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Microbiome and gut stem cell

Juan Gea-Banacloche, Krishna Komanduri, Paul Carpenter, Sophie Paczesny, Stefanie Sarantopoulos, Jo-Anne Young, Nahed El Kassar, Robert Q Le, Kirk Schultz, Linda M Griffith, Bipin Savani, John R Wingard
Immune reconstitution following hematopoietic stem cell transplantation (HCT) beyond one year is not completely understood. Many transplant recipients who are free of graft versus host disease (GVHD) and not receiving any immunosuppression more than a year after transplant seem to be able to mount appropriate immune responses to common pathogens and respond adequately to immunizations. However, two large registry studies over the last two decades seem to indicate that infection is a significant cause of late mortality in some patients, even in the absence of concomitant GVHD...
October 14, 2016: Biology of Blood and Marrow Transplantation
Sachin Goyal, Pratima Nangia-Makker, Lulu Farhana, Yingjie Yu, Adhip Pn Majumdar
Over the past two decades there has been remarkable progress in cancer diagnosis, treatment and screening. The basic mechanisms leading to pathogenesis of various types of cancers are also understood better and some patients, if diagnosed at a particular stage go on to lead a normal pre-diagnosis life. Despite these achievements, racial disparity in some cancers remains a mystery. The higher incidence, aggressiveness and mortality of breast, prostate and colorectal cancers (CRCs) in African-Americans as compared to Caucasian-Americans are now well documented...
September 26, 2016: World Journal of Stem Cells
J Whangbo, J Ritz, A Bhatt
Allogeneic hematopoietic stem cell transplantation (HSCT) is curative for many patients with severe benign and malignant hematologic disorders. The success of allogeneic HSCT is limited by the development of transplant-related complications such as acute graft-versus-host disease (GvHD). Early pre-clinical studies suggested that intestinal microflora contribute to the pathogenesis of acute GvHD, and that growth suppression or eradication of intestinal bacteria prevented the development of acute GvHD even in MHC-mismatched transplants...
August 15, 2016: Bone Marrow Transplantation
Jason W Arnold, Jeffrey Roach, M Andrea Azcarate-Peril
Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking...
July 14, 2016: Trends in Microbiology
Frank Stämmler, Joachim Gläsner, Andreas Hiergeist, Ernst Holler, Daniela Weber, Peter J Oefner, André Gessner, Rainer Spang
BACKGROUND: Next-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of the mammalian gut microbiomes. However, in the absence of a reference, this does not reveal alterations in absolute abundance of specific operational taxonomic units if microbial loads vary across specimens. RESULTS: Here we suggest the spiking of exogenous bacteria into crude specimens to quantify ratios of absolute bacterial abundances. We use the 16S rDNA read counts of the spike-in bacteria to adjust the read counts of endogenous bacteria for changes in total microbial loads...
2016: Microbiome
Joshua E Denny, Whitney L Powell, Nathan W Schmidt
Preservation of health from infectious diseases depends upon both mucosal and systemic immunity via the collaborative effort of innate and adaptive immune responses. The proficiency of host immunity stems from robust defense mechanisms--physical barriers and specialized immune cells--and a failure of these mechanisms leads to pathology. Intriguingly, immunocompetence to pathogens can be shaped by the gut microbiome as recent publications highlight a dynamic interplay between the gut microbiome and host susceptibility to infection...
2016: Frontiers in Cellular and Infection Microbiology
Emmanuel Montassier, Gabriel A Al-Ghalith, Tonya Ward, Stephane Corvec, Thomas Gastinne, Gilles Potel, Phillipe Moreau, Marie France de la Cochetiere, Eric Batard, Dan Knights
BACKGROUND: Bacteremia, or bloodstream infection (BSI), is a leading cause of death among patients with certain types of cancer. A previous study reported that intestinal domination, defined as occupation of at least 30 % of the microbiota by a single bacterial taxon, is associated with BSI in patients undergoing allo-HSCT. However, the impact of the intestinal microbiome before treatment initiation on the risk of subsequent BSI remains unclear. Our objective was to characterize the fecal microbiome collected before treatment to identify microbes that predict the risk of BSI...
2016: Genome Medicine
Andrew E Rosselot, Christian I Hong, Sean R Moore
PURPOSE OF REVIEW: To highlight recent developments in understanding the dynamic relationship between circadian rhythms, the gut microbiome, and gastrointestinal infections. RECENT FINDINGS: In humans and mice, the composition and functions of the intestinal microbiome display diurnal rhythms orchestrated by feeding behaviors and host circadian gene expression. Jet lag, or circadian disruption, perturbs these rhythms to produce gut dysbiosis. When mice are orally infected with Salmonella typhimurium in the morning (the beginning of their rest period) they show higher levels of colonization and gut inflammation vs...
January 2016: Current Opinion in Gastroenterology
P S Heeger
Research reports presented at the American Transplant Congress 2015 provided an array of basic science findings of relevance to the transplant community. Among key themes is the concept that ischemia-reperfusion injury and early posttransplantation inflammation is linked to adaptive alloimmunity and transplant injury. Molecular and cellular mechanisms contributing to these interactions were highlighted. The relevance of understanding how blocking costimulation, including CD40/CD154 interactions, affects various aspects of the alloimmune response was enhanced by the description of preclinical studies demonstrating efficacy of a unique, blocking anti-CD40 monoclonal antibody that could potentially be used in humans...
November 2015: American Journal of Transplantation
Da-Hai Yu, Manasi Gadkari, Quan Zhou, Shiyan Yu, Nan Gao, Yongtao Guan, Deborah Schady, Tony N Roshan, Miao-Hsueh Chen, Eleonora Laritsky, Zhongqi Ge, Hui Wang, Rui Chen, Caroline Westwater, Lynn Bry, Robert A Waterland, Chelsea Moriarty, Cindy Hwang, Alton G Swennes, Sean R Moore, Lanlan Shen
BACKGROUND: DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited. RESULTS: We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we detect extensive dynamic epigenetic changes in intestinal stem cells and their progeny during the suckling period, suggesting postnatal epigenetic development in this stem cell population...
2015: Genome Biology
Qingping Xu, Dominique Mengin-Lecreulx, Xueqian W Liu, Delphine Patin, Carol L Farr, Joanna C Grant, Hsiu-Ju Chiu, Lukasz Jaroszewski, Mark W Knuth, Adam Godzik, Scott A Lesley, Marc-André Elsliger, Ashley M Deacon, Ian A Wilson
UNLABELLED: Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (or dl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l-Ala...
2015: MBio
E Montassier, T Gastinne, P Vangay, G A Al-Ghalith, S Bruley des Varannes, S Massart, P Moreau, G Potel, M F de La Cochetière, E Batard, D Knights
BACKGROUND: Chemotherapy is commonly used as myeloablative conditioning treatment to prepare patients for haematopoietic stem cell transplantation (HSCT). Chemotherapy leads to several side effects, with gastrointestinal (GI) mucositis being one of the most frequent. Current models of GI mucositis pathophysiology are generally silent on the role of the intestinal microbiome. AIM: To identify functional mechanisms by which the intestinal microbiome may play a key role in the pathophysiology of GI mucositis, we applied high-throughput DNA-sequencing analysis to identify microbes and microbial functions that are modulated following chemotherapy...
September 2015: Alimentary Pharmacology & Therapeutics
Stephen M Vindigni, Christina M Surawicz
The intestinal microbiome is critical to digestion, metabolism and protection from pathogenic organisms. Dysbiosis, or alteration of this microbiome, can result in Clostridium difficile infection and may play a role in other conditions. Patients undergoing solid organ transplantation (e.g., kidney, lung, liver, small bowel) and hematopoietic stem cell transplantation have a shift in the gut microbiome with a decrease in predominant organisms, a loss of bacterial diversity and emergence of a new dominant population...
2015: Expert Review of Clinical Immunology
Giovanni C Actis, Rinaldo Pellicano, Floriano Rosina
Despite the level of sophistication they have reached nowadays, the available tools for treatment of inflammatory bowel disease (IBD) can at best chronicize the disease but not cure it. Chances to make leap forward from this hold-back may include designs to reach personalized treatment strategies taking advantage of modern genome associated studies, and shift resources towards unfolding inciting pathogenetic steps rather than continuing to develop drugs that address down-stream phenomena. We have arbitrarily chosen to scrutinize a few projects that may make their way in 2015 and mark the history of IBD research...
May 6, 2015: World Journal of Gastrointestinal Pharmacology and Therapeutics
Melanie Wong
Fifty years ago, in 1964, our understanding of the immune system was very rudimentary. Gell and Coombs had just described classes of hypersensitivity reactions, and Bruton had described and commenced immunoglobulin replacement in agammaglobulinaemia. The distinction between T and B cells was not identified and characterised until the 1960s and 1970s. This was followed by increasing recognition of T and B cell collaboration in immune responses and identification of significant immunodeficiencies. CD4 and CD8 T cells were only recognised in the 1970s and 1980s...
February 2015: Journal of Paediatrics and Child Health
Sabina Lukovac, Clara Belzer, Linette Pellis, Bart J Keijser, Willem M de Vos, Roy C Montijn, Guus Roeselers
UNLABELLED: The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids. We have explored the transcriptional response of organoids upon exposure to short-chain fatty acids (SCFAs) and products generated by two abundant microbiota constituents, Akkermansia muciniphila and Faecalibacterium prausnitzii...
2014: MBio
Henner F Farin, Wouter R Karthaus, Pekka Kujala, Maryam Rakhshandehroo, Gerald Schwank, Robert G J Vries, Eric Kalkhoven, Edward E S Nieuwenhuis, Hans Clevers
Paneth cells (PCs) are terminally differentiated, highly specialized secretory cells located at the base of the crypts of Lieberkühn in the small intestine. Besides their antimicrobial function, PCs serve as a component of the intestinal stem cell niche. By secreting granules containing bactericidal proteins like defensins/cryptdins and lysozyme, PCs regulate the microbiome of the gut. Here we study the control of PC degranulation in primary epithelial organoids in culture. We show that PC degranulation does not directly occur upon stimulation with microbial antigens or bacteria...
June 30, 2014: Journal of Experimental Medicine
R Lu, S Wu, Y-G Zhang, Y Xia, X Liu, Y Zheng, H Chen, K L Schaefer, Z Zhou, M Bissonnette, L Li, J Sun
Salmonella infections can become chronic and increase the risk of cancer. The mechanisms by which specific Salmonella organisms contribute to cancer, however, are still unknown. Live and attenuated Salmonella are used as vectors to target cancer cells, but there have been no systematic studies of the oncogenic potential of chronic Salmonella infections in cancer models. AvrA, a pathogenic product of Salmonella, is inserted into host cells during infection and influences eukaryotic cell pathways. In the current study, we colonized mice with Salmonella AvrA-sufficient or AvrA-deficient Salmonella typhimirium strains and induced inflammation-associated colon cancer by azoxymethane/dextran sulfate sodium (AOM/DSS)...
2014: Oncogenesis
Michael W Rajala, Christa M Patterson, Judith S Opp, Susan K Foltin, Vincent B Young, Martin G Myers
Shifts in the composition of gut bacterial populations can alter host metabolism and may contribute to the pathogenesis of metabolic disorders, including obesity. Mice deficient in leptin action are obese with altered microbiota and increased susceptibility to certain intestinal pathogens. Because antimicrobial peptides (AMPs) secreted by Paneth cells represent a major mechanism by which the host influences the gut microbiome, we examined the mRNA expression of gut AMPs, several of which were decreased in leptin receptor (LepR)-deficient db/db mice, suggesting a potential role for AMP modulation of microbiota composition...
March 2014: Endocrinology
Solat Eslami, Zahra Barzgari, Negar Saliani, Nazli Saeedi, Abolfazl Barzegari
Essentially, people's diet and nutritional status has been changed substantially worldwide and several lines of evidence suggest that these changes are to the detriment of their health. Additionally, it has been well documented that unhealthy diet especially the fast foods, untraditional foods or bad-eating-habits influence the human gut microbiome. The gut microbiota shapes immune responses during human life and affects his/her metabolomic profiles. Furthermore, many studies highlight the molecular pathways that mediate host and symbiont interactions that regulate proper immune function and prevention of cancer in the body...
2012: BioImpacts: BI
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