Results 11 to 20 of about 7,593 (210)

Sizing up metatranscriptomics [PDF]

The ISME Journal, 2012
Abstract A typical marine bacterial cell in coastal seawater contains only ∼200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium’s responses to environmental signals, as well as for ...
Mary Ann, Moran, Brandon, Satinsky, Scott M, Gifford, Haiwei, Luo, Adam, Rivers, Leong-Keat, Chan, Jun, Meng, Bryndan P, Durham, Chen, Shen, Vanessa A, Varaljay, Christa B, Smith, Patricia L, Yager, Brian M, Hopkinson   +12 more
openaire   +2 more sources

Gene finding in metatranscriptomic sequences [PDF]

BMC Bioinformatics, 2014
Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition of the metatranscriptomic sequences will enable us to refine the annotations of the metagenomes, and to study the gene activities and their ...
Wazim Ismail, Yuzhen Ye, Haixu Tang
openaire   +2 more sources

Use of Metatranscriptomics in Microbiome Research [PDF]

Bioinformatics and Biology Insights, 2016
The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes.
Stavros Bashiardes, Gili Zilberman-Schapira, Eran Elinav   +2 more
openaire   +4 more sources

SAMSA2: a standalone metatranscriptome analysis pipeline [PDF]

BMC Bioinformatics, 2017
Abstract Background Complex microbial communities are an area of rapid growth in biology. Metatranscriptomics allows one to investigate the gene activity in an environmental sample via high-throughput sequencing.
Westreich, Samuel T, Treiber, Michelle L, Mills, David A, Korf, Ian, Lemay, Danielle G   +4 more
openaire   +5 more sources

Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication

Microbiology Spectrum, 2022
Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria.
Yang Yu, Wenduo Cheng, Xiaoyuan Chen, Qisen Guo, Huansheng Cao   +4 more
doaj   +1 more source

RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost

mSystems, 2022
Arctic permafrost is thawing due to global warming, with unknown consequences on the microbial inhabitants or associated viruses. DNA viruses have previously been shown to be abundant and active in thawing permafrost, but little is known about RNA ...
Ruonan Wu, Eric M. Bottos, Vincent G. Danna, James C. Stegen, Janet K. Jansson, Michelle R. Davison   +5 more
doaj   +1 more source

Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection

mSphere, 2019
There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease.
David B. Stewart, Justin R. Wright, Maria Fowler, Christopher J. McLimans, Vasily Tokarev, Isabella Amaniera, Owen Baker, Hoi-Tong Wong, Jeff Brabec, Rebecca Drucker, Regina Lamendella   +10 more
doaj   +1 more source

The Osmolyte Ties That Bind: Genomic Insights Into Synthesis and Breakdown of Organic Osmolytes in Marine Microbes

Frontiers in Marine Science, 2021
The production and consumption of organic matter by marine organisms plays a central role in the marine carbon cycle. Labile organic compounds (metabolites) are the major currency of energetic demands and organismal interaction, but these compounds ...
Erin L. McParland, Harriet Alexander, Winifred M. Johnson   +2 more
doaj   +1 more source

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data

Frontiers in Microbiology, 2021
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems.
Chun-Xu Xue, Chun-Xu Xue, Heyu Lin, Xiao-Yu Zhu, Jiwen Liu, Jiwen Liu, Jiwen Liu, Yunhui Zhang, Gary Rowley, Jonathan D. Todd, Meng Li, Xiao-Hua Zhang, Xiao-Hua Zhang, Xiao-Hua Zhang   +13 more
doaj   +1 more source

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

mSystems, 2021
The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples.
Andreas N. Schneider, John Sundh, Görel Sundström, Kerstin Richau, Nicolas Delhomme, Manfred Grabherr, Vaughan Hurry, Nathaniel R. Street   +7 more
doaj   +1 more source