Results 11 to 20 of about 4,884 (222)

SAMSA2: a standalone metatranscriptome analysis pipeline [PDF]

BMC Bioinformatics, 2018
Background Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing.
David A. Mills, Korf, Ian, Lemay, Danielle G, Westreich, Samuel T, Samuel T. Westreich, Ian Korf, Michelle L. Treiber, Danielle G. Lemay, Mills, David A, Treiber, Michelle L   +9 more
core   +7 more sources

Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation. [PDF]

Environ Microbiol Rep
The microbiome profile of freshwater sponges did not broadly change in taxonomy or functional profile based on metatranscriptome analysis prior to and after formation of sponge dormant bodies (gemmules). Results highlight a subset of taxa that likely associate with the sponge host in different ways from facultative to long‐term symbionts.
Strope TA, Easson CG, Fiore CL.
europepmc   +2 more sources

Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota. [PDF]

Mol Nutr Food Res
Mediterranean diet (MD) influences the composition of the gut mycobiome. Key foods of MD are related to bacterial and fungal composition. Combining metagenomics and metatranscriptomics tracks the gene expression profiles of gut microbiota. Metatranscriptomics identifies the transcriptionally active members of the microbiota that overexpressed genes ...
Alvarez-Sala A, Jiménez-Hernández N, Artacho A, Ruiz-Pérez S, Pascual EC, Pons J, Sorlí JV, Corella D, Gosalbes MJ.   +8 more
europepmc   +2 more sources

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.
Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski, Andrey D. Prjibelski   +6 more
doaj   +1 more source

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

BMC Bioinformatics, 2023
Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses.
Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander   +3 more
doaj   +1 more source

Exploring the Change of Host and Microorganism in Chronic Obstructive Pulmonary Disease Patients Based on Metagenomic and Metatranscriptomic Sequencing

Frontiers in Microbiology, 2022
BackgroundChronic obstructive pulmonary disease (COPD) is a universal respiratory disease resulting from the complex interactions between genes and environmental conditions. The process of COPD is deteriorated by repeated episodes of exacerbations, which
Jing Yang, Qiang Zhang, Jun Zhang, Yan Ouyang, Zepeng Sun, Xinlong Liu, Feng Qaio, Li-Qun Xu, Yunfei Niu, Jian Li   +9 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

Targeting RNA with Next‐ and Third‐Generation Sequencing Improves Pathogen Identification in Clinical Samples

Advanced Science, 2021
Fast and accurate identification of microbial pathogens is critical for the proper treatment of infections. Traditional culture‐based diagnosis in clinics is increasingly supplemented by metagenomic next‐generation‐sequencing (mNGS).
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang   +18 more
doaj   +1 more source

Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre

Frontiers in Microbiology, 2021
Open-ocean surface waters host a diverse community of single-celled eukaryotic plankton (protists) consisting of phototrophs, heterotrophs, and mixotrophs. The productivity and biomass of these organisms oscillate over diel cycles, and yet the underlying
Ryan D. Groussman, Sacha N. Coesel, Bryndan P. Durham, Bryndan P. Durham, E. Virginia Armbrust   +4 more
doaj   +1 more source

L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human

Gut Microbes, 2023
Fermented foods and beverages are a significant source of dietary bacteria that enter the gastrointestinal (GI) tract. However, little is known about how these microbes survive and adapt to the small intestinal environment.
Edoardo Zaccaria, Tim Klaassen, Annick M.E. Alleleyn, Jos Boekhorst, Christian Chervaux, Tamara Smokvina, Freddy J. Troost, Michiel Kleerebezem   +7 more
doaj   +1 more source