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Microbiome, crohn

Livia Lindoso, Kajari Mondal, Suresh Venkateswaran, Hari K Somineni, Cortney Ballengee, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace Crandall, Scott Snapper, Shervin Rabizadeh, Joel R Rosh, Neal LeLeiko, Stephen Guthery, David Mack, Richard Kellermayer, Ajay S Gulati, Marian D Pfefferkorn, Dedrick E Moulton, David Keljo, Stanley Cohen, Maria Oliva-Hemker, Melvin B Heyman, Anthony Otley, Susan S Baker, Jonathan S Evans, Barbara S Kirschner, Ashish S Patel, David Ziring, Michael C Stephens, Robert Baldassano, Marla C Dubinsky, James Markowitz, Lee A Denson, Jeffrey Hyams, Subra Kugathasan, Ashwin N Ananthakrishnan
OBJECTIVES: Environmental factors play an important role in the pathogenesis of Crohn's Disease (CD). In particular, by virtue of the instability of the microbiome and development of immunologic tolerance, early life factors may exert the strongest influence on disease risk and phenotype. METHODS: We used data from 1119 CD subjects recruited from RISK inception cohort to examine the impact of early life environment on disease progression. Our primary exposures of interest were breastfeeding in infancy and exposure to maternal, active, or passive smoke...
September 28, 2018: American Journal of Gastroenterology
Miranda G Kiernan, J Calvin Coffey, Kieran McDermott, Paul D Cotter, Raul Cabrera-Rubio, Patrick A Kiely, Colum P Dunne
Background and Aims: Mesenteric lymph nodes are sites in which translocated bacteria incite and progress immunological responses. For this reason, understanding the microbiome of mesenteric lymph nodes in inflammatory bowel disease is important. The bacterial profile of Crohn's disease mesenteric lymph nodes has been analysed using culture-independent methods in only one previous study. This study aimed to investigate the mesenteric lymph node microbiota from both Crohn's disease and ulcerative colitis patients...
September 15, 2018: Journal of Crohn's & Colitis
Bjoern Titz, Raffaella M Gadaleta, Giuseppe Lo Sasso, Ashraf Elamin, Kim Ekroos, Nikolai V Ivanov, Manuel C Peitsch, Julia Hoeng
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD...
September 15, 2018: International Journal of Molecular Sciences
Seyed-Amir Tabatabaeizadeh, Niayesh Tafazoli, Gordon A Ferns, Amir Avan, Majid Ghayour-Mobarhan
Vitamin D has an important role in bone metabolism but recently has been recognized as an immunoregulator, and this has led to investigations on the effect of Vitamin D supplementation in various autoimmune diseases and its anti-inflammatory effects. There is some evidence that Vitamin D can regulate gastrointestinal inflammation. In addition, previous studies have shown that Vitamin D can affect the gut microbiome. The aim of this review is to evaluate the effect of Vitamin D on inflammatory processes, especially its relation to the inflammatory bowel disease (IBD) and gut microbiome...
2018: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
Simon Ghaly, Nadeem O Kaakoush, Frances Lloyd, Lavinia Gordon, Cynthia Forest, Ian C Lawrance, Prue H Hart
Reduced sunlight exposure has been associated with an increased incidence of Crohn's disease and ulcerative colitis. The effect of ultraviolet radiation (UVR) on the faecal microbiome and susceptibility to colitis has not been explored. C57Bl/6 female mice were fed three different vitamin D-containing diets for 24 days before half of the mice in each group were UV-irradiated (1 kJ/m²) for each of four days, followed by twice-weekly irradiation of shaved dorsal skin for 35 days. Faecal DNA was extracted and high-throughput sequencing of the 16S RNA gene performed...
August 11, 2018: Nutrients
Patrick H Bradley, Stephen Nayfach, Katherine S Pollard
The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation...
August 2018: PLoS Computational Biology
Annabel Kleinwort, Paula Döring, Christine Hackbarth, Maciej Patrzyk, Claus-Dieter Heidecke, Tobias Schulze
Diversion colitis (DC) is a frequent clinical condition occurring in patients with bowel segments excluded from the fecal stream as a result of a diverting enterostomy. The etiology of this disease remains ill-defined but appears to differ from that of classical inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. Research aimed to decipher the pathophysiological mechanisms leading to the development of this disease has been severely hampered by the lack of an appropriate murine model...
July 12, 2018: Journal of Visualized Experiments: JoVE
J Rivera-Pinto, J J Egozcue, V Pawlowsky-Glahn, R Paredes, M Noguera-Julian, M L Calle
High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest...
July 2018: MSystems
Emilie H Regner, Neha Ohri, Andrew Stahly, Mark E Gerich, Blair P Fennimore, Diana Ir, Widian K Jubair, Carsten Görg, Janet Siebert, Charles E Robertson, Liron Caplan, Daniel N Frank, Kristine A Kuhn
BACKGROUND: Dysbiosis occurs in spondyloarthritis (SpA) and inflammatory bowel disease (IBD), which is subdivided into Crohn's disease (CD) and ulcerative colitis (UC). The immunologic consequences of alterations in microbiota, however, have not been defined. Intraepithelial lymphocytes (IELs) are T cells within the intestinal epithelium that are in close contact with bacteria and are likely to be modulated by changes in microbiota. We examined differences in human gut-associated bacteria and tested correlation with functional changes in IELs in patients with axial SpA (axSpA), CD, or UC, and in controls...
July 20, 2018: Arthritis Research & Therapy
Jun Miyoshi, Mark Anthony Sofia, Joseph Francis Pierre
Current evidence suggests the etiology of inflammatory bowel diseases (IBD) involves the confluence of host genetic, environmental, and microbial factors that lead to chronic, and often refractory, disease in susceptible individuals. The involvement of microbial triggers in IBD, including Crohn's disease (CD), is increasingly evident with supporting data provided with advancements in metagenomic sequencing that have identified perturbations in microbial structure and function-broadly termed dysbiosis-in CD patients compared with healthy subjects...
July 19, 2018: Clinical Journal of Gastroenterology
Charles N Bernstein, Jessica D Forbes
Background: Since the description of the normal human gut microbiome in healthy individuals using broad-range polymerase chain reaction, there has been great advancement in the techniques used to conduct microbiome research and applications of this research across health, gastrointestinal diseases, and nongastrointestinal diseases. Summary and Key Messages: In inflammatory bowel disease (IBD), studies have reported gut dysbiosis meaning that the microbial composition, diversity, and richness are altered...
November 2017: Inflammatory Intestinal Diseases
Benjamin Wingfield, Sonya Coleman, Thomas M McGinnity, Anthony Bjourson
Inflammatory Bowel Disease (IBD) is an umbrella term for a group of inflammatory diseases of the gastrointestinal tract, including Crohn's Disease and ulcerative colitis. Changes to the intestinal microbiome, the community of micro-organisms that resides in the human gut, have been shown to contribute to the pathogenesis of IBD. IBD diagnosis is often delayed due its non-specific symptoms and because an invasive colonoscopy is required for confirmation, which leads to poor growth in children and worse treatment outcomes...
April 30, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Noam Jacob, Jonathan P Jacobs, Kotaro Kumagai, Connie W Y Ha, Yoshitake Kanazawa, Venu Lagishetty, Katherine Altmayer, Ariel M Hamill, Aimee Von Arx, R Balfour Sartor, Suzanne Devkota, Jonathan Braun, Kathrin S Michelsen, Stephan R Targan, David Q Shih
Tumor necrosis factor-like cytokine 1A (TL1A, TNFSF15) is implicated in inflammatory bowel disease (IBD), modulating the location and severity of intestinal inflammation and fibrosis. TL1A expression is increased in inflamed gut mucosa and associated with fibrostenosing Crohn's disease. Tl1a-overexpression in mice lead to spontaneous ileitis, and exacerbated induced proximal colitis and fibrosis. IBD is associated with shifts in the gut microbiome, but the effect of differing microbial populations and their interaction with TL1A on fibrosis has not been investigated...
September 2018: Mucosal Immunology
Thomas Klag, Jan Wehkamp
New promising treatment options for chronic inflammatory bowel diseases, confirm the expanded pathophysiological understanding in terms of the interactions of the gastrointestinal microbiome with the adaptive and innate immune response and barrier protection. Therefore, these interrelations are focus of research and therapeutic strategies. The following review will give insights into the pathomechanisms, current treatment options and future developments.
July 2018: Deutsche Medizinische Wochenschrift
Ehsaneddin Asgari, Kiavash Garakani, Alice C McHardy, Mohammad R K Mofrad
Motivation: Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture and forensic science...
July 1, 2018: Bioinformatics
Zhe Xun, Qian Zhang, Tao Xu, Ning Chen, Feng Chen
Inflammatory bowel diseases (IBDs) are chronic, idiopathic, relapsing disorders of unclear etiology affecting millions of people worldwide. Aberrant interactions between the human microbiota and immune system in genetically susceptible populations underlie IBD pathogenesis. Despite extensive studies examining the involvement of the gut microbiota in IBD using culture-independent techniques, information is lacking regarding other human microbiome components relevant to IBD. Since accumulated knowledge has underscored the role of the oral microbiota in various systemic diseases, we hypothesized that dissonant oral microbial structure, composition, and function, and different community ecotypes are associated with IBD; and we explored potentially available oral indicators for predicting diseases...
2018: Frontiers in Microbiology
Umut Gazi, Martha Emmanuel Agada, Hanife Ozkayalar, Ceyhun Dalkan, Burcin Sanlidag, Mustafa Asım Safak, Gamze Mocan, Nerin Onder Bahceciler
INTRODUCTION: PFAPA (periodic fever, aphthous stomatitis, pharyngitis and cervical adenitis) is the most frequent non-infectious cause of high fever observed among the European child population. While its cause is still not yet fully identified, PFAPA patients were previously shown to have altered tonsillar microbiome composition. Our study hypothesized that this is associated with a change in antimicrobial peptide (AMP) expression levels, as in the case of Crohn's disease which is another autoinflammatory disorder...
July 2018: International Journal of Pediatric Otorhinolaryngology
Ashleigh Goethel, Kenneth Croitoru, Dana J Philpott
The aetiology and pathogenesis of inflammatory bowel disease (IBD) remains unclear but involves a complex interplay between genetic risk, environmental exposures, the immune system and the gut microbiota. Nearly two decades ago, the first susceptibility gene for Crohn's disease, NOD2, was identified within the IBD 1 locus. Since then, over 230 genetic risk loci have been associated with IBD and yet NOD2 remains the strongest association to date. As an intracellular innate immune sensor of bacteria, investigations into host-microbe interactions, involving both innate and adaptive immune responses, have become of particular interest in understanding the pathogenesis of IBD...
September 2018: Journal of Physiology
Agnieszka Smolinska, Danyta I Tedjo, Lionel Blanchet, Alexander Bodelier, Marieke J Pierik, Ad A M Masclee, Jan Dallinga, Paul H M Savelkoul, Daisy M A E Jonkers, John Penders, Frederik-Jan van Schooten
Microbiota composition and its metabolic capacity are very important for host health. Evidence suggests that gut microbiome is involved in the metabolites production by host-microbiome interaction. These metabolites can be absorbed in blood and excreted in exhaled air. Although, profiles of gut microbiota and exhaled metabolites were associated with gastrointestinal diseases, a direct link between them has not yet been investigated. The aim of the study was to investigate the relation between volatiles in breath and gut microbiome in active and quiescent Crohn's disease (CD) via a multivariate statistical approach...
September 26, 2018: Analytica Chimica Acta
Hamed Khalili, Simon S M Chan, Paul Lochhead, Ashwin N Ananthakrishnan, Andrew R Hart, Andrew T Chan
Crohn's disease and ulcerative colitis, collectively known as IBD, are chronic inflammatory disorders of the gastrointestinal tract. Although the aetiopathogenesis of IBD is largely unknown, it is widely thought that diet has a crucial role in the development and progression of IBD. Indeed, epidemiological and genetic association studies have identified a number of promising dietary and genetic risk factors for IBD. These preliminary studies have led to major interest in investigating the complex interaction between diet, host genetics, the gut microbiota and immune function in the pathogenesis of IBD...
September 2018: Nature Reviews. Gastroenterology & Hepatology
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