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Metatranscriptome

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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/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#2
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28797298/community-characteristics-of-the-gut-microbiomes-of-competitive-cyclists
#3
Lauren M Petersen, Eddy J Bautista, Hoan Nguyen, Blake M Hanson, Lei Chen, Sai H Lek, Erica Sodergren, George M Weinstock
BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28797279/huanglongbing-impairs-the-rhizosphere-to-rhizoplane-enrichment-process-of-the-citrus-root-associated-microbiome
#4
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/28793929/shifts-in-coastal-sediment-oxygenation-cause-pronounced-changes-in-microbial-community-composition-and-associated-metabolism
#5
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28793203/rna-extraction-from-decaying-wood-for-meta-transcriptomic-analyses
#6
Martino Adamo, Samuele Voyron, Mariangela Girlanda, Roland Marmeisse
Wood decomposition is a key step of the terrestrial carbon cycle and of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating to wood decay we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms...
August 9, 2017: Canadian Journal of Microbiology
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/28789673/gene-and-transcript-abundances-of-bacterial-type-iii-secretion-systems-from-the-rumen-microbiome-are-correlated-with-methane-yield-in-sheep
#8
Janine Kamke, Priya Soni, Yang Li, Siva Ganesh, William J Kelly, Sinead C Leahy, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. METHODS: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep...
August 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28782034/effects-of-silver-nanoparticles-on-nitrification-and-associated-nitrous-oxide-production-in-aquatic-environments
#9
Yanling Zheng, Lijun Hou, Min Liu, Silvia E Newell, Guoyu Yin, Chendi Yu, Hongli Zhang, Xiaofei Li, Dengzhou Gao, Juan Gao, Rong Wang, Cheng Liu
Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N2O) production in estuarine sediments...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28777380/sulfide-production-and-oxidation-by-heterotrophic-bacteria-under-aerobic-conditions
#10
Yongzhen Xia, Chuanjuan Lü, Ningke Hou, Yufeng Xin, Jihua Liu, Honglei Liu, Luying Xun
Sulfide (H2S, HS(-) and S(2-)) oxidation to sulfite and thiosulfate by heterotrophic bacteria, using sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO), has recently been reported as a possible detoxification mechanism for sulfide at high levels. Bioinformatic analysis revealed that the sqr and pdo genes were common in sequenced bacterial genomes, implying the sulfide oxidation may have other physiological functions. SQRs have previously been classified into six types. Here we grouped PDOs into three types and showed that some heterotrophic bacteria produced and released H2S from organic sulfur into the headspace during aerobic growth, and others, for example, Pseudomonas aeruginosa PAO1, with sqr and pdo did not release H2S...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28772023/evidence-for-h2-consumption-by-uncultured-desulfobacterales-in-coastal-sediments
#11
Stefan Dyksma, Petra Pjevac, Kin Ovanesov, Marc Mussmann
Molecular hydrogen (H2 ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favorable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments...
August 3, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28769888/unraveling-core-functional-microbiota-in-traditional-solid-state-fermentation-by-high-throughput-amplicons-and-metatranscriptomics-sequencing
#12
Zhewei Song, Hai Du, Yan Zhang, Yan Xu
Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28767318/the-gut-microbiome-and-mental-health-implications-for-anxiety-and-trauma-related-disorders
#13
Stefanie Malan-Muller, Mireia Valles-Colomer, Jeroen Raes, Christopher A Lowry, Soraya Seedat, Sian M J Hemmings
Biological psychiatry research has long focused on the brain in elucidating the neurobiological mechanisms of anxiety- and trauma-related disorders. This review challenges this assumption and suggests that the gut microbiome and its interactome also deserve attention to understand brain disorders and develop innovative treatments and diagnostics in the 21st century. The recent, in-depth characterization of the human microbiome spurred a paradigm shift in human health and disease. Animal models strongly suggest a role for the gut microbiome in anxiety- and trauma-related disorders...
August 2, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28763055/viral-to-metazoan-marine-plankton-nucleotide-sequences-from-the-tara-oceans-expedition
#14
Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédérick Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Mark Wessner, Silvia G Acinas, Marta Royo-Llonch, Francisco M Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E Sieracki, Ramunas Stepanauskas, Matthew B Sullivan, Jennifer R Brum, Melissa B Duhaime, Bonnie T Poulos, Bonnie L Hurwitz, Stéphane Pesant, Eric Karsenti, Patrick Wincker
A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities...
August 1, 2017: Scientific Data
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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