Results 31 to 40 of about 5,063 (236)

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials [PDF]

Scientific Data, 2019
Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized.
Eva Högfors-Rönnholm, Margarita López-Fernández, Stephan Christel, D. Brambilla, M. Huntemann, A. Clum, B. Foster, Bryce J. Foster, S. Roux, K. Palaniappan, N. Varghese, Supratim Mukherjee, T. Reddy, C. Daum, A. Copeland, I-Min A. Chen, N. Ivanova, N. Kyrpides, M. Harmon-Smith, E. Eloe-Fadrosh, D. Lundin, S. Engblom, Mark Dopson   +22 more
semanticscholar   +2 more sources

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

Microbiome, 2018
Background It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon
Samuel Jacquiod, Inês Nunes, Asker Brejnrod, Martin A. Hansen, Peter E. Holm, Anders Johansen, Kristian K. Brandt, Anders Priemé, Søren J. Sørensen   +8 more
doaj   +2 more sources

Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities [PDF]

Nature Communications
Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential.
Evan M. Lee, Nathan P. McNulty, Matthew C. Hibberd, Jiye Cheng, Kazi Ahsan, Hao-Wei Chang, Barak A. Cohen, Jeffrey I. Gordon   +7 more
doaj   +2 more sources

Nf-Core/Magmap: Map Metatranscriptomes to Large Collections of Genomes [PDF]

Bioinformatics
Jarone Pinhassi, Daniel Lundin, George Westmeijer   +2 more
exaly   +2 more sources

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

Frontiers in Bioinformatics, 2023
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments.
Fotis A. Baltoumas, Evangelos Karatzas, David Paez-Espino, Nefeli K. Venetsianou, Eleni Aplakidou, Anastasis Oulas, Robert D. Finn, Sergey Ovchinnikov, Evangelos Pafilis, Nikos C. Kyrpides, Georgios A. Pavlopoulos, Georgios A. Pavlopoulos, Georgios A. Pavlopoulos   +12 more
doaj   +1 more source

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

NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes

Nucleic Acids Research, 2023
The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains.
Fotis A. Baltoumas, E. Karatzas, Si-Rui Liu, S. Ovchinnikov, Yorgos Sofianatos, I-Min A. Chen, N. Kyrpides, G. Pavlopoulos   +7 more
semanticscholar   +1 more source

Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments

Nature Communications, 2022
Microbial nitrogen fixation could be important in the deep sea. Here the authors investigate metagenomes and metatranscriptomes of diazotrophs from deep sea cold seep sediments, reveal greater phylogenetic and functional diversity than hitherto known.
Xiyang Dong, Chuwen Zhang, Yongyi Peng, Hong-Xi Zhang, Ling-Dong Shi, Guangshan Wei, Casey R. J. Hubert, Yong Wang, Chris Greening   +8 more
doaj   +1 more source

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Frontiers in Microbiology, 2022
While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome.
D. Shafranskaya, Varsha Kale, R. Finn, A. Lapidus, Anton I. Korobeynikov, A. Prjibelski   +5 more
semanticscholar   +1 more source

analysis of the deep biosphere metatranscriptomes

, 2023
metatranscriptomes of the deep ...
Zhou Ying-Li, Mara Paraskevi
core   +1 more source