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Gene expression microbiome

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https://www.readbyqxmd.com/read/28220297/what-roles-do-colon-stem-cells-and-gap-junctions-play-in-the-left-and-right-location-of-origin-of-colorectal-cancers
#1
James E Trosko, Heinz-Josef Lenz
This "Commentary" examines an important clinical observation that right-sided colorectal cancers appear less treatable than the left-sided cancers. The concepts of (a) the "initiation/promotion/progression" process, (b) the stem cell hypothesis, (c) the role gap junctional intercellular communication, (d) cancer cells lacking GJIC either because of the non-expression of connexin genes or of non-functional gap junction proteins, and (e) the role of the microbiome in promoting initiated colon stem cells to divide symmetrically or asymmetrically are examined to find an explanation...
February 20, 2017: Journal of Cell Communication and Signaling
https://www.readbyqxmd.com/read/28209760/glucoraphanin-ameliorates-obesity-and-insulin-resistance-through-adipose-tissue-browning-and-reduction-of-metabolic-endotoxemia-in-mice
#2
Naoto Nagata, Liang Xu, Susumu Kohno, Yusuke Ushida, Yudai Aoki, Ryohei Umeda, Nobuo Fuke, Fen Zhuge, Yinhua Ni, Mayumi Nagashimada, Chiaki Takahashi, Hiroyuki Suganuma, Shuichi Kaneko, Tsuguhito Ota
Low-grade sustained inflammation links obesity to insulin resistance and nonalcoholic fatty liver disease (NAFLD). However, therapeutic approaches to improve systemic energy balance and chronic inflammation in obesity are limited. Pharmacological activation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) alleviates obesity and insulin resistance in mice; however, Nrf2 inducers are not clinically available owing to safety concerns. Thus, we examined whether dietary glucoraphanin, a stable precursor of the Nrf2 inducer sulforaphane, ameliorates systemic energy balance, chronic inflammation, insulin resistance, and NAFLD in high-fat diet (HFD)-fed mice...
February 16, 2017: Diabetes
https://www.readbyqxmd.com/read/28197129/the-ecological-role-of-type-three-secretion-systems-in-the-interaction-of-bacteria-with-fungi-in-soil-and-related-habitats-is-diverse-and-context-dependent
#3
REVIEW
Rashid Nazir, Sylvie Mazurier, Pu Yang, Philippe Lemanceau, Jan Dirk van Elsas
Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#4
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28166818/resistant-starch-can-improve-insulin-sensitivity-independently-of-the-gut-microbiota
#5
Laure B Bindels, Rafael R Segura Munoz, João Carlos Gomes-Neto, Valentin Mutemberezi, Inés Martínez, Nuria Salazar, Elizabeth A Cody, Maria I Quintero-Villegas, Hatem Kittana, Clara G de Los Reyes-Gavilán, Robert J Schmaltz, Giulio G Muccioli, Jens Walter, Amanda E Ramer-Tait
BACKGROUND: Obesity-related diseases, including type 2 diabetes and cardiovascular disease, have reached epidemic proportions in industrialized nations, and dietary interventions for their prevention are therefore important. Resistant starches (RS) improve insulin sensitivity in clinical trials, but the mechanisms underlying this health benefit remain poorly understood. Because RS fermentation by the gut microbiota results in the formation of physiologically active metabolites, we chose to specifically determine the role of the gut microbiota in mediating the metabolic benefits of RS...
February 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28157391/microbes-associate-with-host-innate-immune-response-in-idiopathic-pulmonary-fibrosis
#6
Yong Huang, Shwu-Fan Ma, Milena S Espindola, Rekha Vij, Justin M Oldham, Gary B Huffnagle, John R Erb-Downward, Kevin R Flaherty, Beth B Moore, Eric S White, Tong Zhou, Jianrong Li, Yves A Lussier, MeiLan K Han, Naftali Kaminski, Joe G N Garcia, Cory M Hogaboam, Fernando J Martinez, Imre Noth
RATIONALE: Differences in the lung microbial community influence idiopathic pulmonary fibrosis (IPF) progression. Whether the lung microbiome influences IPF host defense remains unknown. OBJECTIVES: To explore the host immune response and microbial interaction in IPF, as they relate to progression-free survival (PFS), fibroblast function, and leukocyte phenotypes. METHODS: Paired microarray gene expression data from peripheral blood mononuclear cells (PBMCs) and 16s rRNA sequencing data from bronchoalveolar lavage (BAL) obtained as part of the COMET-IPF study were used to conduct association pathway analyses...
February 3, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#7
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, Nicola Segata
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling...
January 2017: MSystems
https://www.readbyqxmd.com/read/28133586/possible-health-impacts-of-bt-toxins-and-residues-from-spraying-with-complementary-herbicides-in-genetically-engineered-soybeans-and-risk-assessment-as-performed-by-the-european-food-safety-authority-efsa
#8
REVIEW
Christoph Then, Andreas Bauer-Panskus
BACKGROUND: MON89788 was the first genetically engineered soybean worldwide to express a Bt toxin. Under the brand name Intacta, Monsanto subsequently engineered a stacked trait soybean using MON89788 and MON87701-this stacked soybean expresses an insecticidal toxin and is, in addition, tolerant to glyphosate. After undergoing risk assessment by the European Food Safety Authority (EFSA), the stacked event was authorised for import into the EU in June 2012, including for use in food and feed...
2017: Environmental Sciences Europe
https://www.readbyqxmd.com/read/28125562/o-014-bacterial-sensor-nod2-deletion-causes-th2-inflammatory-bowel-disease-improvement-without-inducing-acute-metatranscriptomic-dysbiosis-in-mice
#9
Alexander Rodriguez-Palacios, Daniele Corridoni, Gabriella Di Stefano, Luca Di Martino, D A Antonopoulos, Eugene Chang, T T Pizarro, Fabio Cominelli
BACKGROUND: Although single nucleotide polymorphisms in the NOD2 (nucleotide-binding oligomerization domain-containing 2) gene have been associated with the pathogenesis of Crohn's disease (CD), little is known about the role of nonpolymorphic wild-type (WT) NOD2 genes in the gut. To date, most animal studies addressing the role of WT NOD2 have been conducted using healthy (ileitis/colitis-free) mouse strains, and have attributed a modulating effect to the gut microbiome, partly based on 16S rRNA sequencing...
February 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28111075/discovery-of-reactive-microbiota-derived-metabolites-that-inhibit-host-proteases
#10
Chun-Jun Guo, Fang-Yuan Chang, Thomas P Wyche, Keriann M Backus, Timothy M Acker, Masanori Funabashi, Mao Taketani, Mohamed S Donia, Stephen Nayfach, Katherine S Pollard, Charles S Craik, Benjamin F Cravatt, Jon Clardy, Christopher A Voigt, Michael A Fischbach
The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the National Institutes of Health Human Microbiome Project (NIH HMP) stool samples, and they are transcribed under conditions of host colonization...
January 26, 2017: Cell
https://www.readbyqxmd.com/read/28096258/regulation-of-glucose-uptake-and-enteroendocrine-function-by-the-intestinal-epithelial-insulin-receptor
#11
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
#12
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
#13
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
#14
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...
January 10, 2017: 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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