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Gene expression microbiome

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https://www.readbyqxmd.com/read/29333342/is-there-a-link-between-aging-and-microbiome-diversity-in-exceptional-mammalian-longevity
#1
Graham M Hughes, John Leech, Sébastien J Puechmaille, Jose V Lopez, Emma C Teeling
A changing microbiome has been linked to biological aging in mice and humans, suggesting a possible role of gut flora in pathogenic aging phenotypes. Many bat species have exceptional longevity given their body size and some can live up to ten times longer than expected with little signs of aging. This study explores the anal microbiome of the exceptionally long-lived Myotis myotis bat, investigating bacterial composition in both adult and juvenile bats to determine if the microbiome changes with age in a wild, long-lived non-model organism, using non-lethal sampling...
2018: PeerJ
https://www.readbyqxmd.com/read/29331497/dietary-antioxidant-micronutrients-alter-mucosal-inflammatory-risk-in-a-murine-model-of-genetic-and-microbial-susceptibility
#2
Joseph F Pierre, Reinhard Hinterleitner, Romain Bouziat, Nathan A Hubert, Vanessa Leone, Jun Miyoshi, Bana Jabri, Eugene B Chang
Inflammatory bowel diseases (IBD) are caused by the convergence of microbial, environmental, and genetic factors. Diet significantly alters these interactions by affecting both the host and microbiome. Using a mucosal inflammatory model that resembles the human condition of ileal pouchitis, we investigated the effects of Control (CONT) or Antioxidant (AOX) diet, containing pharmacologically relevant levels of 4 micronutrients, on disease risk in wild-type and IL-10-/- animals following surgical self-filling (SF) ileal blind loop placement...
December 10, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29330189/targeted-synthesis-and-characterization-of-a-gene-cluster-encoding-nad-p-h-dependent-3%C3%AE-3%C3%AE-and-12%C3%AE-hydroxysteroid-dehydrogenases-from-eggerthella-cag-298-a-gut-metagenomic-sequence
#3
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29315562/hfe-genotype-restricts-the-response-to-paraquat-in-a-mouse-model-of-neurotoxicity
#4
Anne M Nixon, Mark D Meadowcroft, Elizabeth B Neely, Amanda M Snyder, Carson J Purnell, Justin Wright, Regina Lamendella, Wint Nandar, Xuemei Huang, James R Connor
Parkinson's disease (PD) is marked clinically by motor dysfunction and pathologically by dopaminergic cell loss in the substantia nigra (SN) and iron accumulation in the substantia nigra. The driver underlying iron accumulation is unknown and could be genetic or environmental. The HFE protein is critical for the regulation of cellular iron uptake. Mutations within this protein are associated with increased iron accumulation including in the brain. We have focused on the commonly occurring H63D variant of the HFE gene as a disease modifier in a number of neurodegenerative diseases...
January 8, 2018: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29312814/on-revealing-the-gene-targets-of-ebola-virus-micrornas-involved-in-the-human-skin-microbiome
#5
Pei-Chun Hsu, Bin-Hao Chiou, Chun-Ming Huang
Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and has a high mortality rate. Histopathological and immunopathological analyses of Ebola virus have revealed that histopathological changes in skin tissue are associated with various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial for the skin immune shield. The discovery of microRNAs (miRNAs) in Ebola virus implies that immune escape, endothelial cell rupture, and tissue dissolution during Ebola virus infection are a result of the effects of Ebola virus miRNAs...
2018: PeerJ
https://www.readbyqxmd.com/read/29311644/dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome
#6
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G Wilson, Jonathan Braun, Lee A Denson, Subra Kugathasan, Dermot P B McGovern, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period...
January 8, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29303995/local-acetaldehyde-an-essential-role-in-alcohol-related-upper-gastrointestinal-tract-carcinogenesis
#7
REVIEW
Mikko T Nieminen, Mikko Salaspuro
The resident microbiome plays a key role in exposure of the upper gastrointestinal (GI) tract mucosa to acetaldehyde (ACH), a carcinogenic metabolite of ethanol. Poor oral health is a significant risk factor for oral and esophageal carcinogenesis and is characterized by a dysbiotic microbiome. Dysbiosis leads to increased growth of opportunistic pathogens (such as Candida yeasts) and may cause an up to 100% increase in the local ACH production, which is further modified by organ-specific expression and gene polymorphisms of ethanol-metabolizing and ACH-metabolizing enzymes...
January 5, 2018: Cancers
https://www.readbyqxmd.com/read/29300010/acoustic-reporter-genes-for-noninvasive-imaging-of-microorganisms-in-mammalian-hosts
#8
Raymond W Bourdeau, Audrey Lee-Gosselin, Anupama Lakshmanan, Arash Farhadi, Sripriya Ravindra Kumar, Suchita P Nety, Mikhail G Shapiro
The mammalian microbiome has many important roles in health and disease, and genetic engineering is enabling the development of microbial therapeutics and diagnostics. A key determinant of the activity of both natural and engineered microorganisms in vivo is their location within the host organism. However, existing methods for imaging cellular location and function, primarily based on optical reporter genes, have limited deep tissue performance owing to light scattering or require radioactive tracers. Here we introduce acoustic reporter genes, which are genetic constructs that allow bacterial gene expression to be visualized in vivo using ultrasound, a widely available inexpensive technique with deep tissue penetration and high spatial resolution...
January 3, 2018: Nature
https://www.readbyqxmd.com/read/29280960/metagomics-a-web-based-tool-for-peptide-centric-functional-and-taxonomic-analysis-of-metaproteomics-data
#9
Michael Riffle, Damon H May, Emma Timmins-Schiffman, Molly P Mikan, Daniel Jaschob, William Stafford Noble, Brook L Nunn
Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data...
December 27, 2017: Proteomes
https://www.readbyqxmd.com/read/29249928/the-antioxidant-cofactor-alpha-lipoic-acid-may-control-endogenous-formaldehyde-metabolism-in-mammals
#10
Anastasia V Shindyapina, Tatiana V Komarova, Ekaterina V Sheshukova, Natalia M Ershova, Vadim N Tashlitsky, Alexander V Kurkin, Ildar R Yusupov, Garik V Mkrtchyan, Murat Y Shagidulin, Yuri L Dorokhov
The healthy human body contains small amounts of metabolic formaldehyde (FA) that mainly results from methanol oxidation by pectin methylesterase, which is active in a vegetable diet and in the gastrointestinal microbiome. With age, the ability to maintain a low level of FA decreases, which increases the risk of Alzheimer's disease and dementia. It has been shown that 1,2-dithiolane-3-pentanoic acid or alpha lipoic acid (ALA), a naturally occurring dithiol and antioxidant cofactor of mitochondrial α-ketoacid dehydrogenases, increases glutathione (GSH) content and FA metabolism by mitochondrial aldehyde dehydrogenase 2 (ALDH2) thus manifests a therapeutic potential beyond its antioxidant property...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29233893/diversification-of-type-vi-secretion-system-toxins-reveals-ancient-antagonism-among-bee-gut-microbes
#11
Margaret I Steele, Waldan K Kwong, Marvin Whiteley, Nancy A Moran
Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi, a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29218031/crispr-cas-systems-in-bacteroides-fragilis-an-important-pathobiont-in-the-human-gut-microbiome
#12
Mehrdad Tajkarimi, Hannah M Wexler
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29216634/lysine-restriction-affects-feed-intake-and-amino-acid-metabolism-via-gut-microbiome-in-piglets
#13
Jie Yin, Hui Han, Yuying Li, Zhaojin Liu, Yurong Zhao, Rejun Fang, Xingguo Huang, Jie Zheng, Wenkai Ren, Fei Wu, Gang Liu, Xin Wu, Kai Wang, Liping Sun, Chunyong Li, Tiejun Li, Yulong Yin
BACKGROUND/AIMS: Our previous reports suggested that dietary supplementation with lysine influenced intestinal absorption and metabolism of amino acids. In this study, we further investigated the effect of lysine restriction (30%) on feed intake and we also tested the hypothesis that gut microbiome contributed to the potential mechanism of lysine restriction-mediated feeding behavior. Here, we profiled gut microbial communities by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from gut samples as well as growth performance, serum hormones, and intestinal lysine transport in a piglet model...
December 6, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29213261/antibiotic-induced-alterations-in-gut-microbiota-are-associated-with-changes-in-glucose-metabolism-in-healthy-mice
#14
Richard R Rodrigues, Renee L Greer, Xiaoxi Dong, Karen N DSouza, Manoj Gurung, Jia Y Wu, Andrey Morgun, Natalia Shulzhenko
The gut microbiome plays an important role in health and disease. Antibiotics are known to alter gut microbiota, yet their effects on glucose tolerance in lean, normoglycemic mice have not been widely investigated. In this study, we aimed to explore mechanisms by which treatment of lean mice with antibiotics (ampicillin, metronidazole, neomycin, vancomycin, or their cocktail) influences the microbiome and glucose metabolism. Specifically, we sought to: (i) study the effects on body weight, fasting glucose, glucose tolerance, and fasting insulin, (ii) examine the changes in expression of key genes of the bile acid and glucose metabolic pathways in the liver and ileum, (iii) identify the shifts in the cecal microbiota, and (iv) infer interactions between gene expression, microbiome, and the metabolic parameters...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29211769/arsenic-exposure-and-intestinal-microbiota-in-children-from-sirajdikhan-bangladesh
#15
Xiaoxi Dong, Natalia Shulzhenko, Julien Lemaitre, Renee L Greer, Kate Peremyslova, Quazi Quamruzzaman, Mahmudar Rahman, Omar Sharif Ibn Hasan, Sakila Afroz Joya, Mostofa Golam, David C Christiani, Andriy Morgun, Molly L Kile
BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life. RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure...
2017: PloS One
https://www.readbyqxmd.com/read/29192963/reader-reaction-on-the-fast-small-sample-kernel-independence-test-for-microbiome-community-level-association-analysis
#16
Bin Guo, Baolin Wu
Zhan et al. () presented a kernel RV coefficient (KRV) test to evaluate the overall association between host gene expression and microbiome composition, and showed its competitive performance compared to existing methods. In this article, we clarify the close relation of KRV to the existing generalized RV (GRV) coefficient, and show that KRV and GRV have very similar performance. Although the KRV test could control the type I error rate well at 1% and 5% levels, we show that it could largely underestimate p-values at small significance levels leading to significantly inflated type I errors...
November 29, 2017: Biometrics
https://www.readbyqxmd.com/read/29181446/discrete-false-discovery-rate-improves-identification-of-differentially-abundant-microbes
#17
Lingjing Jiang, Amnon Amir, James T Morton, Ruth Heller, Ery Arias-Castro, Rob Knight
Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold...
November 2017: MSystems
https://www.readbyqxmd.com/read/29181381/impact-of-dietary-galacto-oligosaccharide-gos-on-chicken-s-gut-microbiota-mucosal-gene-expression-and-salmonella-colonization
#18
Rebecca-Ayme Hughes, Riawana A Ali, Mary A Mendoza, Hosni M Hassan, Matthew D Koci
Preventing Salmonella colonization in young birds is key to reducing contamination of poultry products for human consumption (eggs and meat). While several Salmonella vaccines have been developed that are capable of yielding high systemic antibodies, it is not clear how effective these approaches are at controlling or preventing Salmonella colonization of the intestinal tract. Effective alternative control strategies are needed to help supplement the bird's ability to prevent Salmonella colonization, specifically by making the cecum less hospitable to Salmonella...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29178599/gut-microbiome-induced-shift-of-acetate-to-butyrate-positively-manages-dysbiosis-in-high-fat-diet
#19
Xu Si, Wenting Shang, Zhongkai Zhou, Padraig Strappe, Bing Wang, Anthony Bird, Chris Blanchard
SCOPE: A recent study revealed the accumulation of gut microbiota-produced acetate (GMPA) led to insulin over-secretion and obesity symptom. To further develop this scientific point, effect of resistant starch (RS) or exogenous acetate carried by RS (RSA) in the gut on metabolic syndrome is investigated using diet-induced obese rats. METHODS AND RESULTS: The metabonomics analysis showed that the gut of rats in RSA group generated more significant butyrate both in serum and feces rather than acetate compared to the rats in RS group, indicating the conversion among metabolites, in particular from acetate to butyrate via gut microbiota...
November 26, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29167663/metagenomic-analysis-of-the-gut-microbiome-of-the-common-black-slug-arion-ater-in-search-of-novel-lignocellulose-degrading-enzymes
#20
Ryan Joynson, Leighton Pritchard, Ekenakema Osemwekha, Natalie Ferry
Some eukaryotes are able to gain access to well-protected carbon sources in plant biomass by exploiting microorganisms in the environment or harbored in their digestive system. One is the land pulmonate Arion ater, which takes advantage of a gut microbial consortium that can break down the widely available, but difficult to digest, carbohydrate polymers in lignocellulose, enabling them to digest a broad range of fresh and partially degraded plant material efficiently. This ability is considered one of the major factors that have enabled A...
2017: Frontiers in Microbiology
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