Results 21 to 30 of about 1,840,918 (247)

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen [PDF]

Nature Communications, 2018
AbstractThe cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-
Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, Timothy J. Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe, Mick Watson   +11 more
openaire   +5 more sources

A comprehensive investigation of metagenome assembly by linked-read sequencing

Microbiome, 2020
Background The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities.
Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu, Shuai Cheng Li   +8 more
doaj   +1 more source

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China

Scientific Data, 2022
AbstractAs a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes ...
Zhou, Lei, Huang, Shihui, Gong, Jiayi, Xu, Peng, Huang, Xiande   +4 more
openaire   +3 more sources

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. [PDF]

PLoS Computational Biology, 2016
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities.
Haixu Tang, Sujun Li, Yuzhen Ye
doaj   +1 more source

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

BMC Bioinformatics, 2021
Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in
Zachary Deng, Eric Delwart
doaj   +1 more source

Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity

mSystems, 2021
Discovery of novel antibiotics is crucial for combating rapidly spreading antimicrobial resistance and new infectious diseases. Most of the clinically used antibiotics are natural products—secondary metabolites produced by soil microbes that can be ...
Shrikant S. Mantri, Timo Negri, Helena Sales-Ortells, Angel Angelov, Silke Peter, Harald Neidhardt, Yvonne Oelmann, Nadine Ziemert   +7 more
doaj   +1 more source

Multilocus sequence typing breathes life into a microbial metagenome [PDF]

, 2006
Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity.
Vandamme Peter, Dowson, Chris G., Mahenthiralingam Eshwar, Dowson Chris G., Adam Baldwin, Pavel Drevinek, Vandamme, Peter, Elke Vanlaere, John J LiPuma, Vanlaere, Elke, Dowson, Christopher G., LiPuma, John J., Drevinek, Pavel, LiPuma John J., Baldwin Adam, Peter Vandamme, Baldwin, Adam, Chris G Dowson, Eshwar Mahenthiralingam, Drevinek Pavel, Vanlaere Elke, Dowson, Chris G, Mahenthiralingam, Eshwar, LiPuma, John J   +23 more
core   +2 more sources

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms [PDF]

, 2013
Eikmeyer FG, Rademacher A, Hanreich A, et al. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms.
Sebastian Jaenicke, Eikmeyer, Felix Gregor ; https://orcid.org/, Zakrzewski, Martha, Schlüter, Andreas, Jaenicke, Sebastian, Antje Rademacher, Maus, Irena, Eikmeyer, Felix G., Alfred Pühler, Hennig, Magdalena, Klocke, Michael, Wibberg, Daniel, Michael Klocke, Andreas Schlüter, Schlüter, Andreas ; https://orcid.org/, Rademacher, Antje, Angelika Hanreich, Martha Zakrzewski, Daniel Wibberg, Magdalena Hennig, Pühler, Alfred, Pühler, Alfred ; https://orcid.org/, Felix G Eikmeyer, Hanreich, Angelika, Irena Maus   +24 more
core   +1 more source

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Nature Biotechnology, 2022
Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities.
Derek M. Bickhart, Mikhail Kolmogorov, Elizabeth Tseng, Daniel M. Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, Ivan Liachko, Shawn T. Sullivan, Sung Bong Shin, Alvah Zorea, Victòria Pascal Andreu, Kevin Panke-Buisse, Marnix H. Medema, Itzhak Mizrahi, Pavel A. Pevzner, Timothy P. L. Smith   +16 more
openaire   +3 more sources

309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula [PDF]

Scientific Data, 2021
AbstractProkaryoplankton genomes from the deep marine sediments are less explored compared to shallow shore sediments. The Gulfs of Kathiawar peninsula experience varied currents and inputs from different on-shore activities. Any perturbations would directly influence the microbiome and their normal homeostasis.
Nathani, Neelam M., Dave, Kaushambee J., Vatsa, Priyanka P., Mahajan, Mayur S., Sharma, Parth, Mootapally, Chandrashekar   +5 more
openaire   +3 more sources