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Gut microbiome

Jong Wha J Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Farhad Hormozdiari, Aldons J Lusis, Eleazar Eskin
A typical GWAS tests correlation between a single phenotype and each genotype one at a time. However, single phenotype analysis might miss unmeasured aspects of complex biological networks. Analyzing many phenotypes simultaneously may increase the power to capture these unmeasured aspects and detect more variants. Several multivariate approaches aim to detect variants related to more than one phenotype, but these current approaches do not consider the effects of population structure. As a result, these approaches may result in a significant amount of false positive identifications...
October 21, 2016: Genetics
R Balfour Sartor, Gary D Wu
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis, via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice...
October 18, 2016: Gastroenterology
Joan B Broderick, James D Moody
The human gut microbiome is the source of not only microbial diversity, but also of interesting chemical reactions and enzymology. An excellent example of this is CutC, an enzyme that makes trimethylamine (TMA). In this issue of Cell Chemical Biology, Bodea et al. (2016) show how CutC uses a glycyl radical to perform C-N bond cleavage needed for TMA production.
October 20, 2016: Cell Chemical Biology
Eric Banan-Mwine Daliri, Shuai Wei, Deog H Oh, Byong H Lee
The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases...
October 21, 2016: Critical Reviews in Food Science and Nutrition
Francesco Savino, Andrea Quartieri, Angela De Marco, Maria Garro, Alberto Amaretti, Stefano Raimondi, Marta Simone, Maddalena Rossi
AIM: This study compared the faecal microbial composition of formula-fed infants who did and did not have colic. METHODS: Faecal samples from formula-fed infants under 16 weeks of age with (n=38) and without (n=39) colic were collected at Department of Pediatrics in Turin, Italy, between February 2014 and October 2015. The pH and faecal ammonia were determined and total bacteria, bifidobacteria, lactic acid bacteria (LAB) and coliforms were quantified by fluorescent in situ hybridisation (FISH)...
October 20, 2016: Acta Paediatrica
Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Sonja C Sawh, Santosh Deshpande, Sandy Jansen, Christopher J Reynaert, Philip M Jones
CONTEXT: Necrotizing enterocolitis (NEC) is the most frequent gastrointestinal emergency in neonates. The microbiome of the preterm gut may regulate the integrity of the intestinal mucosa. Probiotics may positively contribute to mucosal integrity, potentially reducing the risk of NEC in neonates. OBJECTIVE: To perform an updated systematic review and meta-analysis on the efficacy and safety of probiotics for the prevention of NEC in premature infants. DATA SOURCES: Structured searches were performed in: Medline, Embase, and the Cochrane Central Register of Controlled Trials (all via Ovid, from 2013 to January 2015)...
2016: PeerJ
Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight
Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions. The presentation of quantitative effect sizes in addition to P values will improve our ability to perform meta-analysis and to evaluate potentially relevant biological effects...
October 19, 2016: Genome Biology
Philippa Z N Franzini, Jean-Baptiste Ramond, Clarke H Scholtz, Catherine L Sole, Sandra Ronca, Don A Cowan
[This corrects the article DOI: 10.1371/journal.pone.0161118.].
2016: PloS One
Katherine A Dunn, Jessica Moore-Connors, Brad MacIntyre, Andrew Stadnyk, Nikhil A Thomas, Angela Noble, Gamal Mahdi, Mohsin Rashid, Anthony R Otley, Joseph P Bielawski, Johan Van Limbergen
BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn's disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect. METHODS: Fecal samples were collected from 15 pediatric CD patients prior to and after EEN treatment, as well as from 5 healthy controls...
November 2016: Inflammatory Bowel Diseases
Mária Džunková, Giuseppe D'Auria, Hua Xu, Jun Huang, Yinghua Duan, Andrés Moya, Ciarán P Kelly, Xinhua Chen
Antibiotics have significant and long-lasting impacts on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile infection (CDI). Standard therapy using antibiotics is associated with a high rate of disease recurrence, highlighting the need for novel treatment strategies that target toxins, the major virulence factors, rather than the organism itself. Human monoclonal antibodies MK-3415A (actoxumab-bezlotoxumab) to C. difficile toxin A and toxin B, as an emerging non-antibiotic approach, significantly reduced the recurrence of CDI in animal models and human clinical trials...
2016: Frontiers in Cellular and Infection Microbiology
Kaleigh Giles, Benjamin Pluvinage, Alisdair B Boraston
The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution x-ray crystal structure of BpGH50 confirmed its possession of the core (α/β)8 barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues...
October 18, 2016: Proteins
Kristin Nicole Harper
No abstract text is available yet for this article.
October 14, 2016: AIDS
Stephanie M Dillon, Daniel N Frank, Cara C Wilson
HIV-1 infection is associated with substantial damage to the gastrointestinal (GI) tract resulting in structural impairment of the epithelial barrier and a disruption of intestinal homeostasis. The accompanying translocation of microbial products and potentially microbes themselves from the lumen into systemic circulation has been linked to immune activation, inflammation, and HIV-1 disease progression. The importance of microbial translocation in the setting of HIV-1 infection has led to a recent focus on understanding how the communities of microbes that make up the intestinal microbiome are altered during HIV-1 infection and how they interact with mucosal immune cells to contribute to inflammation...
October 14, 2016: AIDS
GwangPyo Ko
Recently, there were dramatically increased interests on human microbiome research worldwide. Human microbiome has been considered as the second genome in addition to our own genome and played very crucial roles in maintaining human health. Human microbiota typically reside on the surface of epithelial cells and play various biological roles ranging from metabolism, immune development, mental health, and to organ development. Since 2008, we have determined the diversity of Korean microbiome and determined the genes and pathways of gut microbiome using Korean Twin Cohort...
September 2016: Journal of Hypertension
Peter Nilsson
A number of chronic disease conditions tend to cluster in families with an increased risk in first-degree relatives, but also an increased risk in second-degree relatives. This fact is most often referred to as the heritability (heredity) of these diseases and explained by the influence of genetic factors, or shared environment, even if the more specific details or mechanism leading to disease are not known. New methods have to be explored in screening studies and register linkage studies to define and measure consequences of a positive family history of disease...
September 2016: Journal of Hypertension
Seungbum Kim, Gary Wang, Gilberto Lobaton, Eric Li, Tao Yang, Mohan Raizada
OBJECTIVE: Our previous studies have demonstrated that gut microbial dysbiosis is linked to high blood pressure in patients. This was associated with decreases in butyrate- and acetate- producing microbial populations. Thus, our objective in this study was to investigate the hypothesis that infusion of butyrate would impact dysbiosis, gut immunity and attenuate hypertension. DESIGN AND METHOD: C57B6 mice were divided into 4 groups; Saline infused, Angiotensin II (750ng/kg/min) infused, Ang II infused and butyrate treated (0...
September 2016: Journal of Hypertension
Martin Hoenigl, Josué Pérez-Santiago, Masato Nakazawa, Michelli Faria de Oliveira, Yonglong Zhang, Malcolm A Finkelman, Scott Letendre, Davey Smith, Sara Gianella
BACKGROUND: The extent of gut microbial translocation, which plays roles in HIV disease progression and non-AIDS comorbidities, appears to vary with the composition of the gut microbiome, particularly the presence of Lactobacillales, which reduce mucosal injury. While low proportions of Lactobacillales in the distal gut microbiome are a very promising indicator of microbial translocation, measurement is expensive and complicated and not feasible for clinical routine. (1→3)-β-d-Glucan (BDG) is a component of most fungal cell walls and might be a surrogate marker for Lactobacillales proportion in the gut and a useful indicator of HIV-associated gut injury...
2016: Frontiers in Immunology
Drew D Kiraly, Deena M Walker, Erin S Calipari, Benoit Labonte, Orna Issler, Catherine J Pena, Efrain A Ribeiro, Scott J Russo, Eric J Nestler
Addiction to cocaine and other psychostimulants represents a major public health crisis. The development and persistence of addictive behaviors comes from a complex interaction of genes and environment - the precise mechanisms of which remain elusive. In recent years a surge of evidence has suggested that the gut microbiome can have tremendous impact on behavioral via the microbiota-gut-brain axis. In this study we characterized the influence of the gut microbiota on cocaine-mediated behaviors. Groups of mice were treated with a prolonged course of non-absorbable antibiotics via the drinking water, which resulted in a substantial reduction of gut bacteria...
October 18, 2016: Scientific Reports
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
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