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Human microbiome

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https://www.readbyqxmd.com/read/28087007/manipulating-the-microbiome
#1
Tammy L Sirich, Timothy W Meyer
The application of molecular methods has provided a new picture of the colon microbial flora, or microbiome. The microbiome has been found to be a complex ecosystem with multiple influences on its human host. In renal medicine, interest has focused on the microbiome as a source of toxic waste chemicals and a stimulant to unwanted systemic inflammation. Early attempts to manipulate the microbiome have yielded limited benefit, but further research is strongly motivated.
February 2017: Kidney International
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#2
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28079170/growth-and-morbidity-of-gambian-infants-are-influenced-by-maternal-milk-oligosaccharides-and-infant-gut-microbiota
#3
Jasmine C C Davis, Zachery T Lewis, Sridevi Krishnan, Robin M Bernstein, Sophie E Moore, Andrew M Prentice, David A Mills, Carlito B Lebrilla, Angela M Zivkovic
Human milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother's HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3'-sialyllactose was found to be a good indicator of infant weight-for-age...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078319/gut-microbiota-inflammation-and-colorectal-cancer
#4
Jun Sun, Ikuko Kato
Although genes contribute to colorectal cancer, the gut microbiota are an important player. Accumulating evidence suggests that chronic infection and the ensuing inflammation contributes to tumor initiation and tumor progression. A variety of bacterial species and tumor-promoting virulence mechanisms have been investigated. Significant advances have been made in understanding the composition and functional capabilities of the gut microbiota and its roles in cancer. In the current review, we discuss the novel roles of microbiota in the progression of colon cancer...
June 2016: Genes & Diseases
https://www.readbyqxmd.com/read/28077947/asthma-and-the-microbiome-defining-the-critical-window-in-early-life
#5
REVIEW
Leah T Stiemsma, Stuart E Turvey
Asthma is a chronic inflammatory immune disorder of the airways affecting one in ten children in westernized countries. The geographical disparity combined with a generational rise in prevalence, emphasizes that changing environmental exposures play a significant role in the etiology of this disease. The microflora hypothesis suggests that early life exposures are disrupting the composition of the microbiota and consequently, promoting immune dysregulation in the form of hypersensitivity disorders. Animal model research supports a role of the microbiota in asthma and atopic disease development...
2017: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/28077565/mahmi-database-a-comprehensive-metahit-based-resource-for-the-study-of-the-mechanism-of-action-of-the-human-microbiota
#6
Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077318/alcohol-microbiome-life-style-influence-alcohol-and-non-alcoholic-organ-damage
#7
REVIEW
Manuela G Neuman, Samuel W French, Samir Zakhari, Stefen Malnick, Helmut K Seitz, Lawrence B Cohen, Mikko Salaspuro, Andreea Voinea Griffin, Andrei Barasch, Irina A Kirpich, Paul G Thomes, Laura W Schrum, Terrence M Donohue, Kusum Kharbanda, Marcus Cruz, Mihai Opris
This paper is based upon the "8th Charles Lieber's Satellite Symposium" organized by Manuela G. Neuman at the Research Society on Alcoholism Annual Meeting, onJune 25, 2016 at New Orleans, Louisiana, USA. The integrative symposium investigated different aspects of alcohol-induced liver disease (ALD) as well as non-alcohol-induced liver disease (NAFLD) and possible repair. We revealedthe basic aspects of alcohol metabolism that may be responsible for the development of liver diseaseas well as the factors that determine the amount, frequency and which type of alcohol misuse leads to liver and gastrointestinal diseases...
January 7, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28077127/navigating-social-and-ethical-challenges-of-biobanking-for-human-microbiome-research
#8
Kim H Chuong, David M Hwang, D Elizabeth Tullis, Valerie J Waters, Yvonne C W Yau, David S Guttman, Kieran C O'Doherty
BACKGROUND: Biobanks are considered to be key infrastructures for research development and have generated a lot of debate about their ethical, legal and social implications (ELSI). While the focus has been on human genomic research, rapid advances in human microbiome research further complicate the debate. DISCUSSION: We draw on two cystic fibrosis biobanks in Toronto, Canada, to illustrate our points. The biobanks have been established to facilitate sample and data sharing for research into the link between disease progression and microbial dynamics in the lungs of pediatric and adult patients...
January 11, 2017: BMC Medical Ethics
https://www.readbyqxmd.com/read/28076867/identifying-host-genetic-variants-associated-with-microbiome-composition-by-testing-multiple-beta-diversity-matrices
#9
Xing Hua, James J Goedert, Maria Teresa Landi, Jianxin Shi
OBJECTIVES: Host genetics have been recently reported to affect human microbiome composition. We previously developed a statistical framework, microbiomeGWAS, to identify host genetic variants associated with microbiome composition by testing a distance matrix. However, statistical power depends on the choice of a microbiome distance matrix. To achieve more robust statistical power, we aim to extend microbiomeGWAS to test the association with many distance matrices, which are defined based on multilevel taxa abundances and phylogenetic information...
2016: Human Heredity
https://www.readbyqxmd.com/read/28074537/neuroblastoma-causes-alterations-of-the-intestinal-microbiome-gut-hormones-inflammatory-cytokines-and-bile-acid-composition
#10
Christoph Castellani, Georg Singer, Margarita Kaiser, Thomas Kaiser, Jianfeng Huang, Daniela Sperl, Karl Kashofer, Guenter Fauler, Barbara Guertl-Lackner, Gerald Höfler, Holger Till
OBJECTIVE: To assess the effect of neuroblastoma (NB) on the intestinal microbiome, metabolism, and inflammatory parameters in a murine model. MATERIALS AND METHODS: Athymic Hsd:Fox1nu mice received subperitoneal implantation of human NB cells (MHH-NB11) (tumor group, TG) or culture medium (sham group). Following 10 weeks of tumor growth, all animals were sacrificed to collect total white adipose tissue (WAT). Luminex assays were performed for gut hormone and inflammation marker analysis...
January 11, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28071710/micropattern-a-web-based-tool-for-microbe-set-enrichment-analysis-and-disease-similarity-calculation-based-on-a-list-of-microbes
#11
Wei Ma, Chuanbo Huang, Yuan Zhou, Jianwei Li, Qinghua Cui
The microbiota colonized on human body is renowned as "a forgotten organ" due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070563/gut-microbiome-of-the-canadian-arctic-inuit
#12
Catherine Girard, Nicolas Tromas, Marc Amyot, B Jesse Shapiro
Diet is a major determinant of community composition in the human gut microbiome, and "traditional" diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome...
January 2017: MSphere
https://www.readbyqxmd.com/read/28069756/inside-out-hiv-the-gut-microbiome-and-the-mucosal-immune-system
#13
REVIEW
Jay Liu, Brett Williams, Daniel Frank, Stephanie M Dillon, Cara C Wilson, Alan L Landay
The components of the human gut microbiome have been found to influence a broad array of pathologic conditions ranging from heart disease to diabetes and even to cancer. HIV infection upsets the delicate balance in the normal host-microbe interaction both through alterations in the taxonomic composition of gut microbial communities as well as through disruption of the normal host response mechanisms. In this article we review the current methods of gut microbiome analysis and the resulting data regarding how HIV infection might change the balance of commensal bacteria in the gut...
January 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28069754/the-influence-of-the-microbiome-on-type-1-diabetes
#14
REVIEW
Alexandra Paun, Christopher Yau, Jayne S Danska
Type 1 diabetes (T1D) is characterized by the autoimmune destruction of pancreatic β cells. The rapid rise in T1D incidence during the past 50 y suggests environmental factors contribute to the disease. The trillion symbiotic microorganisms inhabiting the mammalian gastrointestinal tract (i.e., the microbiota) influence numerous aspects of host physiology. In this study we review the evidence linking perturbations of the gut microbiome to pancreatic autoimmunity. We discuss data from rodent models demonstrating the essential role of the gut microbiota on the development and function of the host's mucosal and systemic immune systems...
January 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28067676/severe-community-acquired-pneumonia-optimal-management
#15
Davide Leoni, Jordi Rello
PURPOSE OF REVIEW: Community-acquired pneumonia (CAP) is the leading cause of mortality among infectious diseases. Several efforts have been implemented to achieve better outcomes, but an important proportion of patients continue dying. This review focuses on the newest research on prognostic factors and diagnostics, opening new perspectives in the management of CAP. RECENT FINDINGS: CAP survival improved in recent years despite an increasing incidence of severe presentations...
January 6, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28065879/structural-zeros-in-high-dimensional-data-with-applications-to-microbiome-studies
#16
Abhishek Kaul, Ori Davidov, Shyamal D Peddada
SUMMARYThis paper is motivated by the recent interest in the analysis of high-dimensional microbiome data. A key feature of these data is the presence of "structural zeros" which are microbes missing from an observation vector due to an underlying biological process and not due to error in measurement. Typical notions of missingness are unable to model these structural zeros. We define a general framework which allows for structural zeros in the model and propose methods of estimating sparse high-dimensional covariance and precision matrices under this setup...
January 8, 2017: Biostatistics
https://www.readbyqxmd.com/read/28063650/performing-skin-microbiome-research-a-method-to-the-madness
#17
REVIEW
Heidi H Kong, Björn Andersson, Thomas Clavel, John E Common, Scott A Jackson, Nathan D Olson, Julia A Segre, Claudia Traidl-Hoffmann
Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis...
January 4, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28063079/the-thyroid-the-eyes-and-the-gut-a-possible-connection
#18
REVIEW
D Covelli, M Ludgate
INTRODUCTION: Graves' disease (GD) is an autoimmune disorder responsible for 60-90% of thyrotoxicosis, with an incidence of 1 to 2 cases per 1000 population per year in England. Graves' orbitopathy (GO) is the most frequent extrathyroidal manifestation, not provoked directly by abnormal thyroid hormone levels, but by the consequence of the underlying autoimmune process. The aetiology of autoimmune disorders is due to an interplay between susceptibility genes and environmental factors, such as infections and stress...
January 7, 2017: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/28052855/syn-004-ribaxamase-an-oral-%C3%AE-lactamase-designed-to-protect-the-gut-microbiome-from-the-deleterious-effects-of-certain-intravenously-administered-%C3%AE-lactam-antibiotics-degrades-ceftriaxone-excreted-into-the-intestine-in-phase-2a-clinical-studies
#19
John F Kokai-Kun, Tracey Roberts, Olivia Coughlin, Eric Sicard, Marianne Rufiange, Richard Fedorak, Christian Carter, Marijke H Adams, James Longstreth, Heidi Whalen, Joseph Sliman
SYN-004 (ribaxamase) is a β-lactamase designed to be orally administered concurrently with intravenous β-lactam antibiotics including most penicillins and cephalosporins. Ribaxamase's anticipated mechanism of action is to degrade excess β-lactam antibiotic that is excreted into the small intestine. This enzymatic inactivation of excreted antibiotic is expected to protect the gut microbiome from disruption and thus prevent undesirable side effects including secondary infections like Clostridium difficile as well as other antibiotic-associated diarrheas...
January 4, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28052549/adsorption-of-norovirus-and-ostreid-herpesvirus-type-1-to-polymer-membranes-for-the-development-of-passive-samplers
#20
Françoise Vincent-Hubert, Benjamin Morga, Tristan Renault, Françoise S Le Guyader
AIMS: This study was performed to develop passive sampling methodology for the detection of two viruses in seawater in the area of shellfish production, The Norovirus (NoV), a human pathogen implicated in gastroenteritis outbreaks linked to oyster consumption and the ostreid herpesvirus type 1 (OsHV-1) a virus associated with mass mortalities of Pacific oysters. METHODS AND RESULTS: Commercially membranes were tested for their capacity to adsorb virus: Zetapor, gauze, nylon, low density polyethylene (LDPE) and Polyvinylidene difluoride (PVDF)...
January 4, 2017: Journal of Applied Microbiology
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