Article
Immunology
Babak Khorsand, Hamid Asadzadeh Aghdaei, Ehsan Nazemalhosseini-Mojarad, Bahareh Nadalian, Banafsheh Nadalian, Hamidreza Houri
Summary: This study found that there are significant changes in the taxonomic and functional composition of Enterobacteriaceae species in the gut of Crohn's disease and ulcerative colitis patients. Particularly, there is a significant increase in the abundance of Escherichia coli and Klebsiella species, which are associated with the development and progression of the diseases.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Samuel Zimmerman, Braden T. Tierney, Chirag J. Patel, Aleksandar D. Kostic
Summary: This study quantified the heterogeneity in microbial gene content across different ecological environments. The researchers identified a large number of nonredundant genes, with the majority occurring in only one sample. They also discovered sets of genes associated with specific ecological environments and highlighted the incompleteness and inaccuracy of previous microbiome gene catalogs.
Article
Gastroenterology & Hepatology
Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Summary: ViroProfiler is a computer analysis tool for analyzing shotgun viral metagenomic data. It can be run on a local or cloud computing environment. It uses containerization technology to ensure computational reproducibility and facilitate collaborative research.
Article
Biochemistry & Molecular Biology
Gerard Serrano-Gomez, Luis Mayorga, Inigo Oyarzun, Joaquim Roca, Natalia Borruel, Francesc Casellas, Encarna Varela, Marta Pozuelo, Kathleen Machiels, Francisco Guarner, Severine Vermeire, Chaysavanh Manichanh
Summary: Crohn's disease (CD) is more dysbiotic than ulcerative colitis (UC), while CD relapse is associated with alterations at the species and metabolic pathway levels, providing biomarkers to discriminate IBD subtypes and predict disease activity. Our study emphasizes the importance of considering relapse-related microbial dysbiosis in IBD patients for better management and treatment strategies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Gastroenterology & Hepatology
Julien Kirchgesner, Rishi J. Desai, Maria C. Schneeweiss, Laurent Beaugerie, Sebastian Schneeweiss, Seoyoung C. Kim
Summary: Combination therapy with vedolizumab and thiopurines is associated with a lower risk of treatment failure compared to vedolizumab monotherapy in patients with CD, but the effect is less pronounced in UC.
Article
Genetics & Heredity
Dasa Jevsinek Skok, Nina Hauptman, Miha Jerala, Nina Zidar
Summary: Ulcerative colitis (UC) and Crohn's disease (CD) involve imbalance in cytokine levels, with INSL5, LEFTY1, and BMP8B identified as potential key genes that may play a role in both diseases and require further investigation for diagnostic potential.
Article
Gastroenterology & Hepatology
Mahasish Shome, Lusheng Song, Stacy Williams, Yunro Chung, Vel Murugan, Jin G. Park, William Faubion, Shabana F. Pasha, Jonathan A. Leighton, Joshua LaBaer, Ji Qiu
Summary: By analyzing the anti-microbial antibody response in patients with inflammatory bowel disease (IBD), we have identified antibody signatures for Crohn's disease (CD) and ulcerative colitis (UC), as well as discovered the associated microorganisms. These findings contribute to our understanding of the role specific microorganisms play in the pathogenesis of IBD and could potentially aid in early and accurate diagnosis.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Microbiology
Da-Yeon Kang, Jong-Lyul Park, Min-Kyung Yeo, Sang-Bum Kang, Jin-Man Kim, Ju Seok Kim, Seon-Young Kim
Summary: Fecal whole-metagenome shotgun (WMS) sequencing was used to differentiate and diagnose Crohn's disease (CD) and ulcerative colitis (UC) through a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) were also identified during the study.
Review
Immunology
Reza Yarani, Ali Shojaeian, Oana Palasca, Nadezhda T. Doncheva, Lars Juhl Jensen, Jan Gorodkin, Flemming Pociot
Summary: This review discusses the differential regulation of miRNAs in inflammatory bowel disease (IBD) and their potential diagnostic and therapeutic applications. Through literature curation and computational analysis, a consensus set of differentially expressed miRNAs in mucosal tissues was obtained. The role of these miRNAs and their potential targets in IBD are highlighted.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Heather J. Galipeau, Alberto Caminero, Williams Turpin, Miriam Bermudez-Brito, Alba Santiago, Josie Libertucci, Marco Constante, Juan Antonio Raygoza Garay, Gaston Rueda, Sarah Armstrong, Alex Clarizio, Michelle Smith, Michael G. Surette, Premysl Bercik, Kenneth Croitoru, Elena F. Verdu
Summary: Increased fecal proteolytic activity was found before the clinical diagnosis of UC, which may serve as a noninvasive biomarker of inflammation associated with changes in gut microbiota. The study suggests potential therapeutic targets for at-risk populations based on antiprotease treatments.
Article
Gastroenterology & Hepatology
Tatsuki Noguchi, Soichiro Ishihara, Motoi Uchino, Hiroki Ikeuchi, Koji Okabayashi, Kitaro Futami, Shinji Tanaka, Hiroki Ohge, Hisashi Nagahara, Kazuhiro Watanabe, Michio Itabashi, Kinya Okamoto, Yoshiki Okita, Tsunekazu Mizushima, Yusuke Mizuuchi, Kazutaka Yamada, Yoshifumi Shimada, Yu Sato, Hideaki Kimura, Kenichi Takahashi, Koya Hida, Yusuke Kinugasa, Junji Okuda, Koji Daito, Fumikazu Koyama, Hideki Ueno, Takayuki Yamamoto, Tsunekazu Hanai, Atsuo Maemoto, Koji Oba, Yoichi Ajioka, Kenichi Sugihara
Summary: Patients with longstanding inflammatory bowel disease, such as ulcerative colitis and Crohn's disease, are at high risk of developing intestinal cancers. This study found significant differences between intestinal cancers associated with ulcerative colitis and Crohn's disease. Crohn's disease-associated cancers were diagnosed at more advanced stages, detected less frequently by surveillance, and had a poorer prognosis compared to those associated with ulcerative colitis.
JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nikolas Dovrolis, Anastasia Moschoviti, Smaragdi Fessatou, George Karamanolis, George Kolios, Maria Gazouli
Summary: This study examines the role of the microbiome in the onset of pediatric inflammatory bowel disease (IBD). Through analyzing the microbiota of nine IBD families, specific patterns of microbial taxa were identified among patients and their families. The results suggest a potential role of maternal factors in the establishment and modulation of the early life microbiome.
Article
Biochemical Research Methods
Florent Clerc, Karli R. Reiding, Noortje de Haan, Carolien A. M. Koeleman, Agnes L. Hipgrave Ederveen, Natalia Manetti, Viktoria Dotz, Vito Annese, Manfred Wuhrer
Summary: This study investigates the associations of immunoglobulin A1 and A2 glycosylation with inflammatory bowel diseases (IBD). Differences in IgA O- and N-glycosylation between patient groups were found to be associated with the diseases, and a statistical model was constructed to predict the disease group of the patients. These findings contribute to the development of noninvasive biomarkers for IBD and improvement in patient care.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Immunology
Yao Wang, Hao Zhuang, Xiao-han Jiang, Rui-han Zou, Hai-yang Wang, Zhi-ning Fan
Summary: Using WGCNA and random forest algorithm, this study identified nine gene signatures associated with the exacerbation of Ulcerative colitis (UC). A novel genotyping scheme was constructed to predict the severity of UC and screen UC patients suitable for CS-IV treatment. Furthermore, a small molecule drug (Exisulind) with potential therapeutic effects for UC was identified, providing new ideas and materials for personalized clinical treatment plans for UC patients.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Vadim Dubinsky, Leah Reshef, Keren Rabinowitz, Karin Yadgar, Lihi Godny, Keren Zonensain, Nir Wasserberg, Iris Dotan, Uri Gophna
Summary: Patients with pouchitis exhibit significant alterations in microbial species, metabolic pathways, and enzyme functions, with specific enrichment of Ruminococcus gnavus strains and depletion in pathways related to butyrate and secondary bile acid synthesis. Microbial feature-based classifiers have been developed to distinguish between patients with a normal pouch and pouchitis, identifying predictive species and genes for pouchitis. The study highlights potential microbial targets for intervention to attenuate small intestinal inflammation in pouchitis and CD.
Article
Oncology
Katherine A. Dunn, Zara Forbrigger, Jessica Connors, Mushfiqur Rahman, Alejandro Cohen, Johan Van Limbergen, Morgan G. Langille, Andrew W. Stadnyk, Joseph P. Bielawski, Susanne L. Penny, Tamara MacDonald, Ketan Kulkarni
Summary: Investigating stool samples from pediatric acute lymphoblastic leukemia patients treated with pegaspargase revealed a significant decline in asparagine, accompanied by changes in 31 microbial genes. These changes involve genes related to amino acid metabolism, nutrient sensing, and pathways associated with cancer.
LEUKEMIA & LYMPHOMA
(2021)
Review
Gastroenterology & Hepatology
Charlotte M. Verburgt, W. Pepijn Heutink, Lot I. M. Kuilboer, Julie D. Dickmann, Faridi S. van Etten-Jamaludin, Marc A. Benninga, Wouter J. de Jonge, Johan E. Van Limbergen, Merit M. Tabbers
Summary: The study evaluated the efficacy and safety of antibiotics in pediatric IBD, finding that azithromycin+metronidazole was more effective in mild-to-moderate Crohn's disease, and the combination of antibiotics and intravenous corticosteroids was more effective in Acute Severe Colitis. No significant drug-related adverse events were reported, but more evidence is needed before widespread implementation in daily practice.
EXPERT REVIEW OF GASTROENTEROLOGY & HEPATOLOGY
(2021)
Article
Gastroenterology & Hepatology
Ruben J. Colman, Ye Xiong, Tomoyuki Mizuno, Jeffrey S. Hyams, Joshua D. Noe, Brendan Boyle, Geert R. D'Haens, Johan van Limbergen, Kelly Chun, Jane Yang, Michael J. Rosen, Lee A. Denson, Alexander A. Vinks, Phillip Minar
Summary: This study evaluated the impact of ATI on infliximab clearance and loss of response, finding that even low levels of ATI can affect drug clearance. The data suggest that dose optimization for low-level ATI can improve infliximab clearance and prevent loss of response.
ALIMENTARY PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Gastroenterology & Hepatology
Thomas Dierikx, Daniel Berkhout, Anat Eck, Sebastian Tims, Johan van Limbergen, Douwe Visser, Marjon de Boer, Nanne de Boer, Daan Touw, Marc Benninga, Nine Schierbeek, Laura Visser, Jan Knol, Guus Roeselers, Johanna de Vries, Tim de Meij
Summary: Cesarean section delivery has a strong impact on infant microbiome colonization, but maternal antibiotic administration before CS does not exacerbate the compromised microbiome. Long-term health effects need to be confirmed by larger studies.
Article
Nutrition & Dietetics
Lara Hart, Charlotte M. Verburgt, Eytan Wine, Mary Zachos, Alisha Poppen, Mallory Chavannes, Johan Van Limbergen, Nikhil Pai
Summary: Inflammatory bowel disease is a chronic autoimmune disorder of the gastrointestinal tract. Nutritional therapy plays an important role in the treatment of IBD due to its influence on the gut microbiome and its safety profile. The increasing incidence of IBD worldwide may be attributed to changes in dietary patterns.
Article
Gastroenterology & Hepatology
Basavaraj Kerur, Karoline Fiedler, Marisa Stahl, Jeffrey Hyams, Michael Stephens, Ying Lu, Marian Pfefferkorn, Raza Alkhouri, Jennifer Strople, Judith Kelsen, Leah Siebold, Alka Goyal, Joel R. Rosh, Neal LeLeiko, Johan Van Limbergen, Anthony L. Guerrerio, Ross M. Maltz, Lina Karam, Eileen Crowley, Anne M. Griffiths, Melvin B. Heyman, Mark Deneau, Keith Benkov, Joshua Noe, Dedrick Moulton, Helen Pappa, Joseph Galanko, Scott Snapper, Aleixo M. Muise, Michael D. Kappelman, Eric Benchimol
Summary: This article describes the utilization and durability of anti-TNF therapy in children with very early onset inflammatory bowel disease (VEOIBD). The study found that the utilization and durability of anti-TNF therapy in VEOIBD children is relatively high and comparable with older children. Having Crohn disease is associated with greater durability compared to UC/IBD-U.
JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION
(2022)
Article
Gastroenterology & Hepatology
Mohammed Ghiboub, Susanne Penny, Charlotte M. Verburgt, Rotem Sigall Boneh, Eytan Wine, Alejandro Cohen, Katherine A. Dunn, Devanand M. Pinto, Marc A. Benninga, Wouter J. de Jonge, Arie Levine, Johan E. Van Limbergen
Summary: The Crohn's disease exclusion diet (CDED) plus partial enteral nutrition (PEN) and exclusive enteral nutrition (EEN) can induce remission in pediatric Crohn's disease. CDED+PEN is better tolerated and able to sustain remission. The remission induced by CDED+PEN is associated with significant changes in inflammatory bowel disease-associated metabolites such as kynurenine, ceramides, amino acids, and others.
Review
Gastroenterology & Hepatology
Jasmijn Z. Jagt, Charlotte M. Verburgt, Ralph de Vries, Nanne K. H. de Boer, Marc A. Benninga, Wouter J. de Jonge, Johan E. van Limbergen, Tim G. J. de Meij
Summary: This systematic review provides evidence for distinct faecal metabolomic profiles in paediatric IBD, but results varied across studies possibly due to differences in study design and applied analytical techniques. Faecal metabolomics could provide more insight into host-microbial interactions in IBD, but further studies with standardized methodologies and reporting are needed.
JOURNAL OF CROHNS & COLITIS
(2022)
Article
Immunology
Katherine A. Dunn, Tamara MacDonald, Gloria J. Rodrigues, Zara Forbrigger, Joseph P. Bielawski, Morgan G. I. Langille, Johan Van Limbergen, Ketan Kulkarni
Summary: Due to decreased immunity, pediatric hematologic-cancer patients often use antibiotics and antifungals to prevent infection. However, the specific effects of these drugs on the gut microbiome of pediatric oncology patients are not well understood. This study found that both antibiotics and antifungals decrease the diversity of the gut microbiome in pediatric patients, and antifungal use is associated with an increase in opportunistic pathogens.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Ruben J. Colman, Tomoyuki Mizuno, Keizo Fukushima, David B. Haslam, Jeffrey S. Hyams, Brendan Boyle, Joshua D. Noe, Geert R. D'Haens, Johan Van Limbergen, Kelly Chun, Jane Yang, Lee A. Denson, Nicholas J. Ollberding, Alexander A. Vinks, Phillip Minar
Summary: This study established a pediatric vedolizumab pharmacokinetic model to optimize dosing. By analyzing fecal microbiota, it was found that an early abundance of butyrate-producing bacteria was associated with patients' response to vedolizumab.
ALIMENTARY PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Biology
Mohammed Ghiboub, Jan Koster, Peter D. Craggs, Andrew Y. F. Li Yim, Anthony Shillings, Sue Hutchinson, Ryan P. Bingham, Kelly Gatfield, Ishtu L. Hageman, Gang Yao, Heather P. O'Keefe, Aaron Coffin, Amish Patel, Lisa A. Sloan, Darren J. Mitchell, Thomas G. Hayhow, Laurent Lunven, Robert J. Watson, Christopher E. Blunt, Lee A. Harrison, Gordon Bruton, Umesh Kumar, Natalie Hamer, John R. Spaull, Danny A. Zwijnenburg, Olaf Welting, Theodorus B. M. Hakvoort, Anje A. Te Velde, Johan van Limbergen, Peter Henneman, Rab K. Prinjha, Menno P. J. de Winther, Nicola R. Harker, David F. Tough, Wouter J. de Jonge
Summary: This study identifies SP140 as a druggable therapeutic target for Crohn's disease and develops the first SP140 inhibitor. Inhibiting SP140 reduces differentiation and activation of inflammatory macrophages while promoting the generation of regulatory macrophages, which is associated with therapeutic response to anti-TNF treatment in CD patients.
Article
Gastroenterology & Hepatology
Elsa A. van Wassenaer, Rick R. van Rijn, Sabrina L. M. Zwetsloot, Floris A. E. de Voogd, Joost van Schuppen, Angelika Kindermann, Tim G. J. de Meij, Johan E. van Limbergen, K. B. Gecse, Geert R. D'Haens, Marc A. Benninga, Bart G. P. Koot
Summary: In this prospective study, two intestinal ultrasound indices were validated and compared for scoring pediatric ulcerative colitis, and the UC-IUS index was found to be more accurate.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Gastroenterology & Hepatology
Charlotte M. Verburgt, Katherine A. Dunn, Mohammed Ghiboub, James D. Lewis, Eytan Wine, Rotem Sigall Boneh, Konstantinos Gerasimidis, Raanan Shamir, Susanne Penny, Devanand M. Pinto, Alejandro Cohen, Paul Bjorndahl, Vaios Svolos, Joseph P. Bielawski, Marc A. Benninga, Wouter J. de Jonge, Johan E. Van Limbergen
Summary: This study found that successful dietary therapy can correct dysbiosis in pediatric Crohn's disease (CD) patients, but 12 weeks of dieting is not enough to achieve complete correction. Composition and metabotype are important and change quickly during the early clinical response to dietary intervention. Correction of dysbiosis may be an important future treatment goal for CD.
JOURNAL OF CROHNS & COLITIS
(2023)
Article
Gastroenterology & Hepatology
Marzieh Akhlaghpour, Talin Haritunians, Shyam K. More, Lisa S. Thomas, Dalton T. Stamps, Shishir Dube, Dalin Li, Shaohong Yang, Carol J. Landers, Emebet Mengesha, Hussein Hamade, Ramachandran Murali, Alka A. Potdar, Andrea J. Wolf, Gregory J. Botwin, Michelle Khrom, Bana Int IBD Genetics, Ashwin N. Ananthakrishnan, William A. Faubion, Bana Jabri, Sergio A. Lira, Rodney D. Newberry, Robert S. Sandler, R. Balfour Sartor, Ramnik J. Xavier, Steven R. Brant, Judy H. Cho, Richard H. Duerr, Mark G. Lazarev, John D. Rioux, L. Philip Schumm, Mark S. Silverberg, Karen Zaghiyan, Phillip Fleshner, Gil Y. Melmed, Eric A. Vasiliauskas, Christina Ha, Shervin Rabizadeh, Gaurav Syal, Nirupama N. Bonthala, David A. Ziring, Stephan R. Targan, Millie D. Long, Dermot P. B. McGovern, Kathrin S. Michelsen
Summary: In this study, a genetic association was found between perianal Crohn's disease (pCD) and a mutation in the CFB gene, which impairs its function and contributes to the occurrence and development of pCD in patients with Crohn's disease.
Article
Pediatrics
Kelly M. A. Dreuning, Joep P. M. Derikx, Johan E. van Limbergen, Frea Kruisinga, Ilan J. N. Koppen
Summary: The infant with chylous ascites was unexpectedly found during surgery for bilateral inguinal hernia repair. With treatment and monitoring, the condition was controlled and the symptoms disappeared, allowing the child to successfully transition to regular feeding.
JOURNAL OF PEDIATRIC SURGERY CASE REPORTS
(2021)
