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Gene expression microbiome

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https://www.readbyqxmd.com/read/28932814/the-gut-commensal-microbiome-of-drosophila-melanogaster-is-modified-by-the-endosymbiont-wolbachia
#1
Rama K Simhadri, Eva M Fast, Rong Guo, Michaela J Schultz, Natalie Vaisman, Luis Ortiz, Joanna Bybee, Barton E Slatko, Horacio M Frydman
Endosymbiotic Wolbachia bacteria and the gut microbiome have independently been shown to affect several aspects of insect biology, including reproduction, development, life span, stem cell activity, and resistance to human pathogens, in insect vectors. This work shows that Wolbachia bacteria, which reside mainly in the fly germline, affect the microbial species present in the fly gut in a lab-reared strain. Drosophila melanogaster hosts two main genera of commensal bacteria-Acetobacter and Lactobacillus. Wolbachia-infected flies have significantly reduced titers of Acetobacter...
September 2017: MSphere
https://www.readbyqxmd.com/read/28929970/bayesian-unidimensional-scaling-for-visualizing-uncertainty-in-high-dimensional-datasets-with-latent-ordering-of-observations
#2
Lan Huong Nguyen, Susan Holmes
BACKGROUND: Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous process, often unknown. Estimating data points' 'natural ordering' and their corresponding uncertainties can help researchers draw insights about the mechanisms involved...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28917668/gut-microbe-mediated-suppression-of-inflammation-associated-colon-carcinogenesis-by-luminal-histamine-production
#3
Chunxu Gao, Bhanu Priya Ganesh, Zhongcheng Shi, Rajesh Rasik Shah, Robert Fultz, Angela Major, Susan Venable, Monica Lugo, Kathleen Hoch, Xiaowei Chen, Anthony Haag, Timothy C Wang, James Versalovic
Microbiome-mediated suppression of carcinogenesis may open new avenues for identification of therapeutic targets and prevention strategies in oncology. Histidine decarboxylase (HDC) deficiency has been shown to promote inflammation-associated colorectal cancer by accumulation of CD11b(+)Gr-1(+) immature myeloid cells, indicating a potential antitumorigenic effect of histamine. Here, we demonstrate that administration of hdc(+)Lactobacillus reuteri in the gut resulted in luminal hdc gene expression and histamine production in the intestines of Hdc(-/-) mice...
September 6, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28912574/distinct-gut-microbiome-patterns-associate-with-consensus-molecular-subtypes-of-colorectal-cancer
#4
Rachel V Purcell, Martina Visnovska, Patrick J Biggs, Sebastian Schmeier, Frank A Frizelle
Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28906277/effect-of-cytomegalovirus-and-epstein-barr-virus-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#5
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: One hundred and eight (108) biopsies from left and right colon (n = 79) and terminal ileum (n = 29) were collected from 19 HIV-infected and 22 HIV-uninfected participants. Levels of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNA were measured by droplet digital PCR. Mucosal gene expression was measured via multiplex-assay...
September 24, 2017: AIDS
https://www.readbyqxmd.com/read/28904640/short-term-dietary-methionine-supplementation-affects-one-carbon-metabolism-and-dna-methylation-in-the-mouse-gut-and-leads-to-altered-microbiome-profiles-barrier-function-gene-expression-and-histomorphology
#6
Isabelle R Miousse, Rupak Pathak, Sarita Garg, Charles M Skinner, Stepan Melnyk, Oleksandra Pavliv, Howard Hendrickson, Reid D Landes, Annie Lumen, Alan J Tackett, Nicolaas E P Deutz, Martin Hauer-Jensen, Igor Koturbash
BACKGROUND: Methionine, a central molecule in one-carbon metabolism, is an essential amino acid required for normal growth and development. Despite its importance to biological systems, methionine is toxic when administered at supra-physiological levels. The aim of this study was to investigate the effects of short-term methionine dietary modulation on the proximal jejunum, the section of the gut specifically responsible for amino acid absorption, in a mouse model. Eight-week-old CBA/J male mice were fed methionine-adequate (MAD; 6...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/28901864/prenatal-stress-enhances-susceptibility-to-allergic-diseases-of-offspring
#7
Maria Moustaki, Sophia Tsabouri, Kostas Priftis, Konstantinos Douros
BACKGROUND AND OBJECTIVES: Maternal prenatal stress (MPS) may result in a range of long-term consequences in the offspring among which is susceptibility to allergic diseases. This review presents the current knowledge on the pathways through which MPS may affect the fetus, and the existing evidence regarding the association between MPS and development of allergy in the offspring. RESULT AND DISCUSSION: A pivotal mediator triggered in response to stress is the release of glucocorticoids (GC)...
September 12, 2017: Endocrine, Metabolic & Immune Disorders Drug Targets
https://www.readbyqxmd.com/read/28889823/epigenetics-and-dohad-from-basics-to-birth-and-beyond
#8
T Bianco-Miotto, J M Craig, Y P Gasser, S J van Dijk, S E Ozanne
Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models...
September 11, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28883813/a-structural-and-functional-elucidation-of-the-rumen-microbiome-influenced-by-various-diets-and-microenvironments
#9
Simon Deusch, Amélia Camarinha-Silva, Jürgen Conrad, Uwe Beifuss, Markus Rodehutscord, Jana Seifert
The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28877764/perilipin-2-modulates-dietary-fat-induced-microbial-global-gene-expression-profiles-in-the-mouse-intestine
#10
Xuejian Xiong, Elise S Bales, Diana Ir, Charles E Robertson, James L McManaman, Daniel N Frank, John Parkinson
BACKGROUND: Intestinal microbiota are critical determinants of obesity and metabolic disease risk. In previous work, we showed that deletion of the cytoplasmic lipid droplet (CLD) protein perilipin-2 (Plin2) modulates gut microbial community structure and abrogates long-term deleterious effects of a high-fat (HF) diet in mice. However, the impact of Plin2 on microbiome function is unknown. RESULTS: Here, we used metatranscriptomics to identify differences in microbiome transcript expression in WT and Plin2-null mice following acute exposure to high-fat/low-carbohydrate (HF) or low-fat/high-carbohydrate (LF) diets...
September 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28873424/dual-specificity-phosphatase-6-deficiency-is-associated-with-impaired-systemic-glucose-tolerance-and-reversible-weight-retardation-in-mice
#11
Katrin Pfuhlmann, Paul T Pfluger, Sonja C Schriever, Timo D Müller, Matthias H Tschöp, Kerstin Stemmer
Here, we aimed to investigate the potential role of DUSP6, a dual specificity phosphatase, that specifically inactivates extracellular signal-regulated kinase (ERK), for the regulation of body weight and glucose homeostasis. We further assessed whether metabolic challenges affect Dusp6 expression in selected brain areas or white adipose tissue. Hypothalamic Dusp6 mRNA levels remained unchanged in chow-fed lean vs. high fat diet (HFD) fed obese C57Bl/6J mice, and in C57Bl/6J mice undergoing prolonged fasting or refeeding with fat free diet (FFD) or HFD...
2017: PloS One
https://www.readbyqxmd.com/read/28870713/dietary-pomegranate-extract-and-inulin-affect-gut-microbiome-differentially-in-mice-fed-an-obesogenic-diet
#12
Song Zhang, Jieping Yang, Susanne M Henning, Rupo Lee, Mark Hsu, Emma Grojean, Rita Pisegna, Austin Ly, David Heber, Zhaoping Li
Growing evidence suggests that dysbiosis of gut microbiota is associated with pathogenesis of a variety of human diseases. Using dietary intervention to shape the composition and metabolism of the gut microbiota is increasingly recognized. In the present study, we investigated the effects of polysaccharide inulin and polyphenol-rich pomegranate extract (PomX) alone or in combination on the cecal microbiota composition and function in a diet induced obesity mouse model. Male C57BL/6 mice were randomly divided into four experimental groups and consumed either high-fat/high-sucrose [HF/HS (32% energy from fat, 25% energy from sucrose, 17% energy from protein)] diet, HF/HS diet supplemented with PomX (0...
September 13, 2017: Anaerobe
https://www.readbyqxmd.com/read/28864748/novel-interactions-between-gut-microbiome-and-host-drug-processing-genes-modify-the-hepatic-metabolism-of-the-environmental-chemicals-pbdes
#13
Cindy Yanfei Li, Soowan Lee, Sara Cade, Li-Jung Kuo, Irvin R Schultz, Deepak K Bhatt, Bhagwat Prasad, Theo K Bammler, Julia Yue Cui
The gut microbiome is a novel frontier in xenobiotic metabolism. Polybrominated diphenyl ethers (PBDEs), especially BDE-47 and BDE-99, are among the most abundant and persistent environmental contaminants that produce a variety of toxicities. Little is known about how the gut microbiome affects the hepatic metabolism of PBDEs and the PBDE-mediated regulation of drug-processing genes (DPGs) in vivo. The goal of this study was to determine the role of gut microbiome in modulating the hepatic biotransformation of PBDEs...
September 1, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/28863779/optimization-of-a-metatranscriptomic-approach-to-study-the-lignocellulolytic-potential-of-the-higher-termite-gut-microbiome
#14
Martyna Marynowska, Xavier Goux, David Sillam-Dussès, Corinne Rouland-Lefèvre, Yves Roisin, Philippe Delfosse, Magdalena Calusinska
BACKGROUND: Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes...
September 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28838324/microbial-regulation-of-microrna-expression-in-the-amygdala-and-prefrontal-cortex
#15
Alan E Hoban, Roman M Stilling, Gerard M Moloney, Rachel D Moloney, Fergus Shanahan, Timothy G Dinan, John F Cryan, Gerard Clarke
BACKGROUND: There is growing evidence for a role of the gut microbiome in shaping behaviour relevant to many psychiatric and neurological disorders. Preclinical studies using germ-free (GF) animals have been essential in contributing to our current understanding of the potential importance of the host microbiome for neurodevelopment and behaviour. In particular, it has been repeatedly demonstrated that manipulation of the gut microbiome modulates anxiety-like behaviours. The neural circuits that underlie anxiety- and fear-related behaviours are complex and heavily depend on functional communication between the amygdala and prefrontal cortex (PFC)...
August 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28821301/space-type-radiation-induces-multimodal-responses-in-the-mouse-gut-microbiome-and-metabolome
#16
David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory Nelson, Martin Hauer-Jensen, Marjan Boerma, Jonathan Braun, Amrita K Cheema
BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel...
August 18, 2017: Microbiome
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#17
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28812142/tcdd-administered-on-activated-carbon-eliminates-bioavailability-and-subsequent-shifts-to-a-key-murine-gut-commensal
#18
Robert D Stedtfeld, J Brett Sallach, Robert B Crawford, Tiffany M Stedtfeld, Maggie R Williams, Hassan Waseem, Cliff T Johnston, Hui Li, Brian J Teppen, Norbert E Kaminski, Stephen A Boyd, James M Tiedje, Syed A Hashsham
Activated carbon (AC) is an increasingly attractive remediation alternative for the sequestration of dioxins at contaminated sites globally. However, the potential for AC to reduce the bioavailability of dioxins in mammals and the residing gut microbiota has received less attention. This question was partially answered in a recent study examining 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced hallmark toxic responses in mice administered with TCDD sequestered by AC or freely available in corn oil by oral gavage...
August 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#19
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28804485/transcriptional-profiling-of-midguts-prepared-from-trypanosoma-t-congolense-positive-glossina-palpalis-palpalis-collected-from-two-distinct-cameroonian-foci-coordinated-signatures-of-the-midguts-remodeling-as-t-congolense-supportive-niches
#20
Jean M Tsagmo Ngoune, Flobert Njiokou, Béatrice Loriod, Ginette Kame-Ngasse, Nicolas Fernandez-Nunez, Claire Rioualen, Jacques van Helden, Anne Geiger
Our previous transcriptomic analysis of Glossina palpalis gambiensis experimentally infected or not with Trypanosoma brucei gambiense aimed to detect differentially expressed genes (DEGs) associated with infection. Specifically, we selected candidate genes governing tsetse fly vector competence that could be used in the context of an anti-vector strategy, to control human and/or animal trypanosomiasis. The present study aimed to verify whether gene expression in field tsetse flies (G. p. palpalis) is modified in response to natural infection by trypanosomes (T...
2017: Frontiers in Immunology
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