SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
TLDR
SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data, is presented, capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.Abstract:
MOTIVATION: The application of Next-Generation Sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The tasks to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. AVAILABILITY: http://bioinfo.lifl.fr/RNA/sortmerna CONTACT: evguenia.kopylova@lifl.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.read more
Citations
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Journal ArticleDOI
Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots.
Belinda C. Martin,Deirdre B. Gleeson,John Statton,Andre R. Siebers,Pauline F. Grierson,Megan H. Ryan,Gary A. Kendrick +6 more
TL;DR: This study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and confirms the importance of the seagrass root environment – a critical, but often overlooked space.
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Metagenome-assembled genomes uncover a global brackish microbiome
Luisa W. Hugerth,John Larsson,Johannes Alneberg,Markus V. Lindh,Catherine Legrand,Jarone Pinhassi,Anders F. Andersson +6 more
TL;DR: In this article, the authors explored an automatic binning approach to reconstruct representative bacterioplankton genomes from metagenomic samples across a time-series in the Baltic Sea.
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FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell
Sebastien Relier,Julie Ripoll,Hélène Guillorit,Amandine Amalric,F. Boissière,Jérôme Vialaret,Aurore Attina,Françoise Debart,Armelle Choquet,Francoise Macari,Emmanuelle Samalin,Jean-Jacques Vasseur,Julie Pannequin,Evelyne Crapez,Christophe Hirtz,Eric Rivals,Amandine Bastide,Alexandre David +17 more
TL;DR: It is shown that the cytoplasmic pool of fat mass and obesity-associated protein (FTO) impedes CSC abilities in colorectal cancer through its m6Am (N6,2’-O-dimethyladenosine) demethylase activity, bringing to light the first biological function of the m6 am modification and its potential adverse consequences for coloreCTal cancer management.
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Metatranscriptomic Analysis of the Mouse Gut Microbiome Response to the Persistent Organic Pollutant 2,3,7,8-Tetrachlorodibenzofuran.
Robert G. Nichols,Jingtao Zhang,Jingwei Cai,Iain A. Murray,Imhoi Koo,Philip B. Smith,Gary H. Perdew,Andrew D. Patterson +7 more
TL;DR: Results suggest that after exposure to 24 µg/kg BW of TCDF, the gut microbiome increases the production of LPS and glutamate to promote localized gut inflammation, potentially using glutamate as a stress response.
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Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast.
TL;DR: The shift from high forage to HG and sampling location had a more significant influence on ruminal bacterial community abundance and structure compared with ADY, and evidence suggested that ADY can increase the abundance of some dominant anaerobic OTU belonging to F. succinogenes and phylum SR1.
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