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microbiome and IBD

Christopher John Kiely, Paul Pavli, Claire Louise O'Brien
Studies of the human intestinal microbiome in patients with inflammatory bowel disease (IBD) consistently show that there are differences (an abnormal or unbalanced microbiome, "dysbiosis") when compared to healthy subjects. We sought to describe changes in the microbiome in individual patients over time, and determine the clinical factors that are associated with significant alteration. Forty-two mucosal biopsies were collected from 20 patients that were spaced an average of 2.4 years apart. These were analysed using bacterial 16S rRNA gene high-throughput sequencing methods...
March 15, 2018: Gut Microbes
Rene Y Choi, Mark Asquith, James T Rosenbaum
PURPOSE OF REVIEW: The intestinal microbiome is thought to play a role in the pathogenesis of inflammatory bowel disease (IBD). There are many shared clinical manifestations between IBD and spondyloarthritis (SpA), of which the most common are peripheral arthritis and uveitis. Clinical overlap along with similar genetics between these diseases suggests a possible shared pathogenetic mechanism, which might center on the intestinal microbiota. In this review, we discuss the available evidence that SpA is a microbiome-driven disease and indicate how SpA-associated uveitis could be tied to gut dysbiosis...
March 13, 2018: Current Opinion in Rheumatology
Andrew Leber, Raquel Hontecillas, Nuria Tubau-Juni, Victoria Zoccoli-Rodriguez, Vida Abedi, Josep Bassaganya-Riera
Interactions among the gut microbiome, dysregulated immune responses, and genetic factors contribute to the pathogenesis of inflammatory bowel disease (IBD). Nlrx1 -/- mice have exacerbated disease severity, colonic lesions, and increased inflammatory markers. Global transcriptomic analyses demonstrate enhanced mucosal antimicrobial defense response, chemokine and cytokine expression, and epithelial cell metabolism in colitic Nlrx1 -/- mice compared to wild-type (WT) mice. Cell-specificity studies using cre-lox mice demonstrate that the loss of NLRX1 in intestinal epithelial cells (IEC) recapitulate the increased sensitivity to DSS colitis observed in whole body Nlrx1 -/- mice...
2018: Frontiers in Immunology
Stanislav Sitkin, Timur Vakhitov, Juris Pokrotnieks
No abstract text is available yet for this article.
March 8, 2018: Journal of Crohn's & Colitis
Rachel Mak'Anyengo, Peter Duewell, Cornelia Reichl, Christine Hörth, Hans-Anton Lehr, Sandra Fischer, Thomas Clavel, Gerald Denk, Simon Hohenester, Sebastian Kobold, Stefan Endres, Max Schnurr, Christian Bauer
Inflammatory bowel disease (IBD) is associated with enhanced levels of the IL-1 family cytokines IL-1β and IL-18, which are activated by the Nlrp3 inflammasome. Here, we investigated the role of inflammasome-driven cytokine release on T cell polarization and DC differentiation in steady state and T cell transfer colitis. In vitro and in vivo data showed that IL-1β induces Th17 polarization and increases GM‑CSF production by T cells. Reduced IL-1β levels in Nlrp3-/- mice correlated with enhanced FLT3L levels and increased frequency of tolerogenic CD103+ DC...
March 8, 2018: JCI Insight
Shlomit David, Carmit Shani Levi, Lulu Fahoum, Yael Ungar, Esther G Meyron-Holtz, Avi Shpigelman, Uri Lesmes
Carrageenan (CGN), a family of marine polysaccharides isolated from seaweeds, has been at the heart of considerable debate in recent years. To date, CGN is generally recognized as safe based on a history of safe use, various acute toxicology studies and some recent chronic toxicology tests. This review offers readers an overview of evidence on CGN characteristics and digestive fate that highlight various gaps in our understanding. Specifically, three unresolved gaps are identified. Firstly, little information can be found on the current levels of public exposure to CGN...
February 22, 2018: Food & Function
Aonghus Lavelle, Harry Sokol
No abstract text is available yet for this article.
February 21, 2018: Nature Reviews. Gastroenterology & Hepatology
Berkeley N Limketkai, Andrea Wolf, Alyssa M Parian
Nutritional strategies have been explored as primary or adjunct therapies for inflammatory bowel disease (IBD). Exclusive enteral nutrition is effective for the induction of remission in Crohn disease and is recommended as a first-line therapy for children. Dietary strategies focus on adjusting the ratio of consumed nutrients that are proinflammatory or antiinflammatory. Treatments with dietary supplements focus on the antiinflammatory effects of the individual supplements (eg, curcumin, omega-3 fatty acids, vitamin D) or their positive effects on the intestinal microbiome (eg, prebiotics, probiotics)...
March 2018: Gastroenterology Clinics of North America
J L Damman, E A Rodriguez, A H Ali, C W Buness, K L Cox, E J Carey, K D Lindor
BACKGROUND AND AIMS: PSC is an autoimmune biliary inflammatory disorder that is often associated with inflammatory bowel disease (IBD), with 50%-75% of patients with PSC having coexisting IBD, most commonly ulcerative colitis. Currently, no medical therapies have been shown to improve the disease course or slow its progression. However, ongoing research has resulted in a growing interest in the use of antibiotics for treatment of PSC, of which vancomycin is the most studied. In this review, we summarise the current evidence on the use of vancomycin in PSC and comment on future research areas of interest...
February 7, 2018: Alimentary Pharmacology & Therapeutics
Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, Amnon Amir, Antonio González, Anupriya Tripathi, Minhu Chen, Gary D Wu, Rob Knight, Hongwei Zhou, Ye Chen
Gut microbiota dysbiosis contributes to the onset and perpetuation of inflammatory bowel disease (IBD). Given that gut microbiotas vary across geography and ethnicity, it remains obscure whether any universal microbial signatures for IBD diagnosis and prognosis evaluation exist irrespective of populations. Here we profiled the fecal microbiota of a series of Chinese IBD patients and combined them with two Western IBD cohorts, PRISM and RISK, for meta-analyses. We found that the gut microbial alteration patterns in IBD are similar among Chinese and Westerners...
January 2018: MSystems
Mingming Yin, Xuebing Yan, Wenhao Weng, Yongzhi Yang, Renyuan Gao, Minfeng Liu, Cheng Pan, Qi Zhu, Hao Li, Qing Wei, Tongyi Shen, Yanlei Ma, Huanlong Qin
BACKGROUND/AIMS: Recent studies have demonstrated that the manipulation of the gut microbiome represents a promising treatment for inflammatory bowel disease (IBD). We previously identified micro integral membrane protein (MIMP) as the smallest domain of surface layer protein from Lactobacillus Plantarum. However, the therapeutic relevance of MIMP in IBD remains unknown. METHODS: We initially employed a dextran sodium sulphate (DSS)-induced colitis model and evaluated the effect of MIMP on the inflammation response, intestinal barrier and gut microbiota using histological examination, Fluorescein isothiocyanate-Dextran detection and pyrosequencing analysis respectively...
January 25, 2018: Cellular Physiology and Biochemistry
Alireza Bolourian, Zahra Mojtahedi
Resistance to a drug and the suppression of inflammatory disorders with immunosuppressive drugs might have happened upon exposure to natural compounds during evolution. Streptomycetes are soil bacteria, but they produce therapeutic drugs. They have been reported to be the low-abundant members of mucosal microbiomes with a higher prevalence in nonhumans ingesting soil compared to humans. Their lower abundance in the human microbiome might be the representations of our current hygienic lifestyle. We suggest that the Streptomyces bacteria producing antiproliferative/immunosuppressive compounds (e...
January 26, 2018: Environmental Microbiology Reports
Alka Goyal, Andrew Yeh, Brian R Bush, Brian A Firek, Leah M Siebold, Matthew Brian Rogers, Adam D Kufen, Michael J Morowitz
Background: The role of fecal microbiota transplant (FMT) in the treatment of pediatric inflammatory bowel disease (IBD) is unknown. The aims of this study were to assess safety, clinical response, and gut microbiome alterations in children with Crohn's disease (CD), ulcerative colitis (UC), or indeterminate colitis (IC). Methods: In this open-label, single-center prospective trial, patients with IBD refractory to medical therapy underwent a single FMT by upper and lower endoscopy...
January 18, 2018: Inflammatory Bowel Diseases
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
Joseph F Pierre, Reinhard Hinterleitner, Romain Bouziat, Nathan A Hubert, Vanessa Leone, Jun Miyoshi, Bana Jabri, Eugene B Chang
Inflammatory bowel diseases (IBD) are caused by the convergence of microbial, environmental, and genetic factors. Diet significantly alters these interactions by affecting both the host and microbiome. Using a mucosal inflammatory model that resembles the human condition of ileal pouchitis, we investigated the effects of Control (CONT) or Antioxidant (AOX) diet, containing pharmacologically relevant levels of 4 micronutrients, on disease risk in wild-type and IL-10-/- animals following surgical self-filling (SF) ileal blind loop placement...
December 10, 2017: Journal of Nutritional Biochemistry
Sandra Maria Barbalho, Ricardo de Alvares Goulart, Ana Luíza de Carvalho Aranão, Pamela Grazielle Correa de Oliveira
Inflammatory bowel diseases (IBDs) are mainly represented by ulcerative colitis and Crohn's disease, and the increase in the incidence tends to follow the rapid industrialization and lifestyle of modern societies. FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) consist of molecules that are poorly absorbed in the small intestine and are fermented by bacteria in the colon leading to symptoms such as bloating, flatulence, diarrhea, and abdominal pain. Reduction of the ingestion of FODMAP could reduce the symptoms and improve the quality of life...
January 12, 2018: Journal of Medicinal Food
Fernando Lopes, Åsa V Keita, Alpana Saxena, Jose Luis Reyes, Nicole Mancini, Ala Al Rajabi, Arthur Wang, Cristiane Baggio, Michael Dicay, Rob van Dalen, Younghee Ahn, Matheus Carneiro, Nathan Peters, Jong M Rho, Wallace MacNaughton, Stephan E Girardin, Humberto Jijon, Dana J Philpott, Johan D Söderholm, Derek M McKay
The gut microbiome contributes to inflammatory bowel disease (IBD), in which bacteria can be present within the epithelium. Epithelial barrier function is decreased in IBD, and dysfunctional epithelial mitochondria and endoplasmic reticulum (ER) stress have been individually associated with IBD. We therefore hypothesized that the combination of ER and mitochondrial stresses significantly disrupt epithelial barrier function. Here, we treated human colonic biopsies, epithelial colonoids, and epithelial cells with an uncoupler of oxidative phosphorylation, dinitrophenol (DNP), with or without the ER stressor tunicamycin, and assessed epithelial barrier function by monitoring internalization and translocation of commensal bacteria...
January 9, 2018: Journal of Biological Chemistry
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G Wilson, Jonathan Braun, Lee A Denson, Subra Kugathasan, Dermot P B McGovern, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period...
January 8, 2018: Nature Microbiology
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
BACKGROUND: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. METHODS: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2...
November 28, 2017: Genome Medicine
Anjelique F Schulfer, Thomas Battaglia, Yelina Alvarez, Luc Bijnens, Victoria E Ruiz, Melody Ho, Serina Robinson, Tonya Ward, Laura M Cox, Arlin B Rogers, Dan Knights, R Balfour Sartor, Martin J Blaser
Antibiotic exposure in children has been associated with the risk of inflammatory bowel disease (IBD). Antibiotic use in children or in their pregnant mother can affect how the intestinal microbiome develops, so we asked whether the transfer of an antibiotic-perturbed microbiota from mothers to their children could affect their risk of developing IBD. Here we demonstrate that germ-free adult pregnant mice inoculated with a gut microbial community shaped by antibiotic exposure transmitted their perturbed microbiota to their offspring with high fidelity...
February 2018: Nature Microbiology
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