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Metatranscriptome

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https://www.readbyqxmd.com/read/28279485/discovering-protein-coding-genes-from-the-environment-time-for-the-eukaryotes
#1
REVIEW
Roland Marmeisse, Harald Kellner, Laurence Fraissinet-Tachet, Patricia Luis
Eukaryotic microorganisms from diverse environments encompass a large number of taxa, many of them still unknown to science. One strategy to mine these organisms for genes of biotechnological relevance is to use a pool of eukaryotic mRNA directly extracted from environmental samples. Recent reports demonstrate that the resulting metatranscriptomic cDNA libraries can be screened by expression in yeast for a wide range of genes and functions from many of the different eukaryotic taxa. In combination with novel emerging high-throughput technologies, we anticipate that this approach should contribute to exploring the functional diversity of the eukaryotic microbiota...
March 6, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28258137/metatranscriptomic-evidence-for-direct-interspecies-electron-transfer-between-geobacter-and-methanothrix-species-in-methanogenic-rice-paddy-soils
#2
Dawn E Holmes, Pravin M Shrestha, David J F Walker, Yan Dang, Kelly P Nevin, Trevor L Woodard, Derek R Lovley
The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNAseq libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET...
March 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28251799/diet-affects-arctic-ground-squirrel-gut-microbial-metatranscriptome-independent-of-community-structure
#3
Jasmine J Hatton, Timothy J Stevenson, C Loren Buck, Khrystyne N Duddleston
We examined the effect of diet on pre-hibernation fattening and the gut microbiota of captive arctic ground squirrels (Urocitellus parryii). We measured body composition across time and gut microbiota density, diversity, and function prior to and after five-weeks on control, high-fat, low-fat (18%, 40%, and 10% energy from fat, respectively), or restricted calorie (50% of control) diets. Squirrels fattened at the same rate and to the same degree on all diets. Additionally, we found no differences in gut microbiota diversity or short chain fatty acid production across time or with diet...
March 2, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28246035/functional-gene-profiling-through-metarnaseq-approach-reveals-diet-dependent-variation-in-rumen-microbiota-of-buffalo-bubalus-bubalis
#4
Ankit T Hinsu, Nidhi R Parmar, Neelam M Nathani, Ramesh J Pandit, Anand B Patel, Amrutlal K Patel, Chaitanya G Joshi
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection...
February 27, 2017: Anaerobe
https://www.readbyqxmd.com/read/28242596/research-progress-of-stoichiogenomics
#5
Lan Yang, Hu Jiangtao, Zhang Yujuan
Stoichiogenomics is a newly arisen research field, which concerns the element usage biases of biological macromolecules at genome, transcriptome, proteome, metabonome levels. Different biological macromolecules have different element compositions and contents. When the supply of some elements was constrained, natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules. This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies, more and more available metagenomic and metatranscriptomic data, and the applications of new analysis strategies...
February 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28235871/metatranscriptomic-profiling-reveals-linkages-between-the-active-rumen-microbiome-and-feed-efficiency-in-beef-cattle
#6
Fuyong Li, Le Luo Guan
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n=10; inefficient, n=10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic datasets...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28218463/closed-reference-metatranscriptomics-enables-in-planta-profiling-of-putative-virulence-activities-in-the-grapevine-trunk-disease-complex
#7
Abraham Morales-Cruz, Gabrielle Allenbeck, Rosa Figueroa-Balderas, Vanessa E Ashworth, Daniel P Lawrence, Renaud Travadon, Rhonda J Smith, Kendra Baumgartner, Philippe E Rolshausen, Dario Cantu
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i...
February 20, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28217745/the-baltic-sea-virome-diversity-and-transcriptional-activity-of-dna-and-rna-viruses
#8
Lisa Zeigler Allen, John P McCrow, Karolina Ininbergs, Christopher L Dupont, Jonathan H Badger, Jeffery M Hoffman, Martin Ekman, Andrew E Allen, Birgitta Bergman, J Craig Venter
Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae...
January 2017: MSystems
https://www.readbyqxmd.com/read/28197133/metatranscriptomics-reveals-the-active-bacterial-and-eukaryotic-fibrolytic-communities-in-the-rumen-of-dairy-cow-fed-a-mixed-diet
#9
Sophie Comtet-Marre, Nicolas Parisot, Pascale Lepercq, Frédérique Chaucheyras-Durand, Pascale Mosoni, Eric Peyretaillade, Ali R Bayat, Kevin J Shingfield, Pierre Peyret, Evelyne Forano
Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28188205/metagenomic-and-metatranscriptomic-analyses-reveal-structure-and-dynamics-of-a-dechlorinating-community-containing-dehalococcoides-mccartyi-and-corrinoid-providing-microorganisms-under-cobalamin-limited-condition
#10
Yujie Men, Ke Yu, Jacob Bælum, Ying Gao, Julien Tremblay, Emmanuel Prestat, Ben Stenuit, Susannah G Tringe, Janet Jansson, Tong Zhang, Lisa Alvarez-Cohen
The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE) - dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28179898/metatranscriptomic-analysis-reveals-unexpectedly-diverse-microbial-metabolism-in-a-biogeochemical-hot-spot-in-an-alluvial-aquifer
#11
Talia N M Jewell, Ulas Karaoz, Markus Bill, Romy Chakraborty, Eoin L Brodie, Kenneth H Williams, Harry R Beller
Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28155666/ribotagger-fast-and-unbiased-16s-18s-profiling-using-whole-community-shotgun-metagenomic-or-metatranscriptome-surveys
#12
Chao Xie, Chin Lui Wesley Goi, Daniel H Huson, Peter F R Little, Rohan B H Williams
BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#13
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/28125587/correction-metatranscriptomic-study-of-common-and-host-specific-patterns-of-gene-expression-between-pines-and-their-symbiotic-ectomycorrhizal-fungi-in-the-genus-suillus
#14
Hui-Ling Liao, Yuan Chen, Rytas Vilgalys
[This corrects the article DOI: 10.1371/journal.pgen.1006348.].
January 2017: PLoS Genetics
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
#15
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/28125344/translating-omics-to-food-microbiology
#16
Aaron M Walsh, Fiona Crispie, Marcus J Claesson, Paul D Cotter
This review examines the applications of omics technologies in food microbiology, with a primary focus on high-throughput sequencing (HTS) technologies. We discuss the different sequencing approaches applicable to the study of food-related microbial isolates and mixed microbial communities in foods, and we provide an overview of the sequencing platforms suitable for each approach. We highlight the potential for genomics, metagenomics, and metatranscriptomics to guide efforts to optimize food fermentations. Additionally, we explore the use of comparative and functional genomics to further our understanding of the mechanisms of probiotic action and we describe the applicability of HTS as a food safety measure...
February 28, 2017: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/28115022/gut-microbial-degradation-of-organophosphate-insecticides-induces-glucose-intolerance-via-gluconeogenesis
#17
Ganesan Velmurugan, Tharmarajan Ramprasath, Krishnan Swaminathan, Gilles Mithieux, Jeyaprakash Rajendhran, Mani Dhivakar, Ayothi Parthasarathy, D D Venkatesh Babu, Leishman John Thumburaj, Allen J Freddy, Vasudevan Dinakaran, Shanavas Syed Mohamed Puhari, Balakrishnan Rekha, Yacob Jenifer Christy, Sivakumar Anusha, Ganesan Divya, Kannan Suganya, Boominathan Meganathan, Narayanan Kalyanaraman, Varadaraj Vasudevan, Raju Kamaraj, Maruthan Karthik, Balakrishnan Jeyakumar, Albert Abhishek, Eldho Paul, Muthuirulan Pushpanathan, Rajamani Koushick Rajmohan, Kumaravel Velayutham, Alexander R Lyon, Subbiah Ramasamy
BACKGROUND: Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. The diabetogenic nature of organophosphates was recently reported but the underlying molecular mechanism is unclear. We aimed to understand the role of gut microbiota in organophosphate-induced hyperglycemia and to unravel the molecular mechanism behind this process. RESULTS: Here we demonstrate a high prevalence of diabetes among people directly exposed to organophosphates in rural India (n = 3080)...
January 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#18
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28094312/unraveling-the-microbial-processes-of-black-band-disease-in-corals-through-integrated-genomics
#19
Yui Sato, Edmund Y S Ling, Dmitrij Turaev, Patrick Laffy, Karen D Weynberg, Thomas Rattei, Bette L Willis, David G Bourne
Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#20
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
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