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Gene expression microbiome

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https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28797279/huanglongbing-impairs-the-rhizosphere-to-rhizoplane-enrichment-process-of-the-citrus-root-associated-microbiome
#5
Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28790923/gut-microbiome-response-to-sucralose-and-its-potential-role-in-inducing-liver-inflammation-in-mice
#6
Xiaoming Bian, Liang Chi, Bei Gao, Pengcheng Tu, Hongyu Ru, Kun Lu
Sucralose is the most widely used artificial sweetener, and its health effects have been highly debated over the years. In particular, previous studies have shown that sucralose consumption can alter the gut microbiota. The gut microbiome plays a key role in processes related to host health, such as food digestion and fermentation, immune cell development, and enteric nervous system regulation. Inflammation is one of the most common effects associated with gut microbiome dysbiosis, which has been linked to a series of human diseases, such as diabetes and obesity...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28790203/the-in-feed-antibiotic-carbadox-induces-phage-gene-transcription-in-the-swine-gut-microbiome
#7
Timothy A Johnson, Torey Looft, Andrew J Severin, Darrell O Bayles, Daniel J Nasko, K Eric Wommack, Adina Howe, Heather K Allen
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28782205/microbiota-derived-tryptophan-indoles-increase-after-gastric-bypass-surgery-and-reduce-intestinal-permeability-in-vitro-and-in-vivo
#8
M Jennis, C R Cavanaugh, G C Leo, J R Mabus, J Lenhard, P J Hornby
BACKGROUND: The diet and microbiome contribute to metabolic disease in part due to increased intestinal inflammation and permeability. Dietary tryptophan is metabolized by both mammalian and bacterial enzymes. Using in vitro, in vivo models, and clinical data, we tested whether bacterial tryptophan indole derivatives underlie the positive benefits of microbiota on inflammation that is associated with metabolic disease. METHODS: In high-fat diet (HFD)-fed mice intestinal permeability and plasma endotoxin levels were measured after indole-3-propionic acid (IPA; 20 mg kg(-1) p...
August 7, 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/28775250/modulation-of-the-tick-gut-milieu-by-a-secreted-tick-protein-favors-borrelia-burgdorferi-colonization
#9
Sukanya Narasimhan, Tim J Schuijt, Nabil M Abraham, Nallakkandi Rajeevan, Jeroen Coumou, Morven Graham, Andrew Robson, Ming-Jie Wu, Sirlei Daffre, Joppe W Hovius, Erol Fikrig
The Lyme disease agent, Borrelia burgdorferi, colonizes the gut of the tick Ixodes scapularis, which transmits the pathogen to vertebrate hosts including humans. Here we show that B. burgdorferi colonization increases the expression of several tick gut genes including pixr, encoding a secreted gut protein with a Reeler domain. RNA interference-mediated silencing of pixr, or immunity against PIXR in mice, impairs the ability of B. burgdorferi to colonize the tick gut. PIXR inhibits bacterial biofilm formation in vitro and in vivo...
August 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28774887/suppressed-hepatic-bile-acid-signalling-despite-elevated-production-of-primary-and-secondary-bile-acids-in-nafld
#10
Na Jiao, Susan S Baker, Adrian Chapa-Rodriguez, Wensheng Liu, Colleen A Nugent, Maria Tsompana, Lucy Mastrandrea, Michael J Buck, Robert D Baker, Robert J Genco, Ruixin Zhu, Lixin Zhu
OBJECTIVE: Bile acids are regulators of lipid and glucose metabolism, and modulate inflammation in the liver and other tissues. Primary bile acids such as cholic acid and chenodeoxycholic acid (CDCA) are produced in the liver, and converted into secondary bile acids such as deoxycholic acid (DCA) and lithocholic acid by gut microbiota. Here we investigated the possible roles of bile acids in non-alcoholic fatty liver disease (NAFLD) pathogenesis and the impact of the gut microbiome on bile acid signalling in NAFLD...
August 3, 2017: Gut
https://www.readbyqxmd.com/read/28771620/a-benign-helminth-alters-the-host-immune-system-and-the-gut-microbiota-in-a-rat-model-system
#11
Laura Wegener Parfrey, Milan Jirků, Radek Šíma, Marie Jalovecká, Bohumil Sak, Karina Grigore, Kateřina Jirků Pomajbíková
Helminths and bacteria are major players in the mammalian gut ecosystem and each influences the host immune system and health. Declines in helminth prevalence and bacterial diversity appear to play a role in the dramatic rise of immune mediated inflammatory diseases (IMIDs) in western populations. Helminths are potent modulators of immune system and their reintroduction is a promising therapeutic avenue for IMIDs. However, the introduction of helminths represents a disturbance for the host and it is important to understand the impact of helminth reintroduction on the host, including the immune system and gut microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/28770064/transcriptomic-differentiation-underlying-marine-to-freshwater-transitions-in-the-south-american-silversides-odontesthes-argentinensis-and-o-%C3%A2-bonariensis-atheriniformes
#12
Lily C Hughes, Gustavo M Somoza, Bryan N Nguyen, James P Bernot, Mariano González-Castro, Juan Martín Díaz de Astarloa, Guillermo Ortí
Salinity gradients are critical habitat determinants for freshwater organisms. Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28761934/metabolic-fingerprints-from-the-human-oral-microbiome-reveal-a-vast-knowledge-gap-of-secreted-small-peptidic-molecules
#13
Anna Edlund, Neha Garg, Hosein Mohimani, Alexey Gurevich, Xuesong He, Wenyuan Shi, Pieter C Dorrestein, Jeffrey S McLean
Recent research indicates that the human microbiota play key roles in maintaining health by providing essential nutrients, providing immune education, and preventing pathogen expansion. Processes underlying the transition from a healthy human microbiome to a disease-associated microbiome are poorly understood, partially because of the potential influences from a wide diversity of bacterium-derived compounds that are illy defined. Here, we present the analysis of peptidic small molecules (SMs) secreted from bacteria and viewed from a temporal perspective...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761060/administration-of-lactobacillus-salivarius-li01-or-pediococcus-pentosaceus-li05-prevents-ccl4-induced-liver-cirrhosis-by-protecting-the-intestinal-barrier-in-rats
#14
Ding Shi, Longxian Lv, Daiqiong Fang, Wenrui Wu, Chenxia Hu, Lichen Xu, Yanfei Chen, Jing Guo, Xinjun Hu, Ang Li, Feifei Guo, Jianzhong Ye, Yating Li, Dewi Andayani, Lanjuan Li
Alterations in the gut microbiome have been reported in liver cirrhosis, and probiotic interventions are considered a potential treatment strategy. This study aimed to evaluate the effects and mechanisms of Lactobacillus salivarius LI01, Pediococcus pentosaceus LI05, Lactobacillus rhamnosus GG, Clostridium butyricum MIYAIRI and Bacillus licheniformis Zhengchangsheng on CCl4-induced cirrhotic rats. Only administration of LI01 or LI05 prevented liver fibrosis and down-regulated the hepatic expression of profibrogenic genes...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28759308/vasopressin-deletion-is-associated-with-sex-specific-shifts-in-the-gut-microbiome
#15
Christopher T Fields, Benoit Chassaing, Matthew J Paul, Andrew T Gewirtz, Geert J de Vries
Brattleboro rats harbor a spontaneous deletion of the arginine-vasopressin (Avp) gene. In addition to diabetes insipidus, these rats exhibit low levels of anxiety and depressive behaviors. Recent work on the gut-brain axis has revealed that gut microbiota can influence anxiety behaviors. Therefore, we studied the effects of Avp gene deletion on gut microbiota. Since Avp gene expression is sexually different, we also examined how Avp deletion affects sex differences in gut microbiota. Males and females show modest but differentiated shifts in taxa abundance across 3 separate Avp deletion genotypes: wildtype (WT), heterozygous (Het) and AVP-deficient Brattleboro (KO) rats...
July 31, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28759253/differential-recognition-of-mtb-specific-epitopes-as-a-function-of-tuberculosis-disease-history
#16
Thomas J Scriba, Chelsea Carpenter, Sebastian Carrasco Pro, John Sidney, Munyaradzi Musvosvi, Virginie Rozot, Grégory Seumois, Sandy L Rosales, Pandurangan Vijayanand, Delia Goletti, Edward Makgotlho, Willem Hanekom, Mark Hatherill, Bjoern Peters, Alessandro Sette, Cecilia S Lindestam Arlehamn
RATIONALE: Individuals with a history of tuberculosis disease are at elevated risk of disease recurrance. The underlying cause is not known, but one explanation is that previous disease results in less effective immunity against Mycobacterium tuberculosis (Mtb). OBJECTIVE: We hypothesized that the repertoire of Mtb-derived epitopes recognized by T cells from individuals with latent Mtb infection (LTBI) differs as a function of previous diagnosis of active tuberculosis (TB) disease...
July 31, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28756121/distal-airway-microbiome-is-associated-with-immunoregulatory-myeloid-cell-responses-in-lung-transplant-recipients
#17
Nirmal S Sharma, Keith M Wille, S Athira, Degui Zhi, Kenneth P Hough, Enrique Diaz-Guzman, Kui Zhang, Ranjit Kumar, Sunad Rangarajan, Peter Eipers, Yong Wang, Ritesh K Srivastava, Jose Vicente Rodriguez Dager, Mohammad Athar, Casey Morrow, Charles W Hoopes, David D Chaplin, Victor J Thannickal, Jessy S Deshane
BACKGROUND: Long-term survival of lung transplant recipients (LTRs) is limited by the occurrence of bronchiolitis obliterans syndrome (BOS). Recent evidence suggests a role for microbiome alterations in the occurrence of BOS, although the precise mechanisms are unclear. In this study we evaluated the relationship between the airway microbiome and distinct subsets of immunoregulatory myeloid-derived suppressor cells (MDSCs) in LTRs. METHODS: Bronchoalveolar lavage (BAL) and simultaneous oral wash and nasal swab samples were collected from adult LTRs...
July 15, 2017: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/28754707/repression-of-salmonella-host-cell-invasion-by-aromatic-small-molecules-from-the-human-fecal-metabolome
#18
Rafael J M Peixoto, Eduardo S Alves, Melody Wang, Rosana B R Ferreira, Alessandra Granato, Jun Han, Hira Gill, Kevan Jacobson, Leandro A Lobo, Regina M C P Domingues, Christoph H Borchers, Julian E Davies, B Brett Finlay, L Caetano M Antunes
The human microbiome is a collection of microorganisms that inhabit every surface of the body that is exposed to the environment, generally coexisting peacefully with their host. These microbes have important functions such as the production of vitamins, maturation of the immune system and protection against pathogens. We have previously shown that a small-molecule extract from the human fecal microbiome has a strong repressive effect on Salmonella enterica serovar Typhimurium host cell invasion by modulating the expression of genes involved in this process...
July 28, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28749495/characterization-of-a-highly-efficient-antibiotic-degrading-metallo-%C3%AE-lactamase-obtained-from-an-uncultured-member-of-a-permafrost-community
#19
Marcelo Monteiro Pedroso, Christopher Selleck, Charmaine Enculescu, Jeffrey R Harmer, Nataša Mitić, Whitney R Craig, Waleed Helweh, Philip Hugenholtz, Gene W Tyson, David L Tierney, James A Larrabee, Gerhard Schenk
Antibiotic resistance is a major global health problem, one that threatens to derail the benefits garnered from arguably the greatest success of modern medicine, the discovery of antibiotics. Among the most potent agents contributing to antibiotic resistance are metallo-β-lactamases (MBLs). The discovery of MBL-like enzymes in microorganisms that are not in contact with the human population is of particular concern as these proteins already have the in-built capacity to inactivate antibiotics, even though they may not need MBL activity for their survival...
August 16, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28721208/new-perspectives-on-the-regulation-of-type-ii-inflammation-in-asthma
#20
REVIEW
Mireya Becerra-Díaz, Marsha Wills-Karp, Nicola M Heller
Asthma is a chronic inflammatory disease of the lungs which has been thought to arise as a result of inappropriately directed T helper type-2 (Th2) immune responses of the lungs to otherwise innocuous inhaled antigens. Current asthma therapeutics are directed towards the amelioration of downstream consequences of type-2 immune responses (i.e. β-agonists) or broad-spectrum immunosuppression (i.e. corticosteroids). However, few approaches to date have been focused on the primary prevention of immune deviation...
2017: F1000Research
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