Results 21 to 30 of about 503,920 (237)

happi: a hierarchical approach to pangenomics inference

Genome Biology, 2023
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms.
Pauline Trinh, David S. Clausen, Amy D. Willis   +2 more
doaj   +1 more source

Terabase-Scale Coassembly of a Tropical Soil Microbiome

Microbiology Spectrum, 2023
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life.
Robert Riley, Robert M. Bowers, Antonio Pedro Camargo, Ashley Campbell, Rob Egan, Emiley A. Eloe-Fadrosh, Brian Foster, Steven Hofmeyr, Marcel Huntemann, Matthew Kellom, Jeffrey A. Kimbrel, Leonid Oliker, Katherine Yelick, Jennifer Pett-Ridge, Asaf Salamov, Neha J. Varghese, Alicia Clum   +16 more
doaj   +1 more source

Shotgun metagenome sequencing and recovery of 444 metagenome-assembled microbial genomes from the biofloc aquaculture system

, 2023
We assembled a total of 444 medium- to high-quality metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 5%, from floc-associated bacterial community (FAB) of a commercial shrimp biofloc aquaculture system, located in South ...
Yeonjung Lim (6645230), Jang-Cheon Cho (518240), Meora Rajeev (11485592), Ilsuk Jung (16468119), Suhyun Kim (226047), Ilnam Kang (518235)   +5 more
core   +1 more source

Metagenome-assembled genomes uncover a global brackish microbiome [PDF]

Genome Biology, 2015
Abstract Microbes are main drivers of biogeochemical cycles in oceans and lakes, yet surprisingly few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Here we used automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea ...
Luisa W. Hugerth, John Larsson, Johannes Alneberg, Markus V. Lindh, Catherine Legrand, Jarone Pinhassi, Anders F. Andersson   +6 more
openaire   +4 more sources

CheckV assesses the quality and completeness of metagenome-assembled viral genomes [PDF]

Nature Biotechnology, 2020
AbstractMillions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses.
Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, Nikos C. Kyrpides   +5 more
openaire   +8 more sources

Metagenomes and metagenome-assembled genomes from <i>Onthophagus taurus</i>. [PDF]

Microbiol Resour Announc
ABSTRACT Shotgun metagenomic sequencing was carried out on Onthophagus taurus larval gut sections, female adult midguts, and pedestals (a maternally provisioned fecal pellet provided to offspring).
Jones JA, Moczek AP, Newton ILG.
europepmc   +3 more sources

Metagenome assembled genomes inventory.

, 2022
Table describing the completeness and degree of contamination of the metagenome assembled genomes generated in this study. (CSV)
Rebecca M. Brotman (8552301), Sarah E. Brown (2501965), Michael T. France (8639613), Anne M. Rompalo (14013989), Jacques Ravel (5502)   +4 more
core   +1 more source

Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa

Microbiology Resource Announcements, 2021
The rhizosphere microbiome plays an essential role in enhancing the growth of plants, raising the need for comprehension of their metabolic abilities. Here, we investigated rhizospheric and bulk soils of maize plants in Mafikeng, South Africa. Metagenome-assembled genomes containing plant growth-promoting genes were reconstructed.
Olubukola O. Babalola, Rebaona R. Molefe, Adenike E. Amoo   +2 more
openaire   +2 more sources

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

Nature Communications, 2022
Here, the authors present SemiBin, a siamese deep neural network framework that incorporates information from reference genomes, able to extract better metagenome-assembled genomes (MAGs) in several host-associated and environmental habitats.
Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, Luis Pedro Coelho   +3 more
doaj   +1 more source

Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories [PDF]

mBio, 2019
In their recent study, Espinoza et al. employ genome-resolved metagenomics to investigate supragingival plaque metagenomes of 88 individuals (1). The 34 metagenome-assembled genomes (MAGs) that the authors report include those that resolve to clades that have largely evaded cultivation efforts, such as Gracilibacteria (formerly GN02) and ...
Alon Shaiber, A. Murat Eren
openaire   +3 more sources