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Microbiome, crohn

Tiffany H Taft, Alyse Bedell, Meredith R Craven, Livia Guadagnoli, Sarah Quinton, Stephen B Hanauer
BACKGROUND: Post-traumatic stress (PTS), or the psycho-physiological response to a traumatic or life-threatening event, is implicated in medical patient outcomes. Emerging evidence suggests a complex relationship between PTS, the brain-gut axis, the gut microbiome, and immune function. Inflammatory bowel disease (IBD) may be susceptible to PTS and its subsequent impacts. To date, no study has evaluated PTS in IBD in the United States. METHODS: Adult patients with IBD were recruited from an outpatient gastroenterology practice, via social media, and via a research recruitment website...
March 7, 2019: Inflammatory Bowel Diseases
Ellen Li, Yuanhao Zhang, Xinyu Tian, Xuefeng Wang, Grace Gathungu, Ashley Wolber, Shehzad S Shiekh, R Balfour Sartor, Nicholas O Davidson, Matthew A Ciorba, Wei Zhu, Leah M Nelson, Charles E Robertson, Daniel N Frank
We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118)...
2019: PloS One
Robert H Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J Gonzalez
Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease...
January 2019: MSystems
Rishi M Goel, Erica M Prosdocimi, Ariella Amar, Yasmin Omar, Michael P Escudier, Jeremy D Sanderson, William G Wade, Natalie J Prescott
BACKGROUND: Orofacial granulomatosis (OFG) is a rare disease characterised by chronic, noncaseating, granulomatous inflammation primarily affecting the oral cavity. Histologically, it is similar to Crohn's disease (CD), and a proportion of patients have both OFG and CD. The cause of OFG remains elusive, but it has been suggested that microbial interactions may be involved. The aim of this study was to compare the salivary microbial composition of subjects with OFG and/or CD and healthy controls...
February 23, 2019: Inflammatory Bowel Diseases
Peter Allan Dobranowski, Chris Tang, Jean Philippe Sauvé, Susan Christine Menzies, Laura May Sly
Inflammatory bowel disease, encompassing both ulcerative colitis and Crohn's disease, is characterized by chronic, relapsing-remitting gastrointestinal inflammation of unknown etiology. SHIP deficient mice develop fully penetrant, spontaneous ileitis at 6 weeks of age, and thus offer a tractable model of Crohn's disease-like inflammation. Since disruptions to the microbiome are implicated in the pathogenesis of Crohn's disease, we conducted a 16S rRNA gene survey of the ileum, cecum, colon, and stool contents of SHIP+/+ and SHIP-/- mice...
February 13, 2019: Gut Microbes
Joby Pulikkan, Agnisrota Mazumder, Tony Grace
Autism spectrum disorder (ASD) is a severe neurodevelopmental or neuropsychiatric disorder with elusive etiology and obscure pathophysiology. Cognitive inabilities, impaired communication, repetitive behavior pattern, and restricted social interaction and communication lead to a debilitating situation in autism. The pattern of co-occurrence of medical comorbidities is most intriguing in autism, compared to any other neurodevelopmental disorders. They have an elevated comorbidity burden among which most frequently are seizures, psychiatric illness, and gastrointestinal disorders...
2019: Advances in Experimental Medicine and Biology
J Alfredo Blakeley-Ruiz, Alison R Erickson, Brandi L Cantarel, Weili Xiong, Rachel Adams, Janet K Jansson, Claire M Fraser, Robert L Hettich
BACKGROUND: The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues...
February 11, 2019: Microbiome
Tzipi Braun, Ayelet Di Segni, Marina BenShoshan, Sandra Neuman, Nina Levhar, Michael Bubis, Orit Picard, Katya Sosnovski, Gilat Efroni, Sarit Farage Barhom, Efrat Glick Saar, Avishay Lahad, Batia Weiss, Doron Yablecovitch, Adi Lahat, Rami Eliakim, Uri Kopylov, Shomron Ben-Horin, Yael Haberman
OBJECTIVES: Crohn's disease (CD) is a chronic relapsing-remitting gut inflammatory disorder with a heterogeneous unpredictable course. Dysbiosis occurs in CD; however, whether microbial dynamics in quiescent CD are instrumental in increasing the risk of a subsequent flare remains undefined. METHODS: We analyzed the long-term dynamics of microbial composition in a prospective observational cohort of patients with quiescent CD (45 cases, 217 samples) over 2 years or until clinical flare occurred, aiming to identify whether changes in the microbiome precede and predict clinical relapse...
February 5, 2019: American Journal of Gastroenterology
Jonathan P Segal, Benjamin H Mullish, Mohammed Nabil Quraishi, Animesh Acharjee, Horace R T Williams, Tariq Iqbal, Ailsa L Hart, Julian R Marchesi
The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these...
2019: Therapeutic Advances in Gastroenterology
Alexandra Paun, Christopher Yau, Shahab Meshkibaf, Michelle C Daigneault, Leili Marandi, Steven Mortin-Toth, Amit Bar-Or, Emma Allen-Vercoe, Philippe Poussier, Jayne S Danska
Microbiome sequence analyses have suggested that changes in gut bacterial composition are associated with autoimmune disease in humans and animal models. However, little is known of the mechanisms through which the gut microbiota influences autoimmune responses to distant tissues. Here, we evaluated systemic antibody responses against cultured human gut bacterial strains to determine whether observed patterns of anticommensal antibody (ACAb) responses are associated with type 1 diabetes (T1D) in two cohorts of pediatric study participants...
February 1, 2019: Science Immunology
Valerie Collij, Floris Imhann, Arnau Vich Vila, Jingyuan Fu, Gerard Dijkstra, Eleonora A M Festen, Michiel D Voskuil, Mark J Daly, Ramnik J Xavier, Cisca Wijmenga, Alexandra Zhernakova, Rinse K Weersma
BACKGROUND: Gene-microbiome interactions are important in aetiology and pathogenesis of inflammatory bowel disease, a chronic inflammatory disorder of the gastrointestinal tract consisting of Crohn's disease and ulcerative colitis. Scarce studies on gene-microbiome interactions show very little overlap in their results. Therefore, it is of utmost importance that gene-microbiome studies are repeated. We aimed to replicate the association between the SLC39A8 [Thr]391 risk allele and gut microbiome composition in patients with inflammatory bowel disease and healthy controls...
2019: PloS One
Eduardo J Contijoch, Graham J Britton, Chao Yang, Ilaria Mogno, Zhihua Li, Ruby Ng, Sean R Llewellyn, Sheela Hira, Crystal Johnson, Keren M Rabinowitz, Revital Barkan, Iris Dotan, Robert P Hirten, Shih-Chen Fu, Yuying Luo, Nancy Yang, Tramy Luong, Philippe R Labrias, Sergio Lira, Inga Peter, Ari Grinspan, Jose C Clemente, Roman Kosoy, Seunghee Kim-Schulze, Xiaochen Qin, Anabella Castillo, Amanda Hurley, Ashish Atreja, Jason Rogers, Farah Fasihuddin, Merjona Saliaj, Amy Nolan, Pamela Reyes-Mercedes, Carina Rodriguez, Sarah Aly, Kenneth Santa-Cruz, Lauren Peters, Mayte Suárez-Fariñas, Ruiqi Huang, Ke Hao, Jun Zhu, Bin Zhang, Bojan Losic, Haritz Irizar, Won-Min Song, Antonio Di Narzo, Wenhui Wang, Benjamin L Cohen, Christopher DiMaio, David Greenwald, Steven Itzkowitz, Aimee Lucas, James Marion, Elana Maser, Ryan Ungaro, Steven Naymagon, Joshua Novak, Brijen Shah, Thomas Ullman, Peter Rubin, James George, Peter Legnani, Shannon E Telesco, Joshua R Friedman, Carrie Brodmerkel, Scott Plevy, Judy H Cho, Jean-Frederic Colombel, Eric E Schadt, Carmen Argmann, Marla Dubinsky, Andrew Kasarskis, Bruce Sands, Jeremiah J Faith
To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis...
January 22, 2019: ELife
Natalie C Knox, Jessica D Forbes, Gary Van Domselaar, Charles N Bernstein
PURPOSE OF REVIEW: This review aims to highlight recent research on the gut microbiome in IBD and the application of microbiome-modulating therapies for the treatment of IBD including the use of the microbiome as an indicator for disease severity and treatment response. RECENT FINDINGS: Despite the high number of gut microbiome studies and emerging evidence supporting the gut microbiome's involvement in disease pathogenesis, no single microorganism has been identified as a pathogenic agent in IBD...
January 19, 2019: Current Treatment Options in Gastroenterology
Bernard C Lo, Samuel B Shin, Diana Canals Hernaez, Ido Refaeli, Hong B Yu, Verena Goebeler, Alissa Cait, William W Mohn, Bruce A Vallance, Kelly M McNagny
The cytokine IL-22 is rapidly induced at barrier surfaces where it regulates host-protective antimicrobial immunity and tissue repair but can also enhance disease severity in some chronic inflammatory settings. Using the chronic Salmonella gastroenteritis model, Ab-mediated neutralization of IL-22 impaired intestinal epithelial barrier integrity and, consequently, exaggerated expression of proinflammatory cytokines. As disease normally resolved, neutralization of IL-22 caused luminal narrowing of the cecum-a feature reminiscent of fibrotic strictures seen in Crohn disease patients...
February 1, 2019: Journal of Immunology: Official Journal of the American Association of Immunologists
Guilherme Piovezani Ramos, Konstantinos A Papadakis
Inflammatory bowel diseases (IBDs), represented by Crohn disease and ulcerative colitis, are associated with major morbidity in Western countries and with increasing incidence in the developing world. Although analysis of the genome of patients with IBD, especially through genome-wide association studies, has unraveled multiple pathways involved in IBD pathogenesis, only part of IBD heritability has been explained by genetic studies. This finding has revealed that environmental factors also play a major role in promoting intestinal inflammation, mostly through their effects in the composition of the microbiome...
January 2019: Mayo Clinic Proceedings
Rosa Reddavide, Ornella Rotolo, Maria Gabriella Caruso, Elisa Stasi, Maria Notarnicola, Chiara Miraglia, Antonio Nouvenne, Tiziana Meschi, Gian Luigi De' Angelis, Francesco Di Mario, Gioacchino Leandro
Inflammatory bowel diseases (IBD) - Crohn's disease (CD) and ulcerative colitis (UC) - are chronic conditions characterised by relapsing inflammation of the gastrointestinal tract. They represent an increasing public health concern and an aetiological enigma due to unknown causal factors. The current knowledge on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to a dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers...
December 17, 2018: Acta Bio-medica: Atenei Parmensis
V Svolos, R Hansen, B Nichols, C Quince, U Z Ijaz, R T Papadopoulou, C A Edwards, D Watson, A Alghamdi, A Brejnrod, C Ansalone, H Duncan, L Gervais, R Tayler, J Salmond, D Bolognini, R Klopfleisch, D R Gaya, S Milling, R K Russell, K Gerasimidis
BACKGROUND & AIMS: Exclusive enteral nutrition (EEN) is the only established dietary treatment for Crohn's disease (CD), but its acceptability is limited. There is a need for novel dietary treatments for CD. METHODS: We evaluated the effects of an individualized, food-based diet (CD-TREAT), with similar composition to EEN, on the gut microbiome, inflammation and clinical response in a rat model, healthy adults, and children with relapsing CD. Twenty-five healthy adults randomly received EEN or CD-TREAT for 7 days, followed by a 14-day washout period, followed by the alternate diet...
December 11, 2018: Gastroenterology
Jessica D Forbes, Chih-Yu Chen, Natalie C Knox, Ruth-Ann Marrie, Hani El-Gabalawy, Teresa de Kievit, Michelle Alfa, Charles N Bernstein, Gary Van Domselaar
BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23)...
December 13, 2018: Microbiome
Zev H Davidovics, Sonia Michail, Maribeth R Nicholson, Larry K Kociolek, Nikhil Pai, Richard Hansen, Tobias Schwerd, Aldo Maspons, Raanan Shamir, Hania Szajewska, Nikhil Thapar, Tim de Meij, Alexis Mosca, Yvan Vandenplas, Stacy A Kahn, Richard Kellermayer
Fecal microbiota transplantation (FMT) is becoming part of the treatment algorithms against recurrent Clostridium difficile infection (rCDI) both in adult and pediatric gastroenterology practice. With our increasing recognition of the critical role the microbiome plays in human health and disease, FMT is also being considered as a potential therapy for other disorders, including inflammatory bowel disease (Crohn disease, ulcerative colitis), graft versus host disease, neuropsychiatric diseases, and metabolic syndrome...
January 2019: Journal of Pediatric Gastroenterology and Nutrition
Eric A Franzosa, Alexandra Sirota-Madi, Julian Avila-Pacheco, Nadine Fornelos, Henry J Haiser, Stefan Reinker, Tommi Vatanen, A Brantley Hall, Himel Mallick, Lauren J McIver, Jenny S Sauk, Robin G Wilson, Betsy W Stevens, Justin M Scott, Kerry Pierce, Amy A Deik, Kevin Bullock, Floris Imhann, Jeffrey A Porter, Alexandra Zhernakova, Jingyuan Fu, Rinse K Weersma, Cisca Wijmenga, Clary B Clish, Hera Vlamakis, Curtis Huttenhower, Ramnik J Xavier
The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients...
December 10, 2018: Nature Microbiology
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