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Gene expression microbiome

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https://www.readbyqxmd.com/read/28096258/regulation-of-glucose-uptake-and-enteroendocrine-function-by-the-intestinal-epithelial-insulin-receptor
#1
Siegfried Ussar, Max-Felix Haering, Shiho Fujisaka, Dominik Lutter, Kevin Y Lee, Ning Li, Georg K Gerber, Lynn Bry, C Ronald Kahn
Insulin and IGF-1 receptors (IR and IGF1R) are major regulators of metabolism and cell growth throughout the body, however, their roles in the intestine remain controversial. Here we show that genetic ablation of the IR or IGF1R in intestinal epithelial cells of mice does not impair intestinal growth or development or the composition of the gut microbiome. However, loss of IR alters intestinal epithelial gene expression, especially in pathways related to glucose uptake and metabolism. More importantly, loss of IR reduces intestinal glucose uptake...
January 17, 2017: Diabetes
https://www.readbyqxmd.com/read/28036141/expression-of-eukaryotic-like-protein-in-the-microbiome-of-sponges
#2
C Díez-Vives, L Moitinho-Silva, S Nielsen, D Reynolds, T Thomas
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28034915/early-life-antibiotic-treatment-enhances-the-pathogenicity-of-cd4-t-cells-during-intestinal-inflammation
#3
Sebastian Scheer, Tiago S Medina, Alex Murison, Matthew D Taves, Frann Antignano, Alistair Chenery, Kiran K Soma, Georgia Perona-Wright, Mathieu Lupien, Cheryl H Arrowsmith, Daniel D De Carvalho, Colby Zaph
The incidence of inflammatory bowel diseases (IBDs) has steadily increased in recent decades-a phenomenon that cannot be explained by genetic mutations alone. Other factors, including the composition of the intestinal microbiome, are potentially important contributors to the increased occurrence of this group of diseases. Previous reports have shown a correlation between early-life antibiotic (Abx) treatment and an increased incidence of IBD. In this report, we investigated the effects of early-life Abx treatments on the pathogenicity of CD4(+) T cells using an experimental T cell transfer model of IBD...
December 29, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28028242/lanthanide-dependent-cross-feeding-of-methane-derived-carbon-is-linked-by-microbial-community-interactions
#4
Sascha M B Krause, Timothy Johnson, Yasodara Samadhi Karunaratne, Yanfen Fu, David A C Beck, Ludmila Chistoserdova, Mary E Lidstrom
The utilization of methane, a potent greenhouse gas, is an important component of local and global carbon cycles that is characterized by tight linkages between methane-utilizing (methanotrophic) and nonmethanotrophic bacteria. It has been suggested that the methanotroph sustains these nonmethanotrophs by cross-feeding, because subsequent products of the methane oxidation pathway, such as methanol, represent alternative carbon sources. We established cocultures in a microcosm model system to determine the mechanism and substrate that underlay the observed cross-feeding in the environment...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28019040/a-small-sample-multivariate-kernel-machine-test-for-microbiome-association-studies
#5
Xiang Zhan, Xingwei Tong, Ni Zhao, Arnab Maity, Michael C Wu, Jun Chen
High-throughput sequencing technologies have enabled large-scale studies of the role of the human microbiome in health conditions and diseases. Microbial community level association test, as a critical step to establish the connection between overall microbiome composition and an outcome of interest, has now been routinely performed in many studies. However, current microbiome association tests all focus on a single outcome. It has become increasingly common for a microbiome study to collect multiple, possibly related, outcomes to maximize the power of discovery...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28013406/simulated-microgravity-affects-some-biological-characteristics-of-lactobacillus-acidophilus
#6
Dongyan Shao, Linbo Yao, Muhammad Shahid Riaz, Jing Zhu, Junling Shi, Mingliang Jin, Qingsheng Huang, Hui Yang
The effects of weightlessness on enteric microorganisms have been extensively studied, but have mainly been focused on pathogens. As a major component of the microbiome of the human intestinal tract, probiotics are important to keep the host healthy. Accordingly, understanding their changes under weightlessness conditions has substantial value. This study was carried out to investigate the characteristics of Lactobacillus acidophilus, a typical probiotic for humans, under simulated microgravity (SMG) conditions...
December 24, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27981307/microbiota-small-rnas-in-inflammatory-bowel-disease
#7
REVIEW
Anca T Filip, Ovidiu Balacescu, Catalin Marian, Andrei Anghel
MiRNAs are a class of potential gene regulators of critical importance in Inflammatory Bowel Disease (IBD). This review aims to present the connection between gut microbiota, probiotics administration and microRNA (miRNA) expression in IBD. It also brings into question cross-kingdom RNAi (RNA interference). Not only that gut host cells garden the intestinal microbiome via miRNA, but also strong evidence supports the idea that different species of bacteria have an impact on the intestinal immune response by modulating miRNA expression...
December 2016: Journal of Gastrointestinal and Liver Diseases: JGLD
https://www.readbyqxmd.com/read/27980034/qsec-inhibition-as-an-antivirulence-approach-for-colitis-associated-bacteria
#8
Michelle G Rooks, Patrick Veiga, Analise Z Reeves, Sydney Lavoie, Koji Yasuda, Yasunari Asano, Kazufumi Yoshihara, Monia Michaud, Leslie Wardwell-Scott, Carey Ann Gallini, Jonathan N Glickman, Nobuyuki Sudo, Curtis Huttenhower, Cammie F Lesser, Wendy S Garrett
Hosts and their microbes have established a sophisticated communication system over many millennia. Within mammalian hosts, this dynamic cross-talk is essential for maintaining intestinal homeostasis. In a genetically susceptible host, dysbiosis of the gut microbiome and dysregulated immune responses are central to the development of inflammatory bowel disease (IBD). Previous surveys of stool from the T-bet(-/-)Rag2(-/-) IBD mouse model revealed microbial features that discriminate between health and disease states...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27935837/patient-specific-bacteroides-genome-variants-in-pouchitis
#9
Joseph H Vineis, Daina L Ringus, Hilary G Morrison, Tom O Delmont, Sushila Dalal, Laura H Raffals, Dionysios A Antonopoulos, David T Rubin, A Murat Eren, Eugene B Chang, Mitchell L Sogin
: A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen...
November 15, 2016: MBio
https://www.readbyqxmd.com/read/27896820/ppar%C3%AE-targeted-oral-cancer-treatment-and-additional-utility-of-genomics-analytic-techniques
#10
Nathan Handley, Jacob Eide, Randall Taylor, Beverly Wuertz, Patrick Gaffney, Frank Ondrey
OBJECTIVE: Peroxisome proliferator-activated receptor γ (PPARγ) agonists have been shown to have anti-proliferative, anti-angiogenic, and proapoptotic effects, leading to interest in their use as cancer therapeutics. Pioglitazone, a U.S. Food and Drug Administration-approved type II diabetes medication and PPARγ agonist, may have a role in adjuvant head-and-neck squamous cell carcinoma treatment or prevention. Therefore, the purpose of this study was: 1) to treat oral cavity cancer cells with the PPARγ activator, pioglitazone, to analyze gene expression changes; and 2) to compare those changes with our preexisting genomic data for development of hypothesis-driven additional basic and clinical studies...
November 29, 2016: Laryngoscope
https://www.readbyqxmd.com/read/27892926/dual-specificity-phosphatase-6-deficiency-regulates-gut-microbiome-and-transcriptome-response-against-diet-induced-obesity-in-mice
#11
Jhen-Wei Ruan, Sarah Statt, Chih-Ting Huang, Yi-Ting Tsai, Cheng-Chin Kuo, Hong-Lin Chan, Yu-Chieh Liao, Tse-Hua Tan, Cheng-Yuan Kao
The gut microbiota plays profound roles in host metabolism and the inflammatory response associated with the development of obesity. Dusp6-deficient mice have been shown to be resistant to diet-induced obesity, but the mechanism behind this remains unclear. 16S ribosomal RNA gene analysis demonstrated that dusp6-deficient mice harbour unique gut microbiota with resistance to diet-induced-obesity-mediated alteration of the gut microbiome. Using a germ-free mouse model, we found that faecal/gut microbiota derived from dusp6-deficient mice significantly increased energy expenditure and reduced weight gain in recipient wild-type mice fed on a high-fat diet...
November 28, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27871908/acetylated-deoxycholic-dca-and-cholic-ca-acids-are-potent-ligands-of-pregnane-x-pxr-receptor
#12
Alejandro Carazo, Lucie Hyrsova, Jan Dusek, Hana Chodounska, Alzbeta Horvatova, Karel Berka, Vaclav Bazgier, Hongying Gan-Schreier, Waleé Chamulitrat, Eva Kudova, Petr Pavek
The Pregnane X (PXR), Vitamin D (VDR) and Farnesoid X (FXR) nuclear receptors have been shown to be receptors of bile acids controlling their detoxification or synthesis. Chenodeoxycholic (CDCA) and lithocholic (LCA) acids are ligands of FXR and VDR, respectively, whereas 3-keto and acetylated derivates of LCA have been described as ligands for all three receptors. In this study, we hypothesized that oxidation or acetylation at position 3, 7 and 12 of bile acids DCA (deoxycholic acid), LCA, CA (cholic acid), and CDCA by detoxification enzymes or microbiome may have an effect on the interactions with bile acid nuclear receptors...
January 4, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/27871240/abo-antigen-and-secretor-statuses-are-not-associated-with-gut-microbiota-composition-in-1-500-twins
#13
Emily R Davenport, Julia K Goodrich, Jordana T Bell, Tim D Spector, Ruth E Ley, Andrew G Clark
BACKGROUND: Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such factor is the ABO antigen. This molecule is not only expressed on the surface of red blood cells, but is also secreted from mucosal surfaces in individuals containing an intact FUT2 gene (secretors)...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27853522/recent-advances-in-entamoeba-biology-rna-interference-drug-discovery-and-gut-microbiome
#14
REVIEW
Pedro Morgado, Dipak Manna, Upinder Singh
In recent years, substantial progress has been made in understanding the molecular and cell biology of the human parasite Entamoeba histolytica, an important pathogen with significant global impact. This review outlines some recent advances in the Entamoeba field in the last five years, focusing on areas that have not recently been discussed in detail: (i) molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis...
2016: F1000Research
https://www.readbyqxmd.com/read/27829448/the-bronchial-epithelial-cell-bacterial-microbiome-and-host-response-in-patients-infected-with-human-immunodeficiency-virus
#15
Marc A Sze, Stella Xu, Janice M Leung, Emily A Vucic, Tawimas Shaipanich, Aida Moghadam, Marianne Harris, Silvia Guillemi, Sunita Sinha, Corey Nislow, Darra Murphy, Cameron Hague, Jonathon Leipsic, Stephen Lam, Wan Lam, Julio S Montaner, Don D Sin, S F Paul Man
BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. METHODS: Two bronchial brush samples were obtained from 21 HIV-infected patients...
November 9, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27825829/metagenomics-probing-pollutant-fate-in-natural-and-engineered-ecosystems
#16
REVIEW
Emna Bouhajja, Spiros N Agathos, Isabelle F George
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field...
December 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27822530/moleculo-long-read-sequencing-facilitates-assembly-and-genomic-binning-from-complex-soil-metagenomes
#17
Richard Allen White, Eric M Bottos, Taniya Roy Chowdhury, Jeremy D Zucker, Colin J Brislawn, Carrie D Nicora, Sarah J Fansler, Kurt R Glaesemann, Kevin Glass, Janet K Jansson
Soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87...
May 2016: MSystems
https://www.readbyqxmd.com/read/27809786/analysis-of-gene-expression-in-the-midgut-of-bombyx-mori-during-the-larval-molting-stage
#18
Bing Yang, Wuren Huang, Jie Zhang, Qiuyun Xu, Shoulin Zhu, Qiaoli Zhang, Brenda T Beerntsen, Hongsheng Song, Erjun Ling
BACKGROUND: Insects can be models for understanding human intestinal infection and pathology. Molting, a special period during which the old insect cuticle is shed and a new one is produced, is crucial for insect development. Holometabolous insects may experience several larva-to-larva moltings to become larger, a pupal molt and adult eclosion to become adults. During the larval molts, they stop feeding and become quiescent. Although the molting larvae become quiescent, it is not known if changes in microbiome, physiology, development and immunity of midguts occur...
November 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27807042/mice-fed-a-high-fat-diet-supplemented-with-resistant-starch-display-marked-shifts-in-the-liver-metabolome-concurrent-with-altered-gut-bacteria
#19
Dorothy A Kieffer, Brian D Piccolo, Maria L Marco, Eun Bae Kim, Michael L Goodson, Michael J Keenan, Tamara N Dunn, Knud Erik Bach Knudsen, Roy J Martin, Sean H Adams
BACKGROUND: High-amylose-maize resistant starch type 2 (HAMRS2) is a fermentable dietary fiber known to alter the gut milieu, including the gut microbiota, which may explain the reported effects of resistant starch to ameliorate obesity-associated metabolic dysfunction. OBJECTIVE: Our working hypothesis was that HAMRS2-induced microbiome changes alter gut-derived signals (i.e., xenometabolites) reaching the liver via the portal circulation, in turn altering liver metabolism by regulating gene expression and other pathways...
December 2016: Journal of Nutrition
https://www.readbyqxmd.com/read/27801835/dietary-gluten-induced-gut-dysbiosis-is-accompanied-by-selective-upregulation-of-micrornas-with-intestinal-tight-junction-and-bacteria-binding-motifs-in-rhesus-macaque-model-of-celiac-disease
#20
Mahesh Mohan, Cheryl-Emiliane T Chow, Caitlin N Ryan, Luisa S Chan, Jason Dufour, Pyone P Aye, James Blanchard, Charles P Moehs, Karol Sestak
The composition of the gut microbiome reflects the overall health status of the host. In this study, stool samples representing the gut microbiomes from 6 gluten-sensitive (GS) captive juvenile rhesus macaques were compared with those from 6 healthy, age- and diet-matched peers. A total of 48 samples representing both groups were studied using V4 16S rRNA gene DNA analysis. Samples from GS macaques were further characterized based on type of diet administered: conventional monkey chow, i.e., wheat gluten-containing diet (GD), gluten-free diet (GFD), barley gluten-derived diet (BOMI) and reduced gluten barley-derived diet (RGB)...
October 28, 2016: Nutrients
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