Botté, Christine Chirat, Bertrand Toussaint. Prebiotic role of softwood hemicellulose in healthy mice model. Journal of Functional Foods 2020; 64 doi: 10.1016/j.jff.2019.103688
140
Georgia Valentina Tita, Cristina Rebeca Fogas, Kinga Cristina Slavescu, Vasile Marcel Tantau, Stefana Arlinda Medan, Daniela Elena Serban. Persistent Gut Microbiota Dysbiosis in Pediatric Crohn’s Disease: A Next-Generation Sequencing Pilot Study. Biomolecules 2026; 16(6) doi: 10.3390/biom16060801
141
142
Andrew Leber, Raquel Hontecillas, Nuria Tubau-Juni, Victoria Zoccoli-Rodriguez, Vida Abedi, Josep Bassaganya-Riera. NLRX1 Modulates Immunometabolic Mechanisms Controlling the Host–Gut Microbiota Interactions during Inflammatory Bowel Disease. Frontiers in Immunology 2018; 9 doi: 10.3389/fimmu.2018.00363
143
Anmol Gulati, Xin Guo. 2022 Medicinal Chemistry Reviews. Medicinal Chemistry Reviews 2022; 57 doi: 10.1021/mc-2022-vol57.ch16
144
Manuela Costanzo, Vincenzo Cesi, Enrica Prete, Anna Negroni, Francesca Palone, Salvatore Cucchiara, Salvatore Oliva, Beatrice Leter, Laura Stronati. Krill oil reduces intestinal inflammation by improving epithelial integrity and impairing adherent-invasive Escherichia coli pathogenicity. Digestive and Liver Disease 2016; 48(1) doi: 10.1016/j.dld.2015.09.012
145
Melissa Arroyo-Mendoza, Hernan Lorenzi, Gregory J. Phillips, Deborah M. Hinton, Melissa M. Kendall. Escherichia coli pathobionts and Crohn’s disease: varied genetic paths leading to similar phenotypes . Journal of Bacteriology 2026; 208(5) doi: 10.1128/jb.00016-26
146
Ava Hosseini, Gillian M. Barlow, Gabriela Leite, Mohamad Rashid, Gonzalo Parodi, Jiajing Wang, Walter Morales, Stacy Weitsman, Ali Rezaie, Mark Pimentel, Ruchi Mathur. Consuming artificial sweeteners may alter the structure and function of duodenal microbial communities. iScience 2023; 26(12) doi: 10.1016/j.isci.2023.108530
147
Rodrick J. Chiodini, Scot E. Dowd, Susan Galandiuk, Brian Davis, Angela Glassing. The predominant site of bacterial translocation across the intestinal mucosal barrier occurs at the advancing disease margin in Crohn's disease.  Microbiology 2016; 162(9) doi: 10.1099/mic.0.000336
148
Maeve E. Krueger, Jake Sondag Boles, Zachary D. Simon, Stephan D. Alvarez, Nikolaus R. McFarland, Michael S. Okun, Ellen M. Zimmermann, Christopher E. Forsmark, Malú Gámez Tansey. Comparative analysis of Parkinson’s and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion. npj Parkinson's Disease 2025; 11(1) doi: 10.1038/s41531-025-00894-4
149
Bahareh Nadalian, Banafsheh Nadalian, Mohammad Reza Zali, Abbas Yadegar. Outer Membrane Vesicles Derived from Adherent-Invasive Escherichia coli Induce Inflammatory Response and Alter the Gene Expression of Junction-Associated Proteins in Human Intestinal Epithelial Cells. Canadian Journal of Infectious Diseases and Medical Microbiology 2024; 2024 doi: 10.1155/2024/2701675
150
Jim Manos. The human microbiome in disease and pathology. APMIS 2022; 130(12) doi: 10.1111/apm.13225
151
152
Giacomo Caio, Lisa Lungaro, Nicola Segata, Matteo Guarino, Giorgio Zoli, Umberto Volta, Roberto De Giorgio. Effect of Gluten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity. Nutrients 2020; 12(6) doi: 10.3390/nu12061832
153
Eric Banan-Mwine Daliri, Fred Kwame Ofosu, Ramachandran Chelliah, Byong Hoon Lee, Deog-Hwan Oh. Health Impact and Therapeutic Manipulation of the Gut Microbiome. High-Throughput 2020; 9(3) doi: 10.3390/ht9030017
154
Yuxiao Chang, Xiang Li, Lei Ding, Chao Yang, Zhiyuan Pan, Ni Han, Yujun Cui, Fachao Zhi, Ruifu Yang, Hong Gao, Yujing Bi. Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues. Engineering 2022; 16 doi: 10.1016/j.eng.2021.03.028
155
G.C. Silveira, B.G. Barbosa, R.A. Arrant, N.C.L. Rosado, M. Dibo, R.S. Yamatogi, L.G. Conceição, P.R.S. Costa, G. Nakazato, R.K.T. Kobayashi, A. Navarro, F.A. Voorwald. Macrolide-responsive histiocytic ulcerative colitis in a French bulldog - clinical and microbiological features - case report. Arquivo Brasileiro de Medicina Veterinária e Zootecnia 2026; 78(3) doi: 10.1590/1678-4162-13478
156
Rafaella F. A. Costa, Maria L. A. Ferrari, Marie-Agnès Bringer, Arlette Darfeuille-Michaud, Flaviano S. Martins, Nicolas Barnich. Characterization of mucosa-associated Escherichia coli strains isolated from Crohn’s disease patients in Brazil. BMC Microbiology 2020; 20(1) doi: 10.1186/s12866-020-01856-x
157
Samvel Sirakanyan, Lena Stepanyan, Elmira Hakobyan, Anush Hovakimyan, Astghik Pepoyan, Marine Balayan. Anticonvulsant drugs and growth kinetics of gut commensal Escherichia coli isolates from familial Mediterranean fever disease patients. Scientific Reports 2026; 16(1) doi: 10.1038/s41598-026-50466-6
158
Khalid A. Abdelhalim, Ataç Uzel, Nalan Gülşen Ünal. Virulence determinants and genetic diversity of adherent-invasive Escherichia coli (AIEC) strains isolated from patients with Crohn's disease. Microbial Pathogenesis 2020; 145 doi: 10.1016/j.micpath.2020.104233
159
Yan-Ni Liang, Jin-Gao Yu, Dong-Bo Zhang, Zhen Zhang, Lang-Lang Ren, Lu-Han Li, Zheng Wang, Zhi-Shu Tang. Indigo Naturalis Ameliorates Dextran Sulfate Sodium-Induced Colitis in Mice by Modulating the Intestinal Microbiota Community. Molecules 2019; 24(22) doi: 10.3390/molecules24224086
160
Ali Shawki, Rocio Ramirez, Marianne R. Spalinger, Paul M. Ruegger, Anica Sayoc-Becerra, Alina N. Santos, Pritha Chatterjee, Vinicius Canale, Jonathan D. Mitchell, John C. Macbeth, Casey M. Gries, Michel L. Tremblay, Ansel Hsiao, James Borneman, Declan F. McCole. The autoimmune susceptibility gene, PTPN2, restricts expansion of a novel mouse adherent-invasive E. coli. Gut Microbes 2020; 11(6) doi: 10.1080/19490976.2020.1775538
161
Christopher S. Vennard, Samson Marvellous Oladeji, Herman O. Sintim. Inhibitors of Cyclic Dinucleotide Phosphodiesterases and Cyclic Oligonucleotide Ring Nucleases as Potential Drugs for Various Diseases. Cells 2025; 14(9) doi: 10.3390/cells14090663
162
Donal Sheehan, Carthage Moran, Fergus Shanahan. The microbiota in inflammatory bowel disease. Journal of Gastroenterology 2015; 50(5) doi: 10.1007/s00535-015-1064-1
163
Aida Heidari, Mohammad Hassan Emami, Fatemeh Maghool, Samane Mohammadzadeh, Parisa Kadkhodaei Elyaderani, Tahereh Safari, Alireza Fahim, Razie Kamali Dolatabadi. Molecular epidemiology, antibiotic resistance profile and frequency of integron 1 and 2 in adherent-invasive Escherichia coli isolates of colorectal cancer patients. Frontiers in Microbiology 2024; 15 doi: 10.3389/fmicb.2024.1366719
164
Giovanna Alexandre Fabiano, Leila Marie Shinn, Adriane Elisabete Costa Antunes. Relationship between Oat Consumption, Gut Microbiota Modulation, and Short-Chain Fatty Acid Synthesis: An Integrative Review. Nutrients 2023; 15(16) doi: 10.3390/nu15163534
165
Qiao Liu, Bohyun Lee, Lei Xie. Small molecule modulation of microbiota: a systems pharmacology perspective. BMC Bioinformatics 2022; 23(S3) doi: 10.1186/s12859-022-04941-2
166
Geeta Kulkarni, Bo Shen. Atlas of Endoscopy Imaging in Inflammatory Bowel Disease. 2020;  doi: 10.1016/B978-0-12-814811-2.00023-2
167
Lacey R. Lopez, Ju-Hyun Ahn, Tomaz Alves, Janelle C. Arthur. Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease. Frontiers in Cellular and Infection Microbiology 2022; 12 doi: 10.3389/fcimb.2022.934619
168
Terence Van Raay, Emma Allen-Vercoe, Robert Allen Britton, Patrice D. Cani. Microbial Interactions and Interventions in Colorectal Cancer. Microbiology Spectrum 2017; 5(3) doi: 10.1128/microbiolspec.BAD-0004-2016
169
Nehal M. El-Deeb, Tamer A.E. Ahmed, Amal D. Premarathna, Vitalijs Rjabovs, Rando Tuvikene, Riadh Hammami, Martine Boulianne, Maxwell T. Hincke. Experimental datasets on the extraction of functional ingredients from seaweeds for controlling bacterial infection. Data in Brief 2025; 60 doi: 10.1016/j.dib.2025.111569
170
Aida Mayorgas, Isabella Dotti, Azucena Salas. Microbial Metabolites, Postbiotics, and Intestinal Epithelial Function. Molecular Nutrition & Food Research 2021; 65(5) doi: 10.1002/mnfr.202000188
171
Abdul Arif Khan, Zakir Khan, Abdul Malik, Mohd Abul Kalam, Phillip Cash, Mohd. Tashfeen Ashraf, Aws Alshamsan. Colorectal cancer-inflammatory bowel disease nexus and felony of Escherichia coli. Life Sciences 2017; 180 doi: 10.1016/j.lfs.2017.05.016
172
Urszula Krupa-Kozak, Natalia Drabińska. Comprehensive Gut Microbiota. 2022;  doi: 10.1016/B978-0-12-819265-8.00036-X
173
Holger Schäffler, Daniel P. R. Herlemann, Christian Alberts, Annika Kaschitzki, Peggy Bodammer, Karen Bannert, Thomas Köller, Philipp Warnke, Bernd Kreikemeyer, Georg Lamprecht. Mucosa‐attached bacterial community in Crohn's disease coheres with the clinical disease activity index. Environmental Microbiology Reports 2016; 8(5) doi: 10.1111/1758-2229.12411
174
Michał Turniak, Beata Sobieszczańska. Diffusely Adhering Escherichia Coli . Postępy Mikrobiologii - Advancements of Microbiology 2019; 58(2) doi: 10.21307/PM-2019.58.2.143
175
Meryl Perlman, Stefania Senger, Smriti Verma, James Carey, Christina S. Faherty. A foundational approach to culture and analyze malnourished organoids. Gut Microbes 2023; 15(2) doi: 10.1080/19490976.2023.2248713
176
Anthony Buisson, Marie-Agnès Bringer, Nicolas Barnich, Emilie Vazeille. Macrophages Versus Escherichia coli. Inflammatory Bowel Diseases 2016; 22(12) doi: 10.1097/MIB.0000000000000946
177
Humaira Rashid, Towfida J. Siddiqua, Biplob Hossain, Abdullah Siddique, Mamun Kabir, Zannatun Noor, Masud Alam, Mamun Ahmed, Rashidul Haque. MicroRNA Expression and Intestinal Permeability in Children Living in a Slum Area of Bangladesh. Frontiers in Molecular Biosciences 2021; 8 doi: 10.3389/fmolb.2021.765301
178
Ke Li, Lina Xu, Mengyue Tian, Ming Yang, Li Jia, Dongmin Zou, Ruonan Liu, Jinliang Du, Yuzhong Ma. The pathogenic potential and genetic attributes of Escherichia coli in milk from dairy cows with subclinical mastitis. Journal of Environmental Science and Health, Part B 2022; 57(11) doi: 10.1080/03601234.2022.2129239
179
Roberta Maria Nicolosi, Graziana Bonincontro, Elena Imperia, Camilla Badiali, Daniela De Vita, Fabio Sciubba, Laura Dugo, Michele Pier Luca Guarino, Annamaria Altomare, Giovanna Simonetti, Gabriella Pasqua. Protective Effect of Procyanidin-Rich Grape Seed Extract against Gram-Negative Virulence Factors. Antibiotics 2023; 12(11) doi: 10.3390/antibiotics12111615
180
Shenglong Xue, Tian Shi, Jinjin Xie, Weidong Liu, Shanxia Yao, Na Li, Huan Liu, Wenjie Kong, Feng Gao. Integrated fecal macrogenomic and metabolomic analyses reveal celiac disease flora and metabolic profiles associated with Chinese populations. Journal of Translational Medicine 2025; 23(1) doi: 10.1186/s12967-025-06991-5
181
Oumaïra Rahmouni, Cécile Vignal, Marie Titécat, Benoît Foligné, Benjamin Pariente, Laurent Dubuquoy, Pierre Desreumaux, Christel Neut. High carriage of adherent invasive E. coli in wildlife and healthy individuals. Gut Pathogens 2018; 10(1) doi: 10.1186/s13099-018-0248-7
182
F. J. Ryan, A. M. Ahern, R. S. Fitzgerald, E. J. Laserna-Mendieta, E. M. Power, A. G. Clooney, K. W. O’Donoghue, P. J. McMurdie, S. Iwai, A. Crits-Christoph, D. Sheehan, C. Moran, B. Flemer, A. L. Zomer, A. Fanning, J. O’Callaghan, J. Walton, A. Temko, W. Stack, L. Jackson, S. A. Joyce, S. Melgar, T. Z. DeSantis, J. T. Bell, F. Shanahan, M. J. Claesson. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nature Communications 2020; 11(1) doi: 10.1038/s41467-020-15342-5
183
Banafsheh Nadalian, Bahareh Nadalian, Hamidreza Houri, Shabnam Shahrokh, Mohammad Abdehagh, Abbas Yadegar, Gholamhossein Ebrahimipour. Phylogrouping and characterization of Escherichia coli isolated from colonic biopsies and fecal samples of patients with flare of inflammatory bowel disease in Iran. Frontiers in Medicine 2022; 9 doi: 10.3389/fmed.2022.985300
184
Yidan Wang, Caiqin Deng, Minmin Sui, Penghao Wei, Bofang Duan, Zhao Li, Fengcai Zou. Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing. Microorganisms 2025; 13(9) doi: 10.3390/microorganisms13092056
185
Kofi Clarke, Dominic Amakye, Jiqing Shi, Shannon Dalessio, Kara DiJoseph, Matthew D. Coates. Empiric Antibiotic Use With Rescue Infliximab Does Not Improve Outcomes in Acute Severe Ulcerative Colitis: A Retrospective Cohort Study. Health Science Reports 2025; 8(8) doi: 10.1002/hsr2.71165
186
Ramón Gómez-Moreno, Rachell Martínez-Ramírez, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Josué Pérez-Santiago, Abel Baerga-Ortiz. Hotspots of Sequence Variability in Gut Microbial Genes Encoding Pro-Inflammatory Factors Revealed by Oligotyping. Frontiers in Genetics 2019; 10 doi: 10.3389/fgene.2019.00631
187
Na Han, Xianhui Peng, Tingting Zhang, Yujun Qiang, Xiuwen Li, Wen Zhang, Laurie E. Comstock. Rapid turnover and short-term blooms of Escherichia coli in the human gut . Journal of Bacteriology 2024; 206(1) doi: 10.1128/jb.00239-23