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Human microbiome

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https://www.readbyqxmd.com/read/29679047/a-quality-improvement-initiative-to-reduce-necrotizing-enterocolitis-across-hospital-systems
#1
Amy T Nathan, Laura Ward, Kurt Schibler, Laurel Moyer, Andrew South, Heather C Kaplan
OBJECTIVE: Necrotizing enterocolitis (NEC) is a devastating intestinal disease in premature infants. Local rates of NEC were unacceptably high. We hypothesized that utilizing quality improvement methodology to standardize care and apply evidence-based practices would reduce our rate of NEC. STUDY DESIGN: A multidisciplinary team used the model for improvement to prioritize interventions. Three neonatal intensive care units (NICUs) developed a standardized feeding protocol for very low birth weight (VLBW) infants, and employed strategies to increase the use of human milk, maximize intestinal perfusion, and promote a healthy microbiome...
April 20, 2018: Journal of Perinatology: Official Journal of the California Perinatal Association
https://www.readbyqxmd.com/read/29676067/significance-of-skin-barrier-dysfunction-in-atopic-dermatitis
#2
REVIEW
Byung Eui Kim, Donald Y M Leung
The epidermis contains epithelial cells, immune cells, and microbes which provides a physical and functional barrier to the protection of human skin. It plays critical roles in preventing environmental allergen penetration into the human body and responsing to microbial pathogens. Atopic dermatitis (AD) is the most common, complex chronic inflammatory skin disease. Skin barrier dysfunction is the initial step in the development of AD. Multiple factors, including immune dysregulation, filaggrin mutations, deficiency of antimicrobial peptides, and skin dysbiosis contribute to skin barrier defects...
May 2018: Allergy, Asthma & Immunology Research
https://www.readbyqxmd.com/read/29675808/help-hope-and-hype-ethical-considerations-of-human-microbiome-research-and-applications
#3
Yonghui Ma, Hua Chen, Canhui Lan, Jianlin Ren
No abstract text is available yet for this article.
April 19, 2018: Protein & Cell
https://www.readbyqxmd.com/read/29675450/engineered-human-gastrointestinal-cultures-to-study-the-microbiome-and-infectious-diseases
#4
REVIEW
Sarah E Blutt, Sue E Crawford, Sasirekha Ramani, Winnie Y Zou, Mary K Estes
New models to study the intestine are key to understanding intestinal diseases and developing novel treatments. Intestinal organ-like culture systems (organoids and enteroids) have substantially advanced the study of the human gastrointestinal tract. Stem cell-derived cultures produce self-organizing structures that contain the multiple differentiated intestinal epithelial cell types including enterocytes, goblet, Paneth, and enteroendocrine cells. Understanding host-microbial interactions is one area in which these cultures are expediting major advancements...
March 2018: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/29674124/diverse-toxic-effectors-are-harbored-by-vgrg-islands-for-interbacterial-antagonism-in-type-vi-secretion-system
#5
Jiale Ma, Min Sun, Zihao Pan, Chengping Lu, Huochun Yao
The type VI secretion system (T6SS) is considered as one of the key competition strategies by injecting toxic effectors for intestinal pathogens to acquire optimal colonization in host gut, a microenviroment with high-density polymicrobial community where bacteria compete for niches and resources. Enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea in human and animals, widely encode T6SS clusters in their genomes. In this report, we first identified VT1, a novel amidase effector in ETEC, significantly hydrolyzed D-lactyl-L-Ala crosslinks between N-acetylmuramoyl and L-Ala in peptidoglycan...
April 16, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29673295/gut-microbiota-metabolism-and-psychopathology-a-critical-review-and-novel-perspectives
#6
Robin N Groen, Nicolien C de Clercq, Max Nieuwdorp, H J Rogier Hoenders, Albert K Groen
Psychiatric disorders are often associated with metabolic comorbidities. However, the mechanisms through which metabolic and psychiatric disorders are connected remain unclear. Pre-clinical studies in rodents indicate that the bidirectional signaling between the intestine and the brain, the so-called microbiome-gut-brain axis, plays an important role in the regulation of both metabolism and behavior. The gut microbiome produces a vast number of metabolites that may be transported into the host and play a part in homeostatic control of metabolism as well as brain function...
April 20, 2018: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29673211/the-role-of-gut-microbiota-in-obesity-and-type-2-and-type-1-diabetes-mellitus-new-insights-into-old-diseases
#7
REVIEW
Igor Alexander Harsch, Peter Christopher Konturek
The investigation of the human microbiome is the most rapidly expanding field in biomedicine. Early studies were undertaken to better understand the role of microbiota in carbohydrate digestion and utilization. These processes include polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production. Recent research has demonstrated that the intricate axis between gut microbiota and the host metabolism is much more complex. Gut microbiota—depending on their composition—have disease-promoting effects but can also possess protective properties...
April 17, 2018: Medical Sciences: Open Access Journal
https://www.readbyqxmd.com/read/29672703/phylogenomic-analysis-of-%C3%AE-lactamase-in-archaea-and-bacteria-enables-the-identification-of-putative-new-members
#8
Vivek Keshri, Arup Panda, Anthony Levasseur, Jean-Marc Rolain, Pierre Pontarotti, Didier Raoult
β-lactamases are enzymes which are commonly produced by bacteria and which degrade the β-lactam ring of β-lactam antibiotics, namely penicillins, cephalosporins, carbapenems, and monobactams, and inactivate these antibiotics. We performed a rational and comprehensive investigation of β-lactamases in different biological databases. In this study, we constructed hidden Markov model profiles as well as the ancestral sequence of four classes of β-lactamases (A, B, C, and D), which were used to identify potential β-lactamases from environmental metagenomic (1206), human microbiome metagenomic (6417), human microbiome reference genome (1310), and NCBI's nonredundant databases (44101)...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29670252/urbanization-and-the-gut-microbiota-in-health-and-inflammatory-bowel-disease
#9
REVIEW
Tao Zuo, Michael A Kamm, Jean-Frédéric Colombel, Siew C Ng
In the 21st century, urbanization represents a major demographic shift in developed and developing countries. Rapid urbanization in the developing world has been associated with an increasing incidence of several autoimmune diseases, including IBD. Patients with IBD exhibit a decrease in the diversity and richness of the gut microbiota, while urbanization attenuates the gut microbial diversity and might have a role in the pathogenesis of IBD. Environmental exposures during urbanization, including Westernization of diet, increased antibiotic use, pollution, improved hygiene status and early-life microbial exposure, have been shown to affect the gut microbiota...
April 18, 2018: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29669589/similarity-of-the-dog-and-human-gut-microbiomes-in-gene-content-and-response-to-diet
#10
Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R Jackson, Qinghong Li, Peer Bork
BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs. RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data)...
April 19, 2018: Microbiome
https://www.readbyqxmd.com/read/29668946/a-system-biology-perspective-on-environment-host-microbe-interactions
#11
Lianmin Chen, Sanzhima Garmaeva, Alexandra Zherankova, Jingyuan Fu, Cisca Wijmenga
A vast, complex and dynamic consortium of microorganisms known as the gut microbiome colonizes the human gut. Over the past few decades we have developed an increased awareness of its important role in human health. In this review we discuss the role of the gut microbiome in complex diseases and the possible causal scenarios behind its interactions with the host genome and environmental factors. We then propose a new analysis framework that combines a systems biology approach, cross-kingdom integration of multiple levels of omics data, and innovative in vitro models to yield an integrated picture of human host-microbe interactions...
April 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29668914/dietary-interventions-to-modulate-the-gut-microbiome-how-far-away-are-we-from-precision-medicine
#12
Francesca De Filippis, Paola Vitaglione, Rosario Cuomo, Roberto Berni Canani, Danilo Ercolini
The importance of the gut microbiome in human health and disease is fully acknowledged. A perturbation in the equilibrium among the different microbial populations living in the gut (dysbiosis) has been associated with the development of several types of diseases. Modulation of the gut microbiome through dietary intervention is an emerging therapeutic and preventive strategy for many conditions. Nevertheless, interpersonal differences in response to therapeutic treatments or dietary regimens are often observed during clinical trials, and recent research has suggested that subject-specific features of the gut microbiota may be responsible...
April 13, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29668831/using-standard-microbiome-reference-groups-to-simplify-beta-diversity-analyses-and-facilitate-independent-validation
#13
Marlena Maziarz, Ruth M Pfeiffer, Yunhu Wan, Mitchell H Gail
Motivation: Comparisons of microbiome communities across populations are often based on pairwise distance measures (beta-diversity). Standard analyses (principal coordinate plots, permutation tests, kernel methods) require access to primary data if another investigator wants to add or compare independent data.We propose using standard reference measurements to simplify microbiome beta-diversity analyses, to make them more transparent, and to facilitate independent validation and comparisons across studies...
April 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29668682/biogeography-and-environmental-conditions-shape-bacteriophage-bacteria-networks-across-the-human-microbiome
#14
Geoffrey D Hannigan, Melissa B Duhaime, Danai Koutra, Patrick D Schloss
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body...
April 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29668558/archaea-microbial-candidates-in-next-generation-probiotics-development
#15
Jean-François Brugère, Wajdi Ben Hania, Marie-Edith Arnal, Céline Ribière, Nathalie Ballet, Pascal Vandeckerkove, Bernard Ollivier, Paul W O'Toole
Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya...
April 17, 2018: Journal of Clinical Gastroenterology
https://www.readbyqxmd.com/read/29668250/the-effects-of-baicalein-on-cortical-pro-inflammatory-cytokines-and-the-intestinal-microbiome-in-senescence-accelerated-mouse-prone-8
#16
Li Gao, Jia-Qi Li, Yu-Zhi Zhou, Xudong Huang, Xue-Mei Qin, Guan-Hua Du
Baicalein, a flavonoid derived from the roots of Scutellariae baicalensis Georgi, has shown health benefits for an array of human diseases including dementia. The senescence-accelerated mouse prone 8 (SAMP8) strain is extensively used as a senile dementia model. To further investigate the effects of baicalein in SAMP8 mice, behavioral testing, biochemical detection and gut microbiota analysis were performed. The results demonstrated that treatment with baicalein ameliorated the senescence status of the SAMP8 mice, as manifested by reducing the grading score of senescence...
April 18, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29666626/next-generation-immune-repertoire-sequencing-as-a-clue-to-elucidate-the-landscape-of-immune-modulation-by-host-gut-microbiome-interactions
#17
Tatsuo Ichinohe, Takahiko Miyama, Takakazu Kawase, Yasuko Honjo, Kazutaka Kitaura, Hiroyuki Sato, Tadasu Shin-I, Ryuji Suzuki
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29666290/viral-diversity-of-house-mice-in-new-york-city
#18
Simon H Williams, Xiaoyu Che, Joel A Garcia, John D Klena, Bohyun Lee, Dorothy Muller, Werner Ulrich, Robert M Corrigan, Stuart Nichol, Komal Jain, W Ian Lipkin
The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera...
April 17, 2018: MBio
https://www.readbyqxmd.com/read/29666289/new-york-city-house-mice-mus-musculus-as-potential-reservoirs-for-pathogenic-bacteria-and-antimicrobial-resistance-determinants
#19
Simon H Williams, Xiaoyu Che, Ashley Paulick, Cheng Guo, Bohyun Lee, Dorothy Muller, Anne-Catrin Uhlemann, Franklin D Lowy, Robert M Corrigan, W Ian Lipkin
House mice ( Mus musculus ) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months...
April 17, 2018: MBio
https://www.readbyqxmd.com/read/29665886/antimicrobial-resistance-from-basic-science-to-translational-innovation
#20
Jun Lin
The rise in antimicrobial resistance (AMR) poses a major threat to animal agriculture and human health. To summarize and update current and emerging AMR issues that are significant for animal health and food safety, this issue presents a virtual AMR symposium consisting of seven review papers. These reviews cover a newly described AMR mechanism in Campylobacter, effects of AMR and microbiome on Campylobacter infection, plasmid-mediated colistin resistance in food-producing animals, the impact of point source or antibiotic residues on the environmental resistome, and potential factors influencing horizontal gene transfer in the intestines of food animals...
December 2017: Animal Health Research Reviews
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