Journal ArticleDOI
Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing
Martha Zakrzewski,Alexander Goesmann,Sebastian Jaenicke,Sebastian Jünemann,Felix Gregor Eikmeyer,Rafael Szczepanowski,Waleed Abu Al-Soud,Søren J. Sørensen,Alfred Pühler,Andreas Schlüter +9 more
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TLDR
It was shown that the most abundant species dominating the community also contributed the majority of the transcripts, and a high transcriptional activity of archaeal species was indicated.About:
This article is published in Journal of Biotechnology.The article was published on 2012-04-30. It has received 208 citations till now. The article focuses on the topics: Metagenomics & Ribosomal DNA.read more
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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
Daniel McDonald,Jose C. Clemente,Justin Kuczynski,Jai Ram Rideout,Jesse Stombaugh,Doug Wendel,Andreas Wilke,Susan M. Huse,John Hufnagle,Folker Meyer,Rob Knight,Rob Knight,J. Gregory Caporaso,J. Gregory Caporaso +13 more
TL;DR: The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications.
Journal ArticleDOI
Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques.
TL;DR: The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability.
Journal ArticleDOI
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
Stefano Campanaro,Laura Treu,Panagiotis Kougias,Davide De Francisci,Giorgio Valle,Irini Angelidaki +5 more
TL;DR: This study dissects the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing, disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes, establishing a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.
Journal ArticleDOI
Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance
TL;DR: This review summarises current insight of syntrophic acetate oxidising microorganisms, their presence and the detection of novel species and relate these observations with operating conditions of the biogas processes in order to explore contributing factors for development of an ammonia-tolerant microbial community that efficiently degrades acetate through the syntrophic pathway.
Journal ArticleDOI
iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite.
TL;DR: Both direct interspecies electron transfer and interspecies H2 transfer were present during methanation of propionate facilitated by magnetite, and most of the up-regulated proteins in methane metabolism were originated from neither Methanosaeta nor Methanosarcina, indicating they were not involved in direct inter species electron transfer.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
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