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Metatranscriptome

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https://www.readbyqxmd.com/read/28694295/in-vivo-analysis-of-the-viable-microbiota-and-helicobacter-pylori-transcriptome-in-gastric-infection-and-early-stages-of-carcinogenesis
#1
Kaisa Thorell, Johan Bengtsson-Palme, Oscar Hsin-Fu Liu, Reyna Victoria Palacios Gonzales, Intawat Nookaew, Linda Rabeneck, Lawrence Paszat, David Y Graham, Jens Nielsen, Samuel B Lundin, Åsa Sjöling
Emerging evidence shows that the human microbiota plays a larger role in disease progression and health than previously anticipated. Helicobacter pylori, the causative agent of gastric cancer and duodenal and gastric ulcers, was early associated with gastric disease, but it has also been proposed that the accompanying microbiota in Helicobacter pylori-infected individuals might affect disease progression and gastric cancer development. In this study, the composition of the transcriptionally active microbial community and the H...
July 10, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28686852/integrated-meta-omic-analyses-of-the-gastrointestinal-tract-microbiome-in-patients-undergoing-allogeneic-hematopoietic-stem-cell-transplantation
#2
Anne Kaysen, Anna Heintz-Buschart, Emilie E L Muller, Shaman Narayanasamy, Linda Wampach, Cédric C Laczny, Norbert Graf, Arne Simon, Katharina Franke, Jörg Bittenbring, Paul Wilmes, Jochen G Schneider
In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes, during allo-HSCT, and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies...
June 20, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28676233/customized-workflow-development-and-data-modularization-concepts-for-rna-sequencing-and-metatranscriptome-experiments
#3
Steffen C Lott, Markus Wolfien, Konstantin Riege, Andrea Bagnacani, Olaf Wolkenhauer, Steve Hoffmann, Wolfgang R Hess
RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses...
July 1, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28674682/the-microbiome-and-blood-pressure-%C3%A2-can-microbes-regulate-our-blood-pressure
#4
REVIEW
Souhaila Al Khodor, Bernd Reichert, Ibrahim F Shatat
The surfaces of the human body are heavily populated by a highly diverse microbial ecosystem termed the microbiota. The largest and richest among these highly heterogeneous populations of microbes is the gut microbiota. The collection of microbes and their genes, called the microbiome, has been studied intensely through the past few years using novel metagenomics, metatranscriptomics, and metabolomics approaches. This has enhanced our understanding of how the microbiome affects our metabolic, immunologic, neurologic, and endocrine homeostasis...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28661199/respiratory-microbiota-and-lower-respiratory-tract-disease
#5
Miguel Lanaspa, Quique Bassat, Marcia Melo Medeiros, Camen Muñoz-Almagro
The respiratory airways harbor a complex succession of ecological niches with distinct but related bacterial communities. Particular challenges of respiratory microbiome research have led to limited scientific output compared to other human microbiomes. Areas covered: In this review, we summarize the current state of knowledge of the bacterial respiratory microbiome, with a particular focus on associations between the respiratory microbiome and lower respiratory tract conditions. Expert commentary: There is growing evidence that the respiratory microbiome is associated with lower respiratory infectious diseases and related conditions...
June 29, 2017: Expert Review of Anti-infective Therapy
https://www.readbyqxmd.com/read/28659879/co-registered-geochemistry-and-metatranscriptomics-reveal-unexpected-distributions-of-microbial-activity-within-a-hydrothermal-vent-field
#6
Heather C Olins, Daniel R Rogers, Christina Preston, William Ussler, Douglas Pargett, Scott Jensen, Brent Roman, James M Birch, Christopher A Scholin, M Fauzi Haroon, Peter R Girguis
Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28656958/virus-host-relationships-of-marine-single-celled-eukaryotes-resolved-from-metatranscriptomics
#7
Mohammad Moniruzzaman, Louie L Wurch, Harriet Alexander, Sonya T Dyhrman, Christopher J Gobler, Steven W Wilhelm
Establishing virus-host relationships has historically relied on culture-dependent approaches. Here we report on the use of marine metatranscriptomics to probe virus-host relationships. Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of polyadenylation-selected RNA sequences from microbial communities dominated by Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts...
June 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/28654333/identification-of-genes-for-synthesis-of-the-blue-pigment-biliverdin-ix%C3%AE-in-the-blue-coral-heliopora-coerulea
#8
Yuki Hongo, Nina Yasuda, Satoshi NagaI
Heliopora coerulea is the only species in the subclass Octocorallia that has a crystalline aragonite skeleton. The skeleton has been reported to contain the blue pigment, biliverdin IXα, which is formed by heme oxygenase (HO) during heme decomposition. There is little information regarding gene expression in H. coerulea; therefore, the biosynthesis pathway for biliverdin IXα is poorly understood. To identify the genes related to heme synthesis and degradation, metatranscripts of H. coerulea and its symbiont Symbiodinium spp...
April 2017: Biological Bulletin
https://www.readbyqxmd.com/read/28632755/potassium-is-a-key-signal-in-host-microbiome-dysbiosis-in-periodontitis
#9
Susan Yost, Ana E Duran-Pinedo, Keerthana Krishnan, Jorge Frias-Lopez
Dysbiosis, or the imbalance in the structural and/or functional properties of the microbiome, is at the origin of important infectious inflammatory diseases such as inflammatory bowel disease (IBD) and periodontal disease. Periodontitis is a polymicrobial inflammatory disease that affects a large proportion of the world's population and has been associated with a wide variety of systemic health conditions, such as diabetes, cardiovascular and respiratory diseases. Dysbiosis has been identified as a key element in the development of the disease...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28607437/single-stranded-rna-viruses-infecting-the-invasive-argentine-ant-linepithema-humile
#10
Monica A M Gruber, Meghan Cooling, James W Baty, Kevin Buckley, Anna Friedlander, Oliver Quinn, Jessica F E J Russell, Alexandra Sébastien, Philip J Lester
Social insects host a diversity of viruses. We examined New Zealand populations of the globally widely distributed invasive Argentine ant (Linepithema humile) for RNA viruses. We used metatranscriptomic analysis, which identified six potential novel viruses in the Dicistroviridae family. Of these, three contigs were confirmed by Sanger sequencing as Linepithema humile virus-1 (LHUV-1), a novel strain of Kashmir bee virus (KBV) and Black queen cell virus (BQCV), while the others were chimeric or misassembled sequences...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607432/characterisation-of-a-stable-laboratory-co-culture-of-acidophilic-nanoorganisms
#11
Susanne Krause, Andreas Bremges, Philipp C Münch, Alice C McHardy, Johannes Gescher
This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the order Thermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA identity of one archaeon is only 91.6% compared to the most closely related isolate Thermogymnomonas acidicola. Hence, this organism is the first member of a new genus...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28602082/linking-genes-to-microbial-biogeochemical-cycling-lessons-from-arsenic
#12
Yong-Guan Zhu, Xi-Mei Xue, Andreas Kappler, Barry P Rosen, Andrew A Meharg
The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species...
June 23, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28561030/metabolic-network-analysis-reveals-microbial-community-interactions-in-anammox-granules
#13
Christopher E Lawson, Sha Wu, Ananda S Bhattacharjee, Joshua J Hamilton, Katherine D McMahon, Ramesh Goel, Daniel R Noguera
Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions...
May 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28548659/metatranscriptomic-analysis-of-prokaryotic-communities-active-in-sulfur-and-arsenic-cycling-in-mono-lake-california-usa
#14
Christian F Edwardson, James T Hollibaugh
This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28546481/metagenomes-and-metatranscriptomes-of-activated-sludge-from-a-sewage-plant-with-or-without-aerobic-granule-enrichment
#15
Julien Crovadore, Vice Soljan, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort
We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28539641/revealing-the-insoluble-metasecretome-of-lignocellulose-degrading-microbial-communities
#16
Anna M Alessi, Susannah M Bird, Joseph P Bennett, Nicola C Oates, Yi Li, Adam A Dowle, Igor Polikarpov, J Peter W Young, Simon J McQueen-Mason, Neil C Bruce
Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28535339/ecophysiological-examination-of-the-lake-erie-microcystis-bloom-in-2014-linkages-between-biology-and-the-water-supply-shutdown-of-toledo-oh
#17
Morgan M Steffen, Timothy W Davis, R Michael L McKay, George S Bullerjahn, Lauren E Krausfeldt, Joshua M A Stough, Michelle L Neitzey, Naomi E Gilbert, Gregory L Boyer, Thomas H Johengen, Duane C Gossiaux, Ashley M Burtner, Danna Palladino, Mark D Rowe, Gregory J Dick, Kevin A Meyer, Shawn Levy, Braden E Boone, Richard P Stumpf, Timothy T Wynne, Paul V Zimba, Danielle Gutierrez, Steven W Wilhelm
Annual cyanobacterial blooms dominated by Microcystis have occurred in western Lake Erie (U.S./Canada) during summer months since 1995. The production of toxins by bloom-forming cyanobacteria can lead to drinking water crises, such as the one experienced by the city of Toledo in August of 2014, when the city was rendered without drinking water for >2 days. It is important to understand the conditions and environmental cues that were driving this specific bloom to provide a scientific framework for management of future bloom events...
June 8, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28526844/identification-of-extracellular-glycerophosphodiesterases-in-pseudomonas-and-their-role-in-soil-organic-phosphorus-remineralisation
#18
Ian D E A Lidbury, Andrew R J Murphy, Tandra D Fraser, Gary D Bending, Alexandra M E Jones, Jonathan D Moore, Andrew Goodall, Mark Tibbett, John P Hammond, David J Scanlan, Elizabeth M H Wellington
In soils, phosphorus (P) exists in numerous organic and inorganic forms. However, plants can only acquire inorganic orthophosphate (Pi), meaning global crop production is frequently limited by P availability. To overcome this problem, rock phosphate fertilisers are heavily applied, often with negative environmental and socio-economic consequences. The organic P fraction of soil contains phospholipids that are rapidly degraded resulting in the release of bioavailable Pi. However, the mechanisms behind this process remain unknown...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515336/the-effects-of-micronutrient-deficiencies-on-bacterial-species-from-the-human-gut-microbiota
#19
Matthew C Hibberd, Meng Wu, Dmitry A Rodionov, Xiaoqing Li, Jiye Cheng, Nicholas W Griffin, Michael J Barratt, Richard J Giannone, Robert L Hettich, Andrei L Osterman, Jeffrey I Gordon
Vitamin and mineral (micronutrient) deficiencies afflict 2 billion people. Although the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the gut microbiota of developing or adult humans. Therefore, we established a community of cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron, or zinc, followed by return to the sufficient diet...
May 17, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#20
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
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