Results 51 to 60 of about 5,063 (236)

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral

Microbiology Spectrum, 2023
Recent deep-ocean exploration has uncovered a variety of cold-water coral (CWC) ecosystems around the world ocean, but it remains unclear how microbiome is associated with these corals at a molecular levels.
Sanqiang Gong, Jiayuan Liang, Xujie Jin, Lijia Xu, Meixia Zhao, Kefu Yu   +5 more
doaj   +1 more source

Diel Patterns in Marine Microbial Metatranscriptomes Reflect Differences in Community Metabolic Activity Over Depth on the Continental Shelf of the North Atlantic

Frontiers in Marine Science, 2022
Microbial community dynamics are influenced not only by biological but also physical and chemical phenomena (e.g., temperature, sunlight, pH, wave energy) that vary on both short and long-time scales. In this study, samples of continental shelf waters of
J. Zehnpfennig, C. Hansel, S. Wankel, C. Sheik, D. Horton, C. Lamborg, D. Learman   +6 more
semanticscholar   +1 more source

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   +6 more sources

Constraining lake ecology via metagenomics, metatranscriptomics, and amplicon sequencing [PDF]

Metabarcoding and Metagenomics
Lake ecosystems are hotspots for important ecosystem functions, yet linking their microbiome to physicochemical parameters remains a challenge. Here, we compare 16S rRNA gene-based amplicon sequencing, metagenomics, and metatranscriptomics across 21 ...
Julia K. Nuy, Till L. V. Bornemann, Daniela Beisser, Alexander J. Probst, Jens Boenigk   +4 more
doaj   +3 more sources

A Methodological Review of Tools That Assess Dust Microbiomes, Metatranscriptomes and the Particulate Chemistry of Indoor Dust

Atmosphere, 2022
Indoor house dust is a blend of organic and inorganic materials, upon which diverse microbial communities such as viruses, bacteria and fungi reside. Adequate moisture in the indoor environment helps microbial communities multiply fast.
Y. Nazzal, F. Howari, Aya Yaslam, Jibran Iqbal, Lina Maloukh, L. Ambika, Ahmed A. Al-Taani, Ijaz Ali, Eman M. Othman, Arshad Jamal, Muhammad Naseem   +10 more
semanticscholar   +1 more source

Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes

Science Advances
Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes.
S. Blaskowski, Marie Roald, P. Berube, R. Braakman, E. Armbrust   +4 more
semanticscholar   +2 more sources

kakapo: easy extraction and annotation of genes from raw RNA-seq reads [PDF]

PeerJ, 2023
kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire ...
Karolis Ramanauskas, Boris Igić
doaj   +2 more sources

Exploring the tymovirids landscape through metatranscriptomics data [PDF]

Archives of Virology, 2021
Abstract Tymovirales is an order of viruses with positive-sense, single-stranded RNA genomes that mostly infect plants, but also fungi and insects. The number of tymovirid sequences has been growing in the last few years with the extensive use of high-throughput sequencing platforms.
Nicolás Bejerman, Humberto Debat
openaire   +2 more sources

Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing

Frontiers in Microbiology, 2018
Biological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is ...
Blaire Steven, Jayne Belnap, Cheryl R. Kuske   +2 more
doaj   +1 more source

Additional file 2 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

, 2022
Additional file 2: Supplementary Table S1. MG_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metagenomes. MG_metadata. Metadata for sequenced metagenomes. MT_FC_annotations.
Martina Aulitto (3744975), Naijia Xiao (14003778), Javier A. Ceja-Navarro (11619023), Yu Gao (69071), Aymerick Eudes (802691), Steven W. Singer (162486), Yu-Wei Wu (16196), Blake A. Simmons (108789), Lauren M. Tom (150584), Beatrice Garcia Rodriguez (14003781), Kai Deng (299054), Trent R. Northen (1413580), Jenny C. Mortimer (5011895), Henrik V. Scheller (4099900), Clifford Louime (14003784), Paul D. Adams (242976)   +15 more
core   +1 more source